In [1]:
# aim: to retrieve compounds from chembl tested against a target
# starting point: UNIPROT ID of target (from e.g. www.rcsb.org)
In [2]:
# some general settngs
import json
import warnings
import logging
In [3]:
# loading chembl package, creating chembl client
import chembl_webresource_client
from chembl_webresource_client import *
from chembl_webresource_client.settings import Settings
from chembl_webresource_client.new_client import new_client as chembl
In [4]:
chembl.target.set_format('json')
In [5]:
# step 1: finding CHEMBL id of target
# we poke a bit around in the data structure
print(dir(chembl))
print(chembl.target)
print(chembl.target[0]['target_components'][0]['accession'] )
['__class__', '__delattr__', '__dict__', '__dir__', '__doc__', '__eq__', '__format__', '__ge__', '__getattribute__', '__gt__', '__hash__', '__init__', '__init_subclass__', '__le__', '__lt__', '__module__', '__ne__', '__new__', '__reduce__', '__reduce_ex__', '__repr__', '__setattr__', '__sizeof__', '__str__', '__subclasshook__', '__weakref__', 'activity', 'assay', 'atc_class', 'binding_site', 'biotherapeutic', 'cell_line', 'chembl_id_lookup', 'compound_record', 'compound_structural_alert', 'description', 'document', 'document_similarity', 'document_term', 'drug', 'drug_indication', 'go_slim', 'image', 'mechanism', 'metabolism', 'molecule', 'molecule_form', 'official', 'organism', 'protein_class', 'similarity', 'source', 'substructure', 'target', 'target_component', 'target_prediction', 'target_relation', 'tissue', 'xref_source']
[{'cross_references': [{'xref_id': 'O43451', 'xref_name': None, 'xref_src': 'canSAR-Target'}, {'xref_id': 'Maltase-glucoamylase', 'xref_name': None, 'xref_src': 'Wikipedia'}], 'organism': 'Homo sapiens', 'pref_name': 'Maltase-glucoamylase', 'species_group_flag': False, 'target_chembl_id': 'CHEMBL2074', 'target_components': [{'accession': 'O43451', 'component_description': 'Maltase-glucoamylase, intestinal', 'component_id': 434, 'component_type': 'PROTEIN', 'relationship': 'SINGLE PROTEIN', 'target_component_synonyms': [{'component_synonym': 'MGA ', 'syn_type': 'GENE_SYMBOL'}, {'component_synonym': 'MGAML', 'syn_type': 'GENE_SYMBOL'}, {'component_synonym': 'MGAM', 'syn_type': 'GENE_SYMBOL'}, {'component_synonym': 'Maltase-glucoamylase, intestinal', 'syn_type': 'UNIPROT'}, {'component_synonym': 'Maltase', 'syn_type': 'UNIPROT'}, {'component_synonym': 'Glucoamylase', 'syn_type': 'UNIPROT'}, {'component_synonym': 'Alpha-glucosidase', 'syn_type': 'UNIPROT'}, {'component_synonym': 'Glucan 1,4-alpha-glucosidase', 'syn_type': 'UNIPROT'}, {'component_synonym': '3.2.1.20', 'syn_type': 'EC_NUMBER'}, {'component_synonym': '3.2.1.3', 'syn_type': 'EC_NUMBER'}]}], 'target_type': 'SINGLE PROTEIN', 'tax_id': 9606}, {'cross_references': [{'xref_id': 'O60706', 'xref_name': None, 'xref_src': 'canSAR-Target'}, {'xref_id': 'ABCC9', 'xref_name': None, 'xref_src': 'Wikipedia'}], 'organism': 'Homo sapiens', 'pref_name': 'Sulfonylurea receptor 2', 'species_group_flag': False, 'target_chembl_id': 'CHEMBL1971', 'target_components': [{'accession': 'O60706', 'component_description': 'ATP-binding cassette sub-family C member 9', 'component_id': 294, 'component_type': 'PROTEIN', 'relationship': 'SINGLE PROTEIN', 'target_component_synonyms': [{'component_synonym': 'SUR2', 'syn_type': 'GENE_SYMBOL'}, {'component_synonym': 'ABCC9', 'syn_type': 'GENE_SYMBOL'}, {'component_synonym': 'ATP-binding cassette sub-family C member 9', 'syn_type': 'UNIPROT'}, {'component_synonym': 'Sulfonylurea receptor 2', 'syn_type': 'UNIPROT'}]}], 'target_type': 'SINGLE PROTEIN', 'tax_id': 9606}, {'cross_references': [{'xref_id': 'CGMP-specific_phosphodiesterase_type_5', 'xref_name': None, 'xref_src': 'Wikipedia'}], 'organism': 'Homo sapiens', 'pref_name': 'Phosphodiesterase 5A', 'species_group_flag': False, 'target_chembl_id': 'CHEMBL1827', 'target_components': [{'accession': 'O76074', 