kinases_in_chembl.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Find UniProt IDs in ChEMBL targets"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Ultimately, we are interested in getting [activity data from ChEMBl](/chembl-27/query_local_chembl-27.ipynb) we need to account for three components:\n",
    "\n",
    "* The compound being measured\n",
    "* The target the compound binds to\n",
    "* The assay where this measurement took place\n",
    "\n",
    "So, to find all activity data stored in ChEMBL that refers to kinases, we have to query for those assays annotated with a certain target.\n",
    "\n",
    "Each of those three components have a unique ChEMBL ID, but so far we only have obtained Uniprot IDs in the `human-kinases` notebook. We need a way to connect Uniprot IDs to ChEMBL target IDs. Fortunately, ChEMBL maintains such a map in their FTP releases. We will parse that file and convert it into a dataframe for easy manipulation."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "from pathlib import Path\n",
    "import urllib.request\n",
    "\n",
    "import chembl_downloader\n",
    "import pandas as pd"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "REPO = (Path(_dh[-1]) / \"..\").resolve()\n",
    "DATA = REPO / 'data'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "# CHEMBL_VERSION = chembl_downloader.latest()\n",
    "CHEMBL_VERSION = 30"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>UniprotID</th>\n",
       "      <th>chembl_targets</th>\n",
       "      <th>description</th>\n",
       "      <th>type</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>P21266</td>\n",
       "      <td>CHEMBL2242</td>\n",
       "      <td>Glutathione S-transferase Mu 3</td>\n",
       "      <td>SINGLE PROTEIN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>O00519</td>\n",
       "      <td>CHEMBL2243</td>\n",
       "      <td>Anandamide amidohydrolase</td>\n",
       "      <td>SINGLE PROTEIN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>P19217</td>\n",
       "      <td>CHEMBL2244</td>\n",
       "      <td>Estrogen sulfotransferase</td>\n",
       "      <td>SINGLE PROTEIN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>P97292</td>\n",
       "      <td>CHEMBL2245</td>\n",
       "      <td>Histamine H2 receptor</td>\n",
       "      <td>SINGLE PROTEIN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>P17342</td>\n",
       "      <td>CHEMBL2247</td>\n",
       "      <td>Atrial natriuretic peptide receptor C</td>\n",
       "      <td>SINGLE PROTEIN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13526</th>\n",
       "      <td>A0A0J5PZ55</td>\n",
       "      <td>CHEMBL4630893</td>\n",
       "      <td>Dihydroorotate dehydrogenase (quinone), mitoch...</td>\n",
       "      <td>SINGLE PROTEIN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13527</th>\n",
       "      <td>Q8NI17</td>\n",
       "      <td>CHEMBL4630894</td>\n",
       "      <td>Interleukin-31 receptor subunit alpha</td>\n",
       "      <td>SINGLE PROTEIN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13528</th>\n",
       "      <td>P43630</td>\n",
       "      <td>CHEMBL4630895</td>\n",
       "      <td>Killer cell immunoglobulin-like receptor 3DL2</td>\n",
       "      <td>SINGLE PROTEIN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13529</th>\n",
       "      <td>A0A0H3HP34</td>\n",
       "      <td>CHEMBL4630896</td>\n",
       "      <td>Enoyl-[acyl-carrier-protein] reductase [NADH]</td>\n",
       "      <td>SINGLE PROTEIN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13530</th>\n",
       "      <td>P28887</td>\n",
       "      <td>CHEMBL4630897</td>\n",
       "      <td>RNA-directed RNA polymerase L</td>\n",
       "      <td>SINGLE PROTEIN</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>13531 rows × 4 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "        UniprotID chembl_targets  \\\n",
       "0          P21266     CHEMBL2242   \n",
       "1          O00519     CHEMBL2243   \n",
       "2          P19217     CHEMBL2244   \n",
       "3          P97292     CHEMBL2245   \n",
       "4          P17342     CHEMBL2247   \n",
       "...           ...            ...   \n",
       "13526  A0A0J5PZ55  CHEMBL4630893   \n",
       "13527      Q8NI17  CHEMBL4630894   \n",
       "13528      P43630  CHEMBL4630895   \n",
       "13529  A0A0H3HP34  CHEMBL4630896   \n",
       "13530      P28887  CHEMBL4630897   \n",
       "\n",
       "                                             description            type  \n",
       "0                         Glutathione S-transferase Mu 3  SINGLE PROTEIN  \n",