'component_description': "cGMP-specific 3',5'-cyclic phosphodiesterase", 'component_id': 124, 'component_type': 'PROTEIN', 'relationship': 'SINGLE PROTEIN', 'target_component_synonyms': [{'component_synonym': 'PDE5', 'syn_type': 'GENE_SYMBOL'}, {'component_synonym': 'PDE5A', 'syn_type': 'GENE_SYMBOL'}, {'component_synonym': "cGMP-specific 3',5'-cyclic phosphodiesterase", 'syn_type': 'UNIPROT'}, {'component_synonym': 'cGMP-binding cGMP-specific phosphodiesterase', 'syn_type': 'UNIPROT'}, {'component_synonym': 'CGB-PDE', 'syn_type': 'UNIPROT'}, {'component_synonym': '3.1.4.35', 'syn_type': 'EC_NUMBER'}]}], 'target_type': 'SINGLE PROTEIN', 'tax_id': 9606}, {'cross_references': [{'xref_id': 'O95180', 'xref_name': None, 'xref_src': 'canSAR-Target'}, {'xref_id': 'CACNA1H', 'xref_name': None, 'xref_src': 'Wikipedia'}], 'organism': 'Homo sapiens', 'pref_name': 'Voltage-gated T-type calcium channel alpha-1H subunit', 'species_group_flag': False, 'target_chembl_id': 'CHEMBL1859', 'target_components': [{'accession': 'O95180', 'component_description': 'Voltage-dependent T-type calcium channel subunit alpha-1H', 'component_id': 167, 'component_type': 'PROTEIN', 'relationship': 'SINGLE PROTEIN', 'target_component_synonyms': [{'component_synonym': 'CACNA1H', 'syn_type': 'GENE_SYMBOL'}, {'component_synonym': 'Voltage-dependent T-type calcium channel subunit alpha-1H', 'syn_type': 'UNIPROT'}, {'component_synonym': 'Low-voltage-activated calcium channel alpha1 3.2 subunit', 'syn_type': 'UNIPROT'}, {'component_synonym': 'Voltage-gated calcium channel subunit alpha Cav3.2', 'syn_type': 'UNIPROT'}]}], 'target_type': 'SINGLE PROTEIN', 'tax_id': 9606}, '...(remaining elements truncated)...']
O43451
In [6]:
# step 2: we search chembl.target list for items that have our 
# uniprot code in chembl.target[]['target_components'][0]['accession'] dictionary
ABL_kinase_uniprotID =  "P42684"
print(ABL_kinase_uniprotID)
chembl_abl_candidates = []
errorcount = 0
for i in range(len(chembl.target)):
    try:
        if chembl.target[i]['target_components'][0]['accession'] ==  ABL_kinase_uniprotID:
            chembl_abl_candidates.append(chembl.target[i])
    except:
        errorcount += 1
print(len(chembl_abl_candidates))    
print(chembl_abl_candidates[0]['target_components'][0]['component_description'],
      chembl_abl_candidates[0]['target_chembl_id'] )

print("for " + str(errorcount) + " targets no accession id was found")        
          
P42684
1
Abelson tyrosine-protein kinase 2 CHEMBL4014
for 4099 targets no accession id was found
In [7]:
# bingo, the component maescription matches, we have found our CHEMBL id
# this code snippet does a similar job, but returns the CHEMBL id for the ABL family of enzymes as well
chembl_abl_candidates_alt = chembl.target.filter(target_components__accession=ABL_kinase_uniprotID)
print ([(x['target_chembl_id'], x['pref_name']) for x in chembl_abl_candidates_alt])
[('CHEMBL4014', 'Tyrosine-protein kinase ABL2'), ('CHEMBL2111414', 'Tyrosine-protein kinase ABL')]
In [8]:
print(chembl.activity)
[{'activity_comment': None, 'activity_id': 31863, 'assay_chembl_id': 'CHEMBL663853', 'assay_description': 'Inhibitory concentration against human DNA topoisomerase II, alpha mediated relaxation of pBR322; no measurable activity', 'assay_type': 'B', 'bao_endpoint': 'BAO_0000190', 'bao_format': 'BAO_0000357', 'bao_label': 'single protein format', 'canonical_smiles': 'o1c(nc2c(cccc12)c3oc4ccccc4n3)c5ccccc5', 'data_validity_comment': None, 'document_chembl_id': 'CHEMBL1137930', 'document_journal': 'Bioorg. Med. Chem. Lett.', 'document_year': 2004, 'ligand_efficiency': None, 'molecule_chembl_id': 'CHEMBL113081', 'parent_molecule_chembl_id': 'CHEMBL113081', 'pchembl_value': None, 'potential_duplicate': False, 'published_relation': '>', 'published_type': 'IC50', 'published_units': 'uM', 'published_value': '100', 'qudt_units': 'http://www.openphacts.org/units/Nanomolar', 'record_id': 206172, 'src_id': 1, 'standard_flag': True, 'standard_relation': '>', 'standard_type': 'IC50', 'standard_units': 'nM', 'standard_value': '100000', 'target_chembl_id': 'CHEMBL1806', 'target_organism': 'Homo sapiens', 'target_pref_name': 'DNA topoisomerase II alpha', 'target_tax_id': '9606', 'uo_units': 'UO_0000065'}, {'activity_comment': None, 'activity_id': 31864, 'assay_chembl_id': 'CHEMBL872937', 'assay_description': 'In vivo inhibitory activity against human Heparanase', 'assay_type': 'B', 'bao_endpoint': 'BAO_0000190', 'bao_format': 'BAO_0000218', 'bao_label': 'organism-based format', 'canonical_smiles': 'Cc1ccc2oc(nc2c1)c3cccc(c3)N4C(=O)c5ccc(cc5C4=O)C(=O)O', 'data_validity_comment': None, 'document_chembl_id': 'CHEMBL1146658', 'document_journal': 'Bioorg. Med. Chem. Lett.', 'document_year': 2004, 'ligand_efficiency': {'bei': '14.06', 'le': '0.26', 'lle': '1.59', 'sei': '5.56'}, 'molecule_chembl_id': 'CHEMBL324340', 'parent_molecule_chembl_id': 'CHEMBL324340', 'pchembl_value': '5.6', 'potential_duplicate': False, 'published_relation': '=', 'published_type': 'IC50', 'published_units': 'uM', 'published_value': '2.5', 'qudt_units': 'http://www.openphacts.org/units/Nanomolar', 'record_id': 208970, 'src_id': 1, 'standard_flag': True, 'standard_relation': '=', 'standard_type': 'IC50', 'standard_units': 'nM', 'standard_value': '2500', 'target_chembl_id': 'CHEMBL3921', 'target_organism': 'Homo sapiens', 'target_pref_name': 'Heparanase', 'target_tax_id': '9606', 'uo_units': 'UO_0000065'}, {'activity_comment': None, 'activity_id': 31865, 'assay_chembl_id': 'CHEMBL693237', 'assay_description': 'In vivo concentration required against angiogenesis in human endothelial cells', 'assay_type': 'F', 'bao_endpoint': 'BAO_0000190', 'bao_format': 'BAO_0000218', 'bao_label': 'organism-based format', 'canonical_smiles': 'Cc1ccc2oc(nc2c1)c3cccc(c3)N4C(=O)c5ccc(cc5C4=O)C(=O)O', 'data_validity_comment': None, 'document_chembl_id': 'CHEMBL1146658', 'document_journal': 'Bioorg. Med. Chem. Lett.', 'document_year': 2004, 'ligand_efficiency': None, 'molecule_chembl_id': 'CHEMBL324340', 'parent_molecule_chembl_id': 'CHEMBL324340', 'pchembl_value': None, 'potential_duplicate': False, 'published_relation': '>', 'published_type': 'IC50', 'published_units': 'uM', 'published_value': '50', 'qudt_units': 'http://www.openphacts.org/units/Nanomolar', 'record_id': 208970, 'src_id': 1, 'standard_flag': True, 'standard_relation': '>', 'standard_type': 'IC50', 'standard_units': 'nM', 'standard_value': '50000', 'target_chembl_id': 'CHEMBL612545', 'target_organism': None, 'target_pref_name': 'Unchecked', 'target_tax_id': None, 'uo_units': 'UO_0000065'}, {'activity_comment': None, 'activity_id': 31866, 'assay_chembl_id': 'CHEMBL872937', 'assay_description': 'In vivo inhibitory activity against human Heparanase', 'assay_type': 'B', 'bao_endpoint': 'BAO_0000190', 'bao_format': 'BAO_0000218', 'bao_label': 'organism-based format', 'canonical_smiles': 'COc1ccc(cc1N2C(=O)c3ccc(cc3C2=O)C(=O)O)c4oc5ccc(cc5n4)c6ccccc6OC', 'data_validity_comment': None, 'document_chembl_id': 'CHEMBL1146658', 'document_journal': 'Bioorg. Med. Chem. Lett.', 'document_year': 2004, 'ligand_efficiency': {'bei': '9.69', 'le': '0.18', 'lle': '0.04', 'sei': '4.23'}, 'molecule_chembl_id': 'CHEMBL109600', 'parent_molecule_chembl_id': 'CHEMBL109600', 'pchembl_value': '5.05', 'potential_duplicate': False, 'published_relation': '=', 'published_type': 'IC50', 'published_units': 'uM', 'published_value': '9', 'qudt_units': 'http://www.openphacts.org/units/Nanomolar', 'record_id': 208987, 'src_id': 1, 'standard_flag': True, 'standard_relation': '=', 'standard_type': 'IC50', 'standard_units': 'nM', 'standard_value': '9000', 'target_chembl_id': 'CHEMBL3921', 'target_organism': 'Homo sapiens', 'target_pref_name': 'Heparanase', 'target_tax_id': '9606', 'uo_units': 'UO_0000065'}, '...(remaining elements truncated)...']