       "1                              Anandamide amidohydrolase  SINGLE PROTEIN  \n",
       "2                              Estrogen sulfotransferase  SINGLE PROTEIN  \n",
       "3                                  Histamine H2 receptor  SINGLE PROTEIN  \n",
       "4                  Atrial natriuretic peptide receptor C  SINGLE PROTEIN  \n",
       "...                                                  ...             ...  \n",
       "13526  Dihydroorotate dehydrogenase (quinone), mitoch...  SINGLE PROTEIN  \n",
       "13527              Interleukin-31 receptor subunit alpha  SINGLE PROTEIN  \n",
       "13528      Killer cell immunoglobulin-like receptor 3DL2  SINGLE PROTEIN  \n",
       "13529      Enoyl-[acyl-carrier-protein] reductase [NADH]  SINGLE PROTEIN  \n",
       "13530                      RNA-directed RNA polymerase L  SINGLE PROTEIN  \n",
       "\n",
       "[13531 rows x 4 columns]"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "uniprot_map = chembl_downloader.get_uniprot_mapping_df(version=CHEMBL_VERSION)\n",
    "uniprot_map = uniprot_map.rename(columns={\n",
    "    \"uniprot_id\": \"UniprotID\",\n",
    "    \"chembl_target_id\": \"chembl_targets\", \n",
    "    \"name\": \"description\", \n",
    "})\n",
    "uniprot_map"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "We join this new information to the human kinases aggregated list from `human-kinases` (all of them, regardless the source):"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>UniprotID</th>\n",
       "      <th>Name</th>\n",
       "      <th>kinhub</th>\n",
       "      <th>klifs</th>\n",
       "      <th>pkinfam</th>\n",
       "      <th>reviewed_uniprot</th>\n",
       "      <th>dunbrack_msa</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>A0A0B4J2F2</td>\n",
       "      <td>SIK1B</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>A4QPH2</td>\n",
       "      <td>PI4KAP2</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>B5MCJ9</td>\n",
       "      <td>TRIM66</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>O00141</td>\n",
       "      <td>SGK1</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>O00238</td>\n",
       "      <td>BMPR1B|BMR1B</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>547</th>\n",
       "      <td>Q9Y616</td>\n",
       "      <td>IRAK3</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>548</th>\n",
       "      <td>Q9Y6E0</td>\n",
       "      <td>STK24</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>549</th>\n",
       "      <td>Q9Y6M4</td>\n",
       "      <td>CSNK1G3|KC1G3</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>550</th>\n",
       "      <td>Q9Y6R4</td>\n",
       "      <td>M3K4|MAP3K4</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>551</th>\n",
       "      <td>Q9Y6S9</td>\n",
       "      <td>RPS6KL1|RPKL1</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>552 rows × 7 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "      UniprotID           Name  kinhub  klifs  pkinfam  reviewed_uniprot  \\\n",
       "0    A0A0B4J2F2          SIK1B   False  False     True              True   \n",
       "1        A4QPH2        PI4KAP2   False   True    False             False   \n",
       "2        B5MCJ9         TRIM66    True  False    False             False   \n",
       "3        O00141           SGK1    True   True     True              True   \n",
       "4        O00238   BMPR1B|BMR1B    True   True     True              True   \n",
       "..          ...            ...     ...    ...      ...               ...   \n",
       "547      Q9Y616          IRAK3    True   True     True              True   \n",
       "548      Q9Y6E0          STK24    True   True     True              True   \n",
       "549      Q9Y6M4  CSNK1G3|KC1G3    True   True     True              True   \n",
       "550      Q9Y6R4    M3K4|MAP3K4    True   True     True              True   \n",
       "551      Q9Y6S9  RPS6KL1|RPKL1    True   True     True              True   \n",
       "\n",
       "     dunbrack_msa  \n",
       "0            True  \n",
       "1           False  \n",
       "2           False  \n",
       "3            True  \n",
       "4            True  \n",
       "..            ...  \n",
       "547          True  \n",
       "548          True  \n",
       "549          True  \n",
       "550          True  \n",
       "551          True  \n",
       "\n",
       "[552 rows x 7 columns]"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "kinases = pd.read_csv(DATA / \"human_kinases.aggregated.csv\", index_col=0)\n",
    "kinases"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "We are only interested in those kinases present in these datasets:\n",
    "\n",
    "* KinHub\n",
    "* KLIFS\n",
    "* PKinFam\n",
    "* Dunbrack's MSA"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>UniprotID</th>\n",
       "      <th>Name</th>\n",
       "      <th>kinhub</th>\n",
       "      <th>klifs</th>\n",
       "      <th>pkinfam</th>\n",
       "      <th>reviewed_uniprot</th>\n",
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       "      <th>0</th>\n",
       "      <td>A0A0B4J2F2</td>\n",
       "      <td>SIK1B</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>A4QPH2</td>\n",
       "      <td>PI4KAP2</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>B5MCJ9</td>\n",
       "      <td>TRIM66</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>O00141</td>\n",
       "      <td>SGK1</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>O00238</td>\n",
       "      <td>BMPR1B|BMR1B</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>547</th>\n",
       "      <td>Q9Y616</td>\n",
       "      <td>IRAK3</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>548</th>\n",
       "      <td>Q9Y6E0</td>\n",
       "      <td>STK24</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>549</th>\n",
       "      <td>Q9Y6M4</td>\n",
       "      <td>CSNK1G3|KC1G3</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>550</th>\n",
       "      <td>Q9Y6R4</td>\n",
       "      <td>M3K4|MAP3K4</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>551</th>\n",
       "      <td>Q9Y6S9</td>\n",
       "      <td>RPS6KL1|RPKL1</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>552 rows × 7 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "      UniprotID           Name  kinhub  klifs  pkinfam  reviewed_uniprot  \\\n",
       "0    A0A0B4J2F2          SIK1B   False  False     True              True   \n",
       "1        A4QPH2        PI4KAP2   False   True    False             False   \n",
       "2        B5MCJ9         TRIM66    True  False    False             False   \n",
       "3        O00141           SGK1    True   True     True              True   \n",
       "4        O00238   BMPR1B|BMR1B    True   True     True              True   \n",
       "..          ...            ...     ...    ...      ...               ...   \n",
       "547      Q9Y616          IRAK3    True   True     True              True   \n",
       "548      Q9Y6E0          STK24    True   True     True              True   \n",
       "549      Q9Y6M4  CSNK1G3|KC1G3    True   True     True              True   \n",
       "550      Q9Y6R4    M3K4|MAP3K4    True   True     True              True   \n",
       "551      Q9Y6S9  RPS6KL1|RPKL1    True   True     True              True   \n",
       "\n",
       "     dunbrack_msa  \n",
       "0            True  \n",
       "1           False  \n",
       "2           False  \n",
       "3            True  \n",
       "4            True  \n",
       "..            ...  \n",
       "547          True  \n",
       "548          True  \n",
       "549          True  \n",
       "550          True  \n",
       "551          True  \n",
       "\n",
       "[552 rows x 7 columns]"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "kinases_subset = kinases[kinases[[\"kinhub\", \"klifs\", \"pkinfam\", \"dunbrack_msa\"]].sum(axis=1) > 0]\n",
    "kinases_subset"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "We would also like to preserve the provenance of the Uniprot assignment, so we will group the provenance columns in a single one now."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>UniprotID</th>\n",
       "      <th>Name</th>\n",
       "      <th>kinhub</th>\n",
       "      <th>klifs</th>\n",
       "      <th>pkinfam</th>\n",
       "      <th>reviewed_uniprot</th>\n",
       "      <th>dunbrack_msa</th>\n",
       "      <th>origin</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>A0A0B4J2F2</td>\n",
       "      <td>SIK1B</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>pkinfam|reviewed_uniprot|dunbrack_msa</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>A4QPH2</td>\n",
       "      <td>PI4KAP2</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>klifs</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>B5MCJ9</td>\n",
       "      <td>TRIM66</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>kinhub</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>O00141</td>\n",
       "      <td>SGK1</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>O00238</td>\n",
       "      <td>BMPR1B|BMR1B</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>547</th>\n",
       "      <td>Q9Y616</td>\n",