In [9]:
# Let's get all measurement for a target
chembl_abl_activities = chembl.activity.filter(target_chembl_id='CHEMBL4014')
print(list(chembl_abl_activities))
[{'activity_comment': 'Not Active', 'activity_id': 1650414, 'assay_chembl_id': 'CHEMBL860899', 'assay_description': 'Average Binding Constant for ABL2; NA=Not Active at 10 uM', 'assay_type': 'B', 'bao_endpoint': 'BAO_0000034', 'bao_format': 'BAO_0000357', 'bao_label': 'single protein format', 'canonical_smiles': 'CS(=O)(=O)CCNCc1oc(cc1)c2ccc3ncnc(Nc4ccc(OCc5cccc(F)c5)c(Cl)c4)c3c2', 'data_validity_comment': None, 'document_chembl_id': 'CHEMBL1144455', 'document_journal': 'Nat. Biotechnol.', 'document_year': 2005, 'ligand_efficiency': None, 'molecule_chembl_id': 'CHEMBL554', 'parent_molecule_chembl_id': 'CHEMBL554', 'pchembl_value': None, 'potential_duplicate': False, 'published_relation': None, 'published_type': 'Kd', 'published_units': None, 'published_value': None, 'qudt_units': None, 'record_id': 405809, 'src_id': 1, 'standard_flag': False, 'standard_relation': None, 'standard_type': 'Kd', 'standard_units': None, 'standard_value': None, 'target_chembl_id': 'CHEMBL4014', 'target_organism': 'Homo sapiens', 'target_pref_name': 'Tyrosine-protein kinase ABL2', 'target_tax_id': '9606', 'uo_units': None}, {'activity_comment': None, 'activity_id': 1650415, 'assay_chembl_id': 'CHEMBL860899', 'assay_description': 'Average Binding Constant for ABL2; NA=Not Active at 10 uM', 'assay_type': 'B', 'bao_endpoint': 'BAO_0000034', 'bao_format': 'BAO_0000357', 'bao_label': 'single protein format', 'canonical_smiles': 'CCOc1cc2ncc(C#N)c(Nc3ccc(F)c(Cl)c3)c2cc1NC(=O)\\C=C\\CN(C)C', 'data_validity_comment': None, 'document_chembl_id': 'CHEMBL1144455', 'document_journal': 'Nat. Biotechnol.', 'document_year': 2005, 'ligand_efficiency': {'bei': '14.52', 'le': '0.28', 'lle': '2.34', 'sei': '7.53'}, 'molecule_chembl_id': 'CHEMBL607707', 'parent_molecule_chembl_id': 'CHEMBL607707', 'pchembl_value': '6.8', 'potential_duplicate': False, 'published_relation': '=', 'published_type': 'Kd', 'published_units': 'uM', 'published_value': '0.16', 'qudt_units': 'http://www.openphacts.org/units/Nanomolar', 'record_id': 405810, 'src_id': 1, 'standard_flag': True, 'standard_relation': '=', 'standard_type': 'Kd', 'standard_units': 'nM', 'standard_value': '160', 'target_chembl_id': 'CHEMBL4014', 'target_organism': 'Homo sapiens', 'target_pref_name': 'Tyrosine-protein kinase ABL2', 'target_tax_id': '9606', 'uo_units': 'UO_0000065'}, {'activity_comment': 'Not Active', 'activity_id': 1650416, 'assay_chembl_id': 'CHEMBL860899', 'assay_description': 'Average Binding Constant for ABL2; NA=Not Active at 10 uM', 'assay_type': 'B', 'bao_endpoint': 'BAO_0000034', 'bao_format': 'BAO_0000357', 'bao_label': 'single protein format', 'canonical_smiles': 'Clc1ccc(Nc2nnc(Cc3ccncc3)c4ccccc24)cc1', 'data_validity_comment': None, 'document_chembl_id': 'CHEMBL1144455', 'document_journal': 'Nat. Biotechnol.', 'document_year': 2005, 'ligand_efficiency': None, 'molecule_chembl_id': 'CHEMBL101253', 'parent_molecule_chembl_id': 'CHEMBL101253', 'pchembl_value': None, 'potential_duplicate': False, 'published_relation': None, 'published_type': 'Kd', 'published_units': None, 'published_value': None, 'qudt_units': None, 'record_id': 405812, 'src_id': 1, 'standard_flag': False, 'standard_relation': None, 'standard_type': 'Kd', 'standard_units': None, 'standard_value': None, 'target_chembl_id': 'CHEMBL4014', 'target_organism': 'Homo sapiens', 'target_pref_name': 'Tyrosine-protein kinase ABL2', 'target_tax_id': '9606', 'uo_units': None}, {'activity_comment': None, 'activity_id': 1650417, 'assay_chembl_id': 'CHEMBL860899', 'assay_description': 'Average Binding Constant for ABL2; NA=Not Active at 10 uM', 'assay_type': 'B', 'bao_endpoint': 'BAO_0000034', 'bao_format': 'BAO_0000357', 'bao_label': 'single protein format', 'canonical_smiles': 'CCN(CC)CCNC(=O)c1c(C)[nH]c(\\C=C\\2/C(=O)Nc3ccc(F)cc23)c1C', 'data_validity_comment': None, 'document_chembl_id': 'CHEMBL1144455', 'document_journal': 'Nat. Biotechnol.', 'document_year': 2005, 'ligand_efficiency': {'bei': '14.86', 'le': '0.28', 'lle': '2.92', 'sei': '7.67'}, 'molecule_chembl_id': 