       "      <td>IRAK3</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>548</th>\n",
       "      <td>Q9Y6E0</td>\n",
       "      <td>STK24</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>549</th>\n",
       "      <td>Q9Y6M4</td>\n",
       "      <td>CSNK1G3|KC1G3</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>550</th>\n",
       "      <td>Q9Y6R4</td>\n",
       "      <td>M3K4|MAP3K4</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>551</th>\n",
       "      <td>Q9Y6S9</td>\n",
       "      <td>RPS6KL1|RPKL1</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>552 rows × 8 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "      UniprotID           Name  kinhub  klifs  pkinfam  reviewed_uniprot  \\\n",
       "0    A0A0B4J2F2          SIK1B   False  False     True              True   \n",
       "1        A4QPH2        PI4KAP2   False   True    False             False   \n",
       "2        B5MCJ9         TRIM66    True  False    False             False   \n",
       "3        O00141           SGK1    True   True     True              True   \n",
       "4        O00238   BMPR1B|BMR1B    True   True     True              True   \n",
       "..          ...            ...     ...    ...      ...               ...   \n",
       "547      Q9Y616          IRAK3    True   True     True              True   \n",
       "548      Q9Y6E0          STK24    True   True     True              True   \n",
       "549      Q9Y6M4  CSNK1G3|KC1G3    True   True     True              True   \n",
       "550      Q9Y6R4    M3K4|MAP3K4    True   True     True              True   \n",
       "551      Q9Y6S9  RPS6KL1|RPKL1    True   True     True              True   \n",
       "\n",
       "     dunbrack_msa                                             origin  \n",
       "0            True              pkinfam|reviewed_uniprot|dunbrack_msa  \n",
       "1           False                                              klifs  \n",
       "2           False                                             kinhub  \n",
       "3            True  kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...  \n",
       "4            True  kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...  \n",
       "..            ...                                                ...  \n",
       "547          True  kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...  \n",
       "548          True  kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...  \n",
       "549          True  kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...  \n",
       "550          True  kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...  \n",
       "551          True  kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...  \n",
       "\n",
       "[552 rows x 8 columns]"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "kinases_subset[\"origin\"] = kinases_subset.apply(lambda s: '|'.join([k for k in [\"kinhub\", \"klifs\", \"pkinfam\", \"reviewed_uniprot\", \"dunbrack_msa\"] if s[k]]), axis=1)\n",
    "kinases_subset"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "We can now merge the needed columns based on the `UniprotID` key."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
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       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>UniprotID</th>\n",
       "      <th>Name</th>\n",
       "      <th>chembl_targets</th>\n",
       "      <th>type</th>\n",
       "      <th>origin</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>A4QPH2</td>\n",
       "      <td>PI4KAP2</td>\n",
       "      <td>CHEMBL4105789</td>\n",
       "      <td>SINGLE PROTEIN</td>\n",
       "      <td>klifs</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>A4QPH2</td>\n",
       "      <td>PI4KAP2</td>\n",
       "      <td>CHEMBL3038509</td>\n",
       "      <td>PROTEIN COMPLEX</td>\n",
       "      <td>klifs</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>O00141</td>\n",
       "      <td>SGK1</td>\n",
       "      <td>CHEMBL2343</td>\n",
       "      <td>SINGLE PROTEIN</td>\n",
       "      <td>kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>O00238</td>\n",
       "      <td>BMPR1B|BMR1B</td>\n",
       "      <td>CHEMBL5476</td>\n",
       "      <td>SINGLE PROTEIN</td>\n",
       "      <td>kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>O00311</td>\n",
       "      <td>CDC7</td>\n",
       "      <td>CHEMBL2111377</td>\n",
       "      <td>PROTEIN COMPLEX</td>\n",
       "      <td>kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1014</th>\n",
       "      <td>Q9Y616</td>\n",
       "      <td>IRAK3</td>\n",