'CHEMBL535', 'parent_molecule_chembl_id': 'CHEMBL535', 'pchembl_value': '5.92', 'potential_duplicate': False, 'published_relation': '=', 'published_type': 'Kd', 'published_units': 'uM', 'published_value': '1.2', 'qudt_units': 'http://www.openphacts.org/units/Nanomolar', 'record_id': 405813, 'src_id': 1, 'standard_flag': True, 'standard_relation': '=', 'standard_type': 'Kd', 'standard_units': 'nM', 'standard_value': '1200', 'target_chembl_id': 'CHEMBL4014', 'target_organism': 'Homo sapiens', 'target_pref_name': 'Tyrosine-protein kinase ABL2', 'target_tax_id': '9606', 'uo_units': 'UO_0000065'}, {'activity_comment': 'Not Active', 'activity_id': 1650418, 'assay_chembl_id': 'CHEMBL860899', 'assay_description': 'Average Binding Constant for ABL2; NA=Not Active at 10 uM', 'assay_type': 'B', 'bao_endpoint': 'BAO_0000034', 'bao_format': 'BAO_0000357', 'bao_label': 'single protein format', 'canonical_smiles': 'COc1cc2c(ncnc2cc1OCCCN3CCCCC3)N4CCN(CC4)C(=O)Nc5ccc(OC(C)C)cc5', 'data_validity_comment': None, 'document_chembl_id': 'CHEMBL1144455', 'document_journal': 'Nat. Biotechnol.', 'document_year': 2005, 'ligand_efficiency': None, 'molecule_chembl_id': 'CHEMBL124660', 'parent_molecule_chembl_id': 'CHEMBL124660', 'pchembl_value': None, 'potential_duplicate': False, 'published_relation': None, 'published_type': 'Kd', 'published_units': None, 'published_value': None, 'qudt_units': None, 'record_id': 405814, 'src_id': 1, 'standard_flag': False, 'standard_relation': None, 'standard_type': 'Kd', 'standard_units': None, 'standard_value': None, 'target_chembl_id': 'CHEMBL4014', 'target_organism': 'Homo sapiens', 'target_pref_name': 'Tyrosine-protein kinase ABL2', 'target_tax_id': '9606', 'uo_units': None}, {'activity_comment': 'Not Active', 'activity_id': 1650419, 'assay_chembl_id': 'CHEMBL860899', 'assay_description': 'Average Binding Constant for ABL2; NA=Not Active at 10 uM', 'assay_type': 'B', 'bao_endpoint': 'BAO_0000034', 'bao_format': 'BAO_0000357', 'bao_label': 'single protein format', 'canonical_smiles': 'CN(C)C[C@@H]1CCn2cc(C3=C(C(=O)NC3=O)c4cn(CCO1)c5ccccc45)c6ccccc26', 'data_validity_comment': None, 'document_chembl_id': 'CHEMBL1144455', 'document_journal': 'Nat. Biotechnol.', 'document_year': 2005, 'ligand_efficiency': None, 'molecule_chembl_id': 'CHEMBL91829', 'parent_molecule_chembl_id': 'CHEMBL91829', 'pchembl_value': None, 'potential_duplicate': False, 'published_relation': None, 'published_type': 'Kd', 'published_units': None, 'published_value': None, 'qudt_units': None, 'record_id': 405815, 'src_id': 1, 'standard_flag': False, 'standard_relation': None, 'standard_type': 'Kd', 'standard_units': None, 'standard_value': None, 'target_chembl_id': 'CHEMBL4014', 'target_organism': 'Homo sapiens', 'target_pref_name': 'Tyrosine-protein kinase ABL2', 'target_tax_id': '9606', 'uo_units': None}, {'activity_comment': None, 'activity_id': 1650420, 'assay_chembl_id': 'CHEMBL860899', 'assay_description': 'Average Binding Constant for ABL2; NA=Not Active at 10 uM', 'assay_type': 'B', 'bao_endpoint': 'BAO_0000034', 'bao_format': 'BAO_0000357', 'bao_label': 'single protein format', 'canonical_smiles': 'CNC(=O)c1cc(Oc2ccc(NC(=O)Nc3ccc(Cl)c(c3)C(F)(F)F)cc2)ccn1', 'data_validity_comment': None, 'document_chembl_id': 'CHEMBL1144455', 'document_journal': 'Nat. 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Lett.', 'document_year': 2016, 'ligand_efficiency': None, 'molecule_chembl_id': 'CHEMBL3758502', 'parent_molecule_chembl_id': 'CHEMBL3758502', 'pchembl_value': None, 'potential_duplicate': None, 'published_relation': '=', 'published_type': 'INH', 'published_units': '%', 'published_value': '69.5', 'qudt_units': 'http://qudt.org/vocab/unit#Percent', 'record_id': 2747903, 'src_id': 1, 'standard_flag': True, 'standard_relation': '=', 'standard_type': 'Inhibition', 'standard_units': '%', 'standard_value': '69.5', 'target_chembl_id': 'CHEMBL4014', 'target_organism': 'Homo sapiens', 'target_pref_name': 'Tyrosine-protein kinase ABL2', 'target_tax_id': '9606', 'uo_units': 'UO_0000187'}, {'activity_comment': None, 'activity_id': 16495333, 'assay_chembl_id': 'CHEMBL3776646', 'assay_description': 'Inhibition of N-terminal His6-tagged recombinant ARG (unknown origin) expressed in baculovirus infected insect Sf9 cells assessed as remaining activity at 1 uM relative to control', 'assay_type': 'B', 'bao_endpoint': 'BAO_0001103', 'bao_format': None, 'bao_label': None, 'canonical_smiles': 'Cn1cc(cn1)c2ccc(Cc3n[nH]c4ccc(cc34)C(=O)N5CCOCC5)cc2', 'data_validity_comment': None, 'document_chembl_id': 'CHEMBL3774357', 'document_journal': 'Bioorg. Med. Chem. Lett.', 'document_year': 2016, 'ligand_efficiency': None, 'molecule_chembl_id': 'CHEMBL3774885', 'parent_molecule_chembl_id': 'CHEMBL3774885', 'pchembl_value': None, 'potential_duplicate': None, 'published_relation': '=', 'published_type': 'Activity', 'published_units': '%', 'published_value': '-15', 'qudt_units': 'http://qudt.org/vocab/unit#Percent', 'record_id': 2763281, 'src_id': 1, 'standard_flag': False, 'standard_relation': '=', 'standard_type': 'Activity', 'standard_units': '%', 'standard_value': '-15', 'target_chembl_id': 'CHEMBL4014', 'target_organism': 'Homo sapiens', 'target_pref_name': 'Tyrosine-protein kinase ABL2', 'target_tax_id': '9606', 'uo_units': 'UO_0000187'}, {'activity_comment': None, 'activity_id': 16508102, 'assay_chembl_id': 'CHEMBL3776646', 'assay_description': 'Inhibition of N-terminal His6-tagged recombinant ARG (unknown origin) expressed in baculovirus infected insect Sf9 cells assessed as remaining activity at 1 uM relative to control', 'assay_type': 'B', 'bao_endpoint': 'BAO_0001103', 'bao_format': None, 'bao_label': None, 'canonical_smiles': 'CNC(=O)c1ccc2[nH]nc(Cc3ccc4c(cnn4C)c3)c2c1', 'data_validity_comment': None, 'document_chembl_id': 'CHEMBL3774357', 'document_journal': 'Bioorg. Med. Chem. Lett.', 'document_year': 2016, 'ligand_efficiency': None, 'molecule_chembl_id': 'CHEMBL3775576', 'parent_molecule_chembl_id': 'CHEMBL3775576', 'pchembl_value': None, 'potential_duplicate': None, 'published_relation': '=', 'published_type': 'Activity', 'published_units': '%', 'published_value': '20', 'qudt_units': 'http://qudt.org/vocab/unit#Percent', 'record_id': 2763260, 'src_id': 1, 'standard_flag': False, 'standard_relation': '=', 'standard_type': 'Activity', 'standard_units': '%', 'standard_value': '20', 'target_chembl_id': 'CHEMBL4014', 'target_organism': 'Homo sapiens', 'target_pref_name': 'Tyrosine-protein kinase ABL2', 'target_tax_id': '9606', 'uo_units': 'UO_0000187'}, {'activity_comment': None, 'activity_id': 16509079, 'assay_chembl_id': 'CHEMBL3776646', 'assay_description': 'Inhibition of N-terminal His6-tagged recombinant ARG (unknown origin) expressed in baculovirus infected insect Sf9 cells assessed as remaining activity at 1 uM relative to control', 'assay_type': 'B', 'bao_endpoint': 'BAO_0001103', 'bao_format': None, 'bao_label': None, 'canonical_smiles': 'Cn1cc(cn1)c2ccc(Cc3n[nH]c4ccc(cc34)C(=O)N5CC[C@@H](O)C5)cc2', 'data_validity_comment': None, 'document_chembl_id': 'CHEMBL3774357', 'document_journal': 'Bioorg. Med. Chem. Lett.', 'document_year': 2016, 'ligand_efficiency': None, 'molecule_chembl_id': 'CHEMBL3775317', 'parent_molecule_chembl_id': 'CHEMBL3775317', 'pchembl_value': None, 'potential_duplicate': None, 'published_relation': '=', 'published_type': 'Activity', 'published_units': '%', 'published_value': '14', 'qudt_units': 'http://qudt.org/vocab/unit#Percent', 'record_id': 2763273, 'src_id': 1, 'standard_flag': False, 'standard_relation': '=', 'standard_type': 'Activity', 'standard_units': '%', 'standard_value': '14', 'target_chembl_id': 'CHEMBL4014', 'target_organism': 'Homo sapiens', 'target_pref_name': 'Tyrosine-protein kinase ABL2', 'target_tax_id': '9606', 'uo_units': 'UO_0000187'}, {'activity_comment': None, 'activity_id': 16593537, 'assay_chembl_id': 'CHEMBL3811540', 'assay_description': 'Inhibition of His-tagged full length human recombinant ARG expressed in baculovirus using Fluorescein-Poly GT as substrate at 100 nM', 'assay_type': 'B', 'bao_endpoint': 'BAO_0000201', 'bao_format': None, 'bao_label': None, 'canonical_smiles': 'COC(=O)c1cc2cc(NCc3cc(NC(=O)c4cc(cc(c4)C(F)(F)F)n5cnc(C)c5)ccc3C)cnc2[nH]1', 'data_validity_comment': None, 'document_chembl_id': 'CHEMBL3808348', 'document_journal': 'J. Med. Chem.', 'document_year': 