       "      <td>CHEMBL4748234</td>\n",
       "      <td>PROTEIN-PROTEIN INTERACTION</td>\n",
       "      <td>kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1015</th>\n",
       "      <td>Q9Y616</td>\n",
       "      <td>IRAK3</td>\n",
       "      <td>CHEMBL4742326</td>\n",
       "      <td>PROTEIN-PROTEIN INTERACTION</td>\n",
       "      <td>kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1016</th>\n",
       "      <td>Q9Y6E0</td>\n",
       "      <td>STK24</td>\n",
       "      <td>CHEMBL5082</td>\n",
       "      <td>SINGLE PROTEIN</td>\n",
       "      <td>kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1017</th>\n",
       "      <td>Q9Y6M4</td>\n",
       "      <td>CSNK1G3|KC1G3</td>\n",
       "      <td>CHEMBL5084</td>\n",
       "      <td>SINGLE PROTEIN</td>\n",
       "      <td>kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1018</th>\n",
       "      <td>Q9Y6R4</td>\n",
       "      <td>M3K4|MAP3K4</td>\n",
       "      <td>CHEMBL4853</td>\n",
       "      <td>SINGLE PROTEIN</td>\n",
       "      <td>kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>1019 rows × 5 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "     UniprotID           Name chembl_targets                         type  \\\n",
       "0       A4QPH2        PI4KAP2  CHEMBL4105789               SINGLE PROTEIN   \n",
       "1       A4QPH2        PI4KAP2  CHEMBL3038509              PROTEIN COMPLEX   \n",
       "2       O00141           SGK1     CHEMBL2343               SINGLE PROTEIN   \n",
       "3       O00238   BMPR1B|BMR1B     CHEMBL5476               SINGLE PROTEIN   \n",
       "4       O00311           CDC7  CHEMBL2111377              PROTEIN COMPLEX   \n",
       "...        ...            ...            ...                          ...   \n",
       "1014    Q9Y616          IRAK3  CHEMBL4748234  PROTEIN-PROTEIN INTERACTION   \n",
       "1015    Q9Y616          IRAK3  CHEMBL4742326  PROTEIN-PROTEIN INTERACTION   \n",
       "1016    Q9Y6E0          STK24     CHEMBL5082               SINGLE PROTEIN   \n",
       "1017    Q9Y6M4  CSNK1G3|KC1G3     CHEMBL5084               SINGLE PROTEIN   \n",
       "1018    Q9Y6R4    M3K4|MAP3K4     CHEMBL4853               SINGLE PROTEIN   \n",
       "\n",
       "                                                 origin  \n",
       "0                                                 klifs  \n",
       "1                                                 klifs  \n",
       "2     kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...  \n",
       "3     kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...  \n",
       "4     kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...  \n",
       "...                                                 ...  \n",
       "1014  kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...  \n",
       "1015  kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...  \n",
       "1016  kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...  \n",
       "1017  kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...  \n",
       "1018  kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...  \n",
       "\n",
       "[1019 rows x 5 columns]"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "merged = pd.merge(kinases_subset[[\"UniprotID\", \"Name\", \"origin\"]], uniprot_map[[\"UniprotID\", \"chembl_targets\", \"type\"]], how=\"inner\", on='UniprotID')[[\"UniprotID\", \"Name\", \"chembl_targets\", \"type\", \"origin\"]]\n",
    "merged"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "~~How is this possible? 969 targets (ChEMBL 28)?!~~\n",
    "\n",
    "Apparently, there's not 1:1 correspondence between UniprotID and ChEMBL ID! Some Uniprot IDs are included in several ChEMBL targets:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "P11802    17\n",
       "P24941    15\n",
       "P35968    11\n",
       "Q00534    11\n",
       "P06493    11\n",
       "          ..\n",
       "O75962     1\n",
       "Q59H18     1\n",
       "Q5JZY3     1\n",
       "Q5MAI5     1\n",
       "Q9Y6R4     1\n",
       "Name: UniprotID, Length: 496, dtype: int64"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "merged.UniprotID.value_counts()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
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       "\n",
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       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>UniprotID</th>\n",
       "      <th>Name</th>\n",
       "      <th>chembl_targets</th>\n",
       "      <th>type</th>\n",
       "      <th>origin</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>221</th>\n",
       "      <td>P11802</td>\n",
       "      <td>CDK4</td>\n",
       "      <td>CHEMBL331</td>\n",
       "      <td>SINGLE PROTEIN</td>\n",
       "      <td>kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>222</th>\n",
       "      <td>P11802</td>\n",
       "      <td>CDK4</td>\n",
       "      <td>CHEMBL2095942</td>\n",
       "      <td>PROTEIN COMPLEX</td>\n",
       "      <td>kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>223</th>\n",
       "      <td>P11802</td>\n",
       "      <td>CDK4</td>\n",
       "      <td>CHEMBL2111326</td>\n",
       "      <td>SELECTIVITY GROUP</td>\n",
       "      <td>kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>224</th>\n",
       "      <td>P11802</td>\n",
       "      <td>CDK4</td>\n",
       "      <td>CHEMBL1907601</td>\n",
       "      <td>PROTEIN COMPLEX</td>\n",
       "      <td>kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>225</th>\n",
       "      <td>P11802</td>\n",
       "      <td>CDK4</td>\n",
       "      <td>CHEMBL3301385</td>\n",
       "      <td>PROTEIN COMPLEX</td>\n",
       "      <td>kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>226</th>\n",
       "      <td>P11802</td>\n",
       "      <td>CDK4</td>\n",
       "      <td>CHEMBL4523686</td>\n",
       "      <td>PROTEIN-PROTEIN INTERACTION</td>\n",
       "      <td>kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>227</th>\n",
       "      <td>P11802</td>\n",
       "      <td>CDK4</td>\n",
       "      <td>CHEMBL4523715</td>\n",
       "      <td>PROTEIN-PROTEIN INTERACTION</td>\n",
       "      <td>kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>228</th>\n",
       "      <td>P11802</td>\n",
       "      <td>CDK4</td>\n",
       "      <td>CHEMBL4523732</td>\n",
       "      <td>PROTEIN-PROTEIN INTERACTION</td>\n",
       "      <td>kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>229</th>\n",
       "      <td>P11802</td>\n",
       "      <td>CDK4</td>\n",
       "      <td>CHEMBL3038472</td>\n",
       "      <td>PROTEIN COMPLEX</td>\n",
       "      <td>kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>230</th>\n",
       "      <td>P11802</td>\n",
       "      <td>CDK4</td>\n",
       "      <td>CHEMBL4523963</td>\n",
       "      <td>SELECTIVITY GROUP</td>\n",
       "      <td>kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>231</th>\n",
       "      <td>P11802</td>\n",
       "      <td>CDK4</td>\n",
       "      <td>CHEMBL3559691</td>\n",
       "      <td>PROTEIN FAMILY</td>\n",
       "      <td>kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>232</th>\n",
       "      <td>P11802</td>\n",
       "      <td>CDK4</td>\n",
       "      <td>CHEMBL3038517</td>\n",
       "      <td>PROTEIN FAMILY</td>\n",
       "      <td>kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>233</th>\n",
       "      <td>P11802</td>\n",
       "      <td>CDK4</td>\n",
       "      <td>CHEMBL4106184</td>\n",
       "      <td>PROTEIN FAMILY</td>\n",
       "      <td>kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>234</th>\n",
       "      <td>P11802</td>\n",
       "      <td>CDK4</td>\n",
       "      <td>CHEMBL4630748</td>\n",
       "      <td>PROTEIN-PROTEIN INTERACTION</td>\n",
       "      <td>kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>235</th>\n",
       "      <td>P11802</td>\n",
       "      <td>CDK4</td>\n",
       "      <td>CHEMBL3885548</td>\n",
       "      <td>PROTEIN COMPLEX</td>\n",
       "      <td>kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>236</th>\n",
       "      <td>P11802</td>\n",
       "      <td>CDK4</td>\n",
       "      <td>CHEMBL3885553</td>\n",
       "      <td>PROTEIN FAMILY</td>\n",
       "      <td>kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>237</th>\n",
       "      <td>P11802</td>\n",
       "      <td>CDK4</td>\n",
       "      <td>CHEMBL3885554</td>\n",
       "      <td>PROTEIN COMPLEX</td>\n",
       "      <td>kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "    UniprotID  Name chembl_targets                         type  \\\n",
       "221    P11802  CDK4      CHEMBL331               SINGLE PROTEIN   \n",
       "222    P11802  CDK4  CHEMBL2095942              PROTEIN COMPLEX   \n",
       "223    P11802  CDK4  CHEMBL2111326            SELECTIVITY GROUP   \n",
       "224    P11802  CDK4  CHEMBL1907601              PROTEIN COMPLEX   \n",
       "225    P11802  CDK4  CHEMBL3301385              PROTEIN COMPLEX   \n",
       "226    P11802  CDK4  CHEMBL4523686  PROTEIN-PROTEIN INTERACTION   \n",
       "227    P11802  CDK4  CHEMBL4523715  PROTEIN-PROTEIN INTERACTION   \n",
       "228    P11802  CDK4  CHEMBL4523732  PROTEIN-PROTEIN INTERACTION   \n",