2016, 'ligand_efficiency': None, 'molecule_chembl_id': 'CHEMBL3808884', 'parent_molecule_chembl_id': 'CHEMBL3808884', 'pchembl_value': None, 'potential_duplicate': None, 'published_relation': '<', 'published_type': 'INH', 'published_units': '%', 'published_value': '40', 'qudt_units': 'http://qudt.org/vocab/unit#Percent', 'record_id': 2780310, 'src_id': 1, 'standard_flag': True, 'standard_relation': '<', 'standard_type': 'Inhibition', 'standard_units': '%', 'standard_value': '40', 'target_chembl_id': 'CHEMBL4014', 'target_organism': 'Homo sapiens', 'target_pref_name': 'Tyrosine-protein kinase ABL2', 'target_tax_id': '9606', 'uo_units': 'UO_0000187'}, {'activity_comment': None, 'activity_id': 16613759, 'assay_chembl_id': 'CHEMBL3816552', 'assay_description': 'Inhibition of human ABL2 at 1 uM using [EAIYAAPFAKKK] as substrate', 'assay_type': 'B', 'bao_endpoint': 'BAO_0000201', 'bao_format': None, 'bao_label': None, 'canonical_smiles': 'CNS(=O)(=O)c1ccc(N(C)C)c(Nc2ncnc3cc(OC)c(OC)cc23)c1', 'data_validity_comment': None, 'document_chembl_id': 'CHEMBL3813650', 'document_journal': 'Bioorg. Med. Chem. Lett.', 'document_year': 2016, 'ligand_efficiency': None, 'molecule_chembl_id': 'CHEMBL3815093', 'parent_molecule_chembl_id': 'CHEMBL3815093', 'pchembl_value': None, 'potential_duplicate': None, 'published_relation': '=', 'published_type': 'INH', 'published_units': '%', 'published_value': '4', 'qudt_units': 'http://qudt.org/vocab/unit#Percent', 'record_id': 2781972, 'src_id': 1, 'standard_flag': True, 'standard_relation': '=', 'standard_type': 'Inhibition', 'standard_units': '%', 'standard_value': '4', 'target_chembl_id': 'CHEMBL4014', 'target_organism': 'Homo sapiens', 'target_pref_name': 'Tyrosine-protein kinase ABL2', 'target_tax_id': '9606', 'uo_units': 'UO_0000187'}, {'activity_comment': None, 'activity_id': 16618280, 'assay_chembl_id': 'CHEMBL3817005', 'assay_description': 'Inhibition of full length recombinant human C-terminal His-tagged cytoplasmic ARG expressed in baculovirus expression system at 1 uM relative to control', 'assay_type': 'B', 'bao_endpoint': 'BAO_0000201', 'bao_format': None, 'bao_label': None, 'canonical_smiles': 'CC1(C)OCCn2c1nc3c(nc(nc23)c4cnc(N)nc4)N5CCOCC5', 'data_validity_comment': None, 'document_chembl_id': 'CHEMBL3813614', 'document_journal': 'ACS Med. Chem. Lett.', 'document_year': 2016, 'ligand_efficiency': None, 'molecule_chembl_id': 'CHEMBL3813842', 'parent_molecule_chembl_id': 'CHEMBL3813842', 'pchembl_value': None, 'potential_duplicate': None, 'published_relation': '<', 'published_type': 'INH', 'published_units': '%', 'published_value': '50', 'qudt_units': 'http://qudt.org/vocab/unit#Percent', 'record_id': 2781546, 'src_id': 1, 'standard_flag': True, 'standard_relation': '<', 'standard_type': 'Inhibition', 'standard_units': '%', 'standard_value': '50', 'target_chembl_id': 'CHEMBL4014', 'target_organism': 'Homo sapiens', 'target_pref_name': 'Tyrosine-protein kinase ABL2', 'target_tax_id': '9606', 'uo_units': 'UO_0000187'}, {'activity_comment': None, 'activity_id': 16619677, 'assay_chembl_id': 'CHEMBL3820245', 'assay_description': 'Inhibition of recombinant human full length His-tagged ARG expressed in Baculovirus at 1 uM relative to control', 'assay_type': 'B', 'bao_endpoint': 'BAO_0000201', 'bao_format': None, 'bao_label': None, 'canonical_smiles': 'CN(C)C[C@@H](NC(=O)N1Cc2c(Nc3nc(C)nc4ccsc34)n[nH]c2C1(C)C)c5ccccc5', 'data_validity_comment': None, 'document_chembl_id': 'CHEMBL3817726', 'document_journal': 'J. Med. Chem.', 'document_year': 2016, 'ligand_efficiency': None, 'molecule_chembl_id': 'CHEMBL3128043', 'parent_molecule_chembl_id': 'CHEMBL3128043', 'pchembl_value': None, 'potential_duplicate': None, 'published_relation': '>', 'published_type': 'INH', 'published_units': '%', 'published_value': '75', 'qudt_units': 'http://qudt.org/vocab/unit#Percent', 'record_id': 2783846, 'src_id': 1, 'standard_flag': True, 'standard_relation': '>', 'standard_type': 'Inhibition', 'standard_units': '%', 'standard_value': '75', 'target_chembl_id': 'CHEMBL4014', 'target_organism': 'Homo sapiens', 'target_pref_name': 'Tyrosine-protein kinase ABL2', 'target_tax_id': '9606', 'uo_units': 