       "229    P11802  CDK4  CHEMBL3038472              PROTEIN COMPLEX   \n",
       "230    P11802  CDK4  CHEMBL4523963            SELECTIVITY GROUP   \n",
       "231    P11802  CDK4  CHEMBL3559691               PROTEIN FAMILY   \n",
       "232    P11802  CDK4  CHEMBL3038517               PROTEIN FAMILY   \n",
       "233    P11802  CDK4  CHEMBL4106184               PROTEIN FAMILY   \n",
       "234    P11802  CDK4  CHEMBL4630748  PROTEIN-PROTEIN INTERACTION   \n",
       "235    P11802  CDK4  CHEMBL3885548              PROTEIN COMPLEX   \n",
       "236    P11802  CDK4  CHEMBL3885553               PROTEIN FAMILY   \n",
       "237    P11802  CDK4  CHEMBL3885554              PROTEIN COMPLEX   \n",
       "\n",
       "                                                origin  \n",
       "221  kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...  \n",
       "222  kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...  \n",
       "223  kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...  \n",
       "224  kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...  \n",
       "225  kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...  \n",
       "226  kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...  \n",
       "227  kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...  \n",
       "228  kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...  \n",
       "229  kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...  \n",
       "230  kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...  \n",
       "231  kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...  \n",
       "232  kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...  \n",
       "233  kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...  \n",
       "234  kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...  \n",
       "235  kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...  \n",
       "236  kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...  \n",
       "237  kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...  "
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "merged[merged.UniprotID == \"P11802\"]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "... and some ChEMBL targets include several kinases (e.g. chimeric proteins):"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>UniprotID</th>\n",
       "      <th>Name</th>\n",
       "      <th>chembl_targets</th>\n",
       "      <th>type</th>\n",
       "      <th>origin</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>113</th>\n",
       "      <td>P00519</td>\n",
       "      <td>ABL1</td>\n",
       "      <td>CHEMBL2096618</td>\n",
       "      <td>CHIMERIC PROTEIN</td>\n",
       "      <td>kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>209</th>\n",
       "      <td>P11274</td>\n",
       "      <td>BCR</td>\n",
       "      <td>CHEMBL2096618</td>\n",
       "      <td>CHIMERIC PROTEIN</td>\n",
       "      <td>kinhub|klifs</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "    UniprotID  Name chembl_targets              type  \\\n",
       "113    P00519  ABL1  CHEMBL2096618  CHIMERIC PROTEIN   \n",
       "209    P11274   BCR  CHEMBL2096618  CHIMERIC PROTEIN   \n",
       "\n",
       "                                                origin  \n",
       "113  kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...  \n",
       "209                                       kinhub|klifs  "
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "merged[merged.chembl_targets == \"CHEMBL2096618\"]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "This is due to the different `type` values:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "SINGLE PROTEIN                 494\n",
       "PROTEIN FAMILY                 247\n",
       "PROTEIN COMPLEX                121\n",
       "PROTEIN-PROTEIN INTERACTION    108\n",
       "SELECTIVITY GROUP               22\n",
       "CHIMERIC PROTEIN                16\n",
       "PROTEIN COMPLEX GROUP           11\n",
       "Name: type, dtype: int64"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "merged.type.value_counts()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "If we focus on `SINGLE PROTEIN` types:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>UniprotID</th>\n",
       "      <th>Name</th>\n",
       "      <th>chembl_targets</th>\n",
       "      <th>type</th>\n",
       "      <th>origin</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>A4QPH2</td>\n",
       "      <td>PI4KAP2</td>\n",
       "      <td>CHEMBL4105789</td>\n",
       "      <td>SINGLE PROTEIN</td>\n",
       "      <td>klifs</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>O00141</td>\n",
       "      <td>SGK1</td>\n",
       "      <td>CHEMBL2343</td>\n",
       "      <td>SINGLE PROTEIN</td>\n",
       "      <td>kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>O00238</td>\n",
       "      <td>BMPR1B|BMR1B</td>\n",
       "      <td>CHEMBL5476</td>\n",
       "      <td>SINGLE PROTEIN</td>\n",
       "      <td>kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>O00311</td>\n",
       "      <td>CDC7</td>\n",
       "      <td>CHEMBL5443</td>\n",
       "      <td>SINGLE PROTEIN</td>\n",
       "      <td>kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>O00329</td>\n",
       "      <td>PIK3CD</td>\n",
       "      <td>CHEMBL3130</td>\n",
       "      <td>SINGLE PROTEIN</td>\n",
       "      <td>klifs|pkinfam</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1012</th>\n",
       "      <td>Q9Y5S2</td>\n",
       "      <td>MRCKB|CDC42BPB</td>\n",
       "      <td>CHEMBL5052</td>\n",
       "      <td>SINGLE PROTEIN</td>\n",
       "      <td>kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1013</th>\n",
       "      <td>Q9Y616</td>\n",
       "      <td>IRAK3</td>\n",
       "      <td>CHEMBL5081</td>\n",
       "      <td>SINGLE PROTEIN</td>\n",
       "      <td>kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1016</th>\n",
       "      <td>Q9Y6E0</td>\n",
       "      <td>STK24</td>\n",
       "      <td>CHEMBL5082</td>\n",
       "      <td>SINGLE PROTEIN</td>\n",
       "      <td>kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1017</th>\n",
       "      <td>Q9Y6M4</td>\n",
       "      <td>CSNK1G3|KC1G3</td>\n",
       "      <td>CHEMBL5084</td>\n",
       "      <td>SINGLE PROTEIN</td>\n",
       "      <td>kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1018</th>\n",
       "      <td>Q9Y6R4</td>\n",
       "      <td>M3K4|MAP3K4</td>\n",
       "      <td>CHEMBL4853</td>\n",
       "      <td>SINGLE PROTEIN</td>\n",
       "      <td>kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>494 rows × 5 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "     UniprotID            Name chembl_targets            type  \\\n",
       "0       A4QPH2         PI4KAP2  CHEMBL4105789  SINGLE PROTEIN   \n",
       "2       O00141            SGK1     CHEMBL2343  SINGLE PROTEIN   \n",
       "3       O00238    BMPR1B|BMR1B     CHEMBL5476  SINGLE PROTEIN   \n",
       "5       O00311            CDC7     CHEMBL5443  SINGLE PROTEIN   \n",
       "7       O00329          PIK3CD     CHEMBL3130  SINGLE PROTEIN   \n",
       "...        ...             ...            ...             ...   \n",
       "1012    Q9Y5S2  MRCKB|CDC42BPB     CHEMBL5052  SINGLE PROTEIN   \n",
       "1013    Q9Y616           IRAK3     CHEMBL5081  SINGLE PROTEIN   \n",
       "1016    Q9Y6E0           STK24     CHEMBL5082  SINGLE PROTEIN   \n",
       "1017    Q9Y6M4   CSNK1G3|KC1G3     CHEMBL5084  SINGLE PROTEIN   \n",
       "1018    Q9Y6R4     M3K4|MAP3K4     CHEMBL4853  SINGLE PROTEIN   \n",
       "\n",
       "                                                 origin  \n",
       "0                                                 klifs  \n",
       "2     kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...  \n",
       "3     kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...  \n",
       "5     kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...  \n",
       "7                                         klifs|pkinfam  \n",
       "...                                                 ...  \n",
       "1012  kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...  \n",
       "1013  kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...  \n",
       "1016  kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...  \n",
       "1017  kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...  \n",
       "1018  kinhub|klifs|pkinfam|reviewed_uniprot|dunbrack...  \n",
       "\n",
       "[494 rows x 5 columns]"
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "merged[merged.type == \"SINGLE PROTEIN\"]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "... we end up with a total of 491 targets (ChEMBL 28), which is more acceptable.\n",
    "\n",
    "For that reason, we will only save records corresponding to `type == SINGLE PROTEIN`"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [],
   "source": [
    "merged[merged.type == \"SINGLE PROTEIN\"].to_csv(DATA /  f\"human_kinases_and_chembl_targets.chembl_{CHEMBL_VERSION}.csv\", index=False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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