'UO_0000187'}, {'activity_comment': None, 'activity_id': 16621477, 'assay_chembl_id': 'CHEMBL3820470', 'assay_description': 'Inhibition of ARG (unknown origin) incubated for 1 hr by spectrophotometric analysis', 'assay_type': 'B', 'bao_endpoint': 'BAO_0000190', 'bao_format': None, 'bao_label': None, 'canonical_smiles': 'CN1C(=O)COc2c1cnc3ccc(Sc4nnc5c(F)cc(cn45)c6cnn(C)c6)cc23', 'data_validity_comment': None, 'document_chembl_id': 'CHEMBL3817824', 'document_journal': 'Bioorg. Med. Chem.', 'document_year': 2016, 'ligand_efficiency': None, 'molecule_chembl_id': 'CHEMBL3818247', 'parent_molecule_chembl_id': 'CHEMBL3818247', 'pchembl_value': None, 'potential_duplicate': None, 'published_relation': '>', 'published_type': 'IC50', 'published_units': 'nM', 'published_value': '30000', 'qudt_units': 'http://www.openphacts.org/units/Nanomolar', 'record_id': 2784915, 'src_id': 1, 'standard_flag': True, 'standard_relation': '>', 'standard_type': 'IC50', 'standard_units': 'nM', 'standard_value': '30000', 'target_chembl_id': 'CHEMBL4014', 'target_organism': 'Homo sapiens', 'target_pref_name': 'Tyrosine-protein kinase ABL2', 'target_tax_id': '9606', 'uo_units': 'UO_0000065'}, {'activity_comment': None, 'activity_id': 16622192, 'assay_chembl_id': 'CHEMBL3820470', 'assay_description': 'Inhibition of ARG (unknown origin) incubated for 1 hr by spectrophotometric analysis', 'assay_type': 'B', 'bao_endpoint': 'BAO_0000190', 'bao_format': None, 'bao_label': None, 'canonical_smiles': 'CN[C@@H]1C[C@H]2O[C@@](C)([C@@H]1OC)n3c4ccccc4c5c6CNC(=O)c6c7c8ccccc8n2c7c35', 'data_validity_comment': None, 'document_chembl_id': 'CHEMBL3817824', 'document_journal': 'Bioorg. Med. Chem.', 'document_year': 2016, 'ligand_efficiency': None, 'molecule_chembl_id': 'CHEMBL388978', 'parent_molecule_chembl_id': 'CHEMBL388978', 'pchembl_value': '7.12', 'potential_duplicate': None, 'published_relation': '=', 'published_type': 'IC50', 'published_units': 'nM', 'published_value': '75.9', 'qudt_units': 'http://www.openphacts.org/units/Nanomolar', 'record_id': 2783100, 'src_id': 1, 'standard_flag': True, 'standard_relation': '=', 'standard_type': 'IC50', 'standard_units': 'nM', 'standard_value': '75.9', 'target_chembl_id': 'CHEMBL4014', 'target_organism': 'Homo sapiens', 'target_pref_name': 'Tyrosine-protein kinase ABL2', 'target_tax_id': '9606', 'uo_units': 'UO_0000065'}]
In [10]:
import xmltodict
In [11]:
# next, we are retrieving details from the assay the activity was measured in
# we keep binding and functional assays
# compounds of 10nM or better are considered as actives
# compounds of 10mycroM or worse are considered as inactives
chembl.assay.set_format('xml')
selected_actives = []
selected_decoys = []
for i in range(len(chembl_abl_activities)):
    x = chembl_abl_activities[i]
    ID = (x['assay_chembl_id'])
    details = chembl.assay.get(ID)
    d=xmltodict.parse(details)
    if(int(d['assay']['confidence_score']) == 9):
        if (d['assay']['assay_type'] in ['B','F']):
            if str(x['standard_units']) == 'nM':
                if float(x['standard_value']) < 10:
                    selected_actives.append(x['canonical_smiles'])
                elif float(x['standard_value']) > 10000:
                    selected_decoys.append(x['canonical_smiles'])
#selected_actives = set(selected_actives)            
print (len(selected_actives), len(selected_decoys)) 
selected_actives = set(selected_actives)
with open("ABL_smi","w") as fh:
    count = 0
    for e in selected_actives:
        print(e)
        count+=1
        fh.write(e + "\n")
14 2
COc1cc(Nc2c(cnc3cc(OCCCN4CCN(C)CC4)c(OC)cc23)C#N)c(Cl)cc1Cl
CSc1cccc(Nc2ncc3C=C(C(=O)N(C)c3n2)c4c(Cl)cccc4Cl)c1
CN1CCN(Cc2ccc(NC(=O)Nc3cc(C#Cc4cnc5cnccn45)n(C)n3)cc2C(F)(F)F)CC1
CN1CCN(Cc2ccc(cc2)C(=O)Nc3ccc(C)c(Nc4nccc(n4)c5cccnc5)c3)CC1
Cc1nc(Nc2ncc(s2)C(=O)Nc3c(C)cccc3Cl)cc(n1)N4CCN(CCO)CC4
CN1CCN(Cc2ccc(NC(=O)Nc3cc(C#Cc4cnc5cccnn45)n(C)n3)cc2C(F)(F)F)CC1
CN1CCN(Cc2ccc(NC(=O)c3ccc(C)c(c3)C#Cc4cncc5nccn45)cc2C(F)(F)F)CC1
CN1CCN(Cc2ccc(cc2C(F)(F)F)C(=O)Nc3ccc(C)c(c3)C#Cc4cnc5cccnn45)CC1
CCN1CCN(Cc2ccc(NC(=O)Nc3ccc(Oc4cc(NC)ncn4)cc3)cc2C(F)(F)F)CC1
CN1CCN(CC1)c2cc(Nc3cc(C)[nH]n3)nc(Sc4ccc(NC(=O)C5CC5)cc4)n2
In [ ]: