Working with Molecules from ZINC and ChEMBL¶
Graphein provides utilities for retrieving molecules and metadata from ZINC and ChEMBL
The ZINC database is a curated collection of commercially available chemical compounds prepared especially for virtual screening.
ChEMBL or ChEMBLdb is a manually curated chemical database of bioactive molecules with drug-like properties. It is maintained by the European Bioinformatics Institute, of the European Molecular Biology Laboratory
[2]:
# Install Graphein if necessary
# !pip install graphein[extras]
[3]:
import graphein.molecule as gm
ZINC¶
Mapping between SMILEs and ZINC IDs.¶
[4]:
#NBVAL_SKIP
gm.get_smiles_from_zinc("ZINC01234567", backend="zinc15") #Backend allows specification of which ZINC release to use
[4]:
'C[C@H]1CCCCN1CC#CC(O)(c1ccccc1)c1ccccc1'
We can also map a SMILE string back to ZINC identifiers.
N.B. we may obtain multiple ZINC IDs. In the example below, we retrieve two ZINC IDs for the two enantiomers of the specified molecule
[5]:
#NBVAL_SKIP
gm.get_zinc_id_from_smile("C[C@H]1CCCCN1CC#CC(O)(c1ccccc1)c1ccccc1")
[5]:
['ZINC000001234567', 'ZINC000001234568']
Constructing Graphs¶
We can also retrieve the molecular graphs directly from the ZINC ID
[6]:
#NBVAL_SKIP
g = gm.construct_graph(zinc_id="ZINC000001234567")
g.graph["rdmol"]
[6]:
[8]:
#NBVAL_SKIP
g = gm.construct_graph(zinc_id="ZINC000001234568")
g.graph["rdmol"]
[8]:
[18]:
#NBVAL_SKIP
# Here we retrieve the above molecule, generate a 3D conformer and visualise it
config = gm.MoleculeGraphConfig(edge_construction_functions=[gm.add_atom_bonds])
g = gm.construct_graph(zinc_id="ZINC000001234568", generate_conformer=True, config=config)
gm.plotly_molecular_graph(g)
Data type cannot be displayed: application/vnd.plotly.v1+json
ChEMBL¶
Similarly, we can map between ChEMBL identifiers and SMILEs. We can also add ChEMBLs rich metadata to the graph
[6]:
#NBVAL_SKIP
gm.get_smiles_from_chembl("CHEMBL1234")
WARNING [bioservices:ChEMBL:119]: The URL (https://www.ebi.ac.uk/chembl/api/data) provided cannot be reached.
[6]:
'CC(=O)N(O)CCCCCNC(=O)CCC(=O)N(O)CCCCCNC(=O)CCC(=O)N(O)CCCCCN.CS(=O)(=O)O'
[7]:
#NBVAL_SKIP
gm.get_chembl_id_from_smiles("CC(=O)N(O)CCCCCNC(=O)CCC(=O)N(O)CCCCCNC(=O)CCC(=O)N(O)CCCCCN.CS(=O)(=O)O")
WARNING [bioservices:ChEMBL:119]: The URL (https://www.ebi.ac.uk/chembl/api/data) provided cannot be reached.
WARNING [bioservices:ChEMBL:119]: The URL (https://www.ebi.ac.uk/chembl/api/data) provided cannot be reached.
[7]:
'CHEMBL1234'
Constructing Graphs from ChEMBL¶
[9]:
#NBVAL_SKIP
g = gm.construct_graph(chembl_id="CHEMBL1234")
g.graph["rdmol"]
WARNING [bioservices:ChEMBL:119]: The URL (https://www.ebi.ac.uk/chembl/api/data) provided cannot be reached.
WARNING [bioservices:ChEMBL:119]: The URL (https://www.ebi.ac.uk/chembl/api/data) provided cannot be reached.
WARNING [bioservices:ChEMBL:119]: The URL (https://www.ebi.ac.uk/chembl/api/data) provided cannot be reached.
WARNING [bioservices:ChEMBL:119]: The URL (https://www.ebi.ac.uk/chembl/api/data) provided cannot be reached.
[9]:
Retrieving Metadata from ChEMBL¶
We can retrieve metadata from chembl both functionally and via the graph construction config.
[13]:
#NBVAL_SKIP
# Functionally
g = gm.add_chembl_metadata(g)
print(g.graph["chembl_metadata"])
WARNING [bioservices:ChEMBL:119]: The URL (https://www.ebi.ac.uk/chembl/api/data) provided cannot be reached.
WARNING [bioservices:ChEMBL:119]: The URL (https://www.ebi.ac.uk/chembl/api/data) provided cannot be reached.
WARNING [bioservices:ChEMBL:119]: The URL (https://www.ebi.ac.uk/chembl/api/data) provided cannot be reached.
WARNING [bioservices:ChEMBL:119]: The URL (https://www.ebi.ac.uk/chembl/api/data) provided cannot be reached.
WARNING [bioservices:ChEMBL:119]: The URL (https://www.ebi.ac.uk/chembl/api/data) provided cannot be reached.
WARNING [bioservices:ChEMBL:119]: The URL (https://www.ebi.ac.uk/chembl/api/data) provided cannot be reached.
WARNING [bioservices:ChEMBL:119]: The URL (https://www.ebi.ac.uk/chembl/api/data) provided cannot be reached.
WARNING [bioservices:ChEMBL:119]: The URL (https://www.ebi.ac.uk/chembl/api/data) provided cannot be reached.
{'atc_classifications': [], 'availability_type': 1, 'biotherapeutic': None, 'black_box_warning': 0, 'chebi_par_id': 31460, 'chirality': 2, 'cross_references': [{'xref_id': 'deferoxamine%20mesylate', 'xref_name': 'deferoxamine mesylate', 'xref_src': 'DailyMed'}, {'xref_id': '11112937', 'xref_name': 'SID: 11112937', 'xref_src': 'PubChem'}, {'xref_id': '11533050', 'xref_name': 'SID: 11533050', 'xref_src': 'PubChem'}, {'xref_id': '124882730', 'xref_name': 'SID: 124882730', 'xref_src': 'PubChem'}, {'xref_id': '144204292', 'xref_name': 'SID: 144204292', 'xref_src': 'PubChem'}, {'xref_id': '170464752', 'xref_name': 'SID: 170464752', 'xref_src': 'PubChem'}, {'xref_id': '26747967', 'xref_name': 'SID: 26747967', 'xref_src': 'PubChem'}], 'dosed_ingredient': True, 'first_approval': 1968, 'first_in_class': 0, 'helm_notation': None, 'indication_class': 'Antidote (to iron poisoning); Chelating Agent', 'inorganic_flag': 0, 'max_phase': 4, 'molecule_chembl_id': 'CHEMBL1234', 'molecule_hierarchy': {'molecule_chembl_id': 'CHEMBL1234', 'parent_chembl_id': 'CHEMBL556'}, 'molecule_properties': {'alogp': '0.92', 'aromatic_rings': 0, 'cx_logd': '-3.64', 'cx_logp': '-3.37', 'cx_most_apka': '7.92', 'cx_most_bpka': '10.21', 'full_molformula': 'C26H52N6O11S', 'full_mwt': '656.80', 'hba': 9, 'hba_lipinski': 14, 'hbd': 6, 'hbd_lipinski': 7, 'heavy_atoms': 39, 'molecular_species': 'BASE', 'mw_freebase': '560.69', 'mw_monoisotopic': '560.3534', 'num_lipinski_ro5_violations': 3, 'num_ro5_violations': 2, 'psa': '205.84', 'qed_weighted': '0.06', 'ro3_pass': 'N', 'rtb': 23}, 'molecule_structures': {'canonical_smiles': 'CC(=O)N(O)CCCCCNC(=O)CCC(=O)N(O)CCCCCNC(=O)CCC(=O)N(O)CCCCCN.CS(=O)(=O)O', 'molfile': '\n RDKit 2D\n\n 44 42 0 0 0 0 0 0 0 0999 V2000\n 8.4417 0.9708 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.5667 0.5208 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 7.7167 -4.3792 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 10.5792 0.5708 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 2.7042 0.9125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.5667 -0.3250 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n 7.7167 0.5375 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n 8.4417 -3.9750 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n -0.1583 0.9250 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 8.4417 1.7833 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 7.0125 -3.9750 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 9.1542 0.5500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1.2792 0.9250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 2.7042 1.7375 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 11.3042 0.9833 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 10.5792 -0.2542 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n 3.4292 0.5000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n 2.0000 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 9.8750 0.9708 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 9.1667 -4.4250 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 7.7167 -0.2875 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 1.2792 -0.7250 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n -1.5833 -4.0375 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n 7.7167 -5.2250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 7.0125 0.9583 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -0.1583 -0.7375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 8.4417 -3.1500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 4.1417 0.9250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 9.8750 -0.6542 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -1.5833 -3.2125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 6.2917 0.5333 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -0.1583 -1.5625 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 9.1542 -2.7292 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 4.8625 0.5208 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 9.8750 -1.4917 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -0.8625 -2.8000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 5.5792 0.9375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 9.1542 -1.9042 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -0.8625 -1.9750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 13.4750 -2.4292 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0\n 13.0667 -1.7125 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 13.8667 -3.1500 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 14.1917 -2.0250 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 12.7500 -2.8250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 2 13 1 0\n 3 8 1 0\n 4 19 1 0\n 5 17 1 0\n 6 2 1 0\n 7 1 1 0\n 8 27 1 0\n 9 2 2 0\n 10 1 2 0\n 11 3 2 0\n 12 1 1 0\n 13 18 1 0\n 14 5 2 0\n 15 4 2 0\n 16 4 1 0\n 17 28 1 0\n 18 5 1 0\n 19 12 1 0\n 20 8 1 0\n 21 7 1 0\n 22 6 1 0\n 23 30 1 0\n 24 3 1 0\n 25 7 1 0\n 26 6 1 0\n 27 33 1 0\n 28 34 1 0\n 29 16 1 0\n 30 36 1 0\n 31 25 1 0\n 32 26 1 0\n 33 38 1 0\n 34 37 1 0\n 35 29 1 0\n 36 39 1 0\n 37 31 1 0\n 38 35 1 0\n 39 32 1 0\n 41 40 2 0\n 42 40 2 0\n 43 40 1 0\n 44 40 1 0\nM END\n\n> <chembl_id>\nCHEMBL1234\n\n> <chembl_pref_name>\nDEFEROXAMINE MESYLATE\n\n', 'standard_inchi': 'InChI=1S/C25H48N6O8.CH4O3S/c1-21(32)29(37)18-9-3-6-16-27-22(33)12-14-25(36)31(39)20-10-4-7-17-28-23(34)11-13-24(35)30(38)19-8-2-5-15-26;1-5(2,3)4/h37-39H,2-20,26H2,1H3,(H,27,33)(H,28,34);1H3,(H,2,3,4)', 'standard_inchi_key': 'IDDIJAWJANBQLJ-UHFFFAOYSA-N'}, 'molecule_synonyms': [{'molecule_synonym': 'BA-33112', 'syn_type': 'RESEARCH_CODE', 'synonyms': 'BA-33112'}, {'molecule_synonym': 'Deferoxamine mesilate', 'syn_type': 'JAN', 'synonyms': 'DEFEROXAMINE MESILATE'}, {'molecule_synonym': 'Deferoxamine mesilate', 'syn_type': 'OTHER', 'synonyms': 'DEFEROXAMINE MESILATE'}, {'molecule_synonym': 'Deferoxamine mesylate', 'syn_type': 'FDA', 'synonyms': 'DEFEROXAMINE MESYLATE'}, {'molecule_synonym': 'Deferoxamine mesylate', 'syn_type': 'OTHER', 'synonyms': 'DEFEROXAMINE MESYLATE'}, {'molecule_synonym': 'Deferoxamine mesylate', 'syn_type': 'TRADE_NAME', 'synonyms': 'DEFEROXAMINE MESYLATE'}, {'molecule_synonym': 'Deferoxamine mesylate', 'syn_type': 'USAN', 'synonyms': 'DEFEROXAMINE MESYLATE'}, {'molecule_synonym': 'Deferoxamine mesylate', 'syn_type': 'USP', 'synonyms': 'DEFEROXAMINE MESYLATE'}, {'molecule_synonym': 'Deferoxamine methanesulfonate', 'syn_type': 'MERCK_INDEX', 'synonyms': 'DEFEROXAMINE METHANESULFONATE'}, {'molecule_synonym': 'Deferoxamini mesilas', 'syn_type': 'OTHER', 'synonyms': 'DEFEROXAMINI MESILAS'}, {'molecule_synonym': 'Desferal', 'syn_type': 'TRADE_NAME', 'synonyms': 'Desferal'}, {'molecule_synonym': 'Desferal Mesylate', 'syn_type': 'TRADE_NAME', 'synonyms': 'Desferal Mesylate'}, {'molecule_synonym': 'Desferrioxamine mesilate', 'syn_type': 'BAN', 'synonyms': 'DESFERRIOXAMINE MESILATE'}, {'molecule_synonym': 'Desferrioxamine mesilate', 'syn_type': 'BNF', 'synonyms': 'DESFERRIOXAMINE MESILATE'}, {'molecule_synonym': 'Desferrioxamine Mesylate', 'syn_type': 'TRADE_NAME', 'synonyms': 'Desferrioxamine Mesylate'}, {'molecule_synonym': 'Desferrioxamine mesylate', 'syn_type': 'OTHER', 'synonyms': 'DESFERRIOXAMINE MESYLATE'}, {'molecule_synonym': 'NSC-756718', 'syn_type': 'RESEARCH_CODE', 'synonyms': 'NSC-756718'}], 'molecule_type': 'Small molecule', 'natural_product': 0, 'oral': False, 'parenteral': True, 'polymer_flag': 0, 'pref_name': 'DEFEROXAMINE MESYLATE', 'prodrug': 0, 'structure_type': 'MOL', 'therapeutic_flag': True, 'topical': False, 'usan_stem': None, 'usan_stem_definition': None, 'usan_substem': None, 'usan_year': 1966, 'withdrawn_class': None, 'withdrawn_country': None, 'withdrawn_flag': False, 'withdrawn_reason': None, 'withdrawn_year': None}
[15]:
# Via Config
config = gm.MoleculeGraphConfig(graph_metadata_functions=[gm.add_chembl_metadata])
g = gm.construct_graph(chembl_id="CHEMBL1234", config=config)
g.graph["chembl_metadata"]
WARNING [bioservices:ChEMBL:119]: The URL (https://www.ebi.ac.uk/chembl/api/data) provided cannot be reached.
WARNING [bioservices:ChEMBL:119]: The URL (https://www.ebi.ac.uk/chembl/api/data) provided cannot be reached.
WARNING [bioservices:ChEMBL:119]: The URL (https://www.ebi.ac.uk/chembl/api/data) provided cannot be reached.
WARNING [bioservices:ChEMBL:119]: The URL (https://www.ebi.ac.uk/chembl/api/data) provided cannot be reached.
WARNING [bioservices:ChEMBL:119]: The URL (https://www.ebi.ac.uk/chembl/api/data) provided cannot be reached.
WARNING [bioservices:ChEMBL:119]: The URL (https://www.ebi.ac.uk/chembl/api/data) provided cannot be reached.
WARNING [bioservices:ChEMBL:119]: The URL (https://www.ebi.ac.uk/chembl/api/data) provided cannot be reached.
WARNING [bioservices:ChEMBL:119]: The URL (https://www.ebi.ac.uk/chembl/api/data) provided cannot be reached.
WARNING [bioservices:ChEMBL:119]: The URL (https://www.ebi.ac.uk/chembl/api/data) provided cannot be reached.
WARNING [bioservices:ChEMBL:119]: The URL (https://www.ebi.ac.uk/chembl/api/data) provided cannot be reached.
WARNING [bioservices:ChEMBL:119]: The URL (https://www.ebi.ac.uk/chembl/api/data) provided cannot be reached.
WARNING [bioservices:ChEMBL:119]: The URL (https://www.ebi.ac.uk/chembl/api/data) provided cannot be reached.
WARNING [bioservices:ChEMBL:119]: The URL (https://www.ebi.ac.uk/chembl/api/data) provided cannot be reached.
WARNING [bioservices:ChEMBL:119]: The URL (https://www.ebi.ac.uk/chembl/api/data) provided cannot be reached.
WARNING [bioservices:ChEMBL:119]: The URL (https://www.ebi.ac.uk/chembl/api/data) provided cannot be reached.
WARNING [bioservices:ChEMBL:119]: The URL (https://www.ebi.ac.uk/chembl/api/data) provided cannot be reached.
WARNING [bioservices:ChEMBL:119]: The URL (https://www.ebi.ac.uk/chembl/api/data) provided cannot be reached.
WARNING [bioservices:ChEMBL:119]: The URL (https://www.ebi.ac.uk/chembl/api/data) provided cannot be reached.
WARNING [bioservices:ChEMBL:119]: The URL (https://www.ebi.ac.uk/chembl/api/data) provided cannot be reached.
WARNING [bioservices:ChEMBL:119]: The URL (https://www.ebi.ac.uk/chembl/api/data) provided cannot be reached.
WARNING [bioservices:ChEMBL:119]: The URL (https://www.ebi.ac.uk/chembl/api/data) provided cannot be reached.
[15]:
{'atc_classifications': [],
'availability_type': 1,
'biotherapeutic': None,
'black_box_warning': 0,
'chebi_par_id': 31460,
'chirality': 2,
'cross_references': [{'xref_id': 'deferoxamine%20mesylate',
'xref_name': 'deferoxamine mesylate',
'xref_src': 'DailyMed'},
{'xref_id': '11112937', 'xref_name': 'SID: 11112937', 'xref_src': 'PubChem'},
{'xref_id': '11533050', 'xref_name': 'SID: 11533050', 'xref_src': 'PubChem'},
{'xref_id': '124882730',
'xref_name': 'SID: 124882730',
'xref_src': 'PubChem'},
{'xref_id': '144204292',
'xref_name': 'SID: 144204292',
'xref_src': 'PubChem'},
{'xref_id': '170464752',
'xref_name': 'SID: 170464752',
'xref_src': 'PubChem'},
{'xref_id': '26747967',
'xref_name': 'SID: 26747967',
'xref_src': 'PubChem'}],
'dosed_ingredient': True,
'first_approval': 1968,
'first_in_class': 0,
'helm_notation': None,
'indication_class': 'Antidote (to iron poisoning); Chelating Agent',
'inorganic_flag': 0,
'max_phase': 4,
'molecule_chembl_id': 'CHEMBL1234',
'molecule_hierarchy': {'molecule_chembl_id': 'CHEMBL1234',
'parent_chembl_id': 'CHEMBL556'},
'molecule_properties': {'alogp': '0.92',
'aromatic_rings': 0,
'cx_logd': '-3.64',
'cx_logp': '-3.37',
'cx_most_apka': '7.92',
'cx_most_bpka': '10.21',
'full_molformula': 'C26H52N6O11S',
'full_mwt': '656.80',
'hba': 9,
'hba_lipinski': 14,
'hbd': 6,
'hbd_lipinski': 7,
'heavy_atoms': 39,
'molecular_species': 'BASE',
'mw_freebase': '560.69',
'mw_monoisotopic': '560.3534',
'num_lipinski_ro5_violations': 3,
'num_ro5_violations': 2,
'psa': '205.84',
'qed_weighted': '0.06',
'ro3_pass': 'N',
'rtb': 23},
'molecule_structures': {'canonical_smiles': 'CC(=O)N(O)CCCCCNC(=O)CCC(=O)N(O)CCCCCNC(=O)CCC(=O)N(O)CCCCCN.CS(=O)(=O)O',
'molfile': '\n RDKit 2D\n\n 44 42 0 0 0 0 0 0 0 0999 V2000\n 8.4417 0.9708 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.5667 0.5208 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 7.7167 -4.3792 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 10.5792 0.5708 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 2.7042 0.9125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.5667 -0.3250 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n 7.7167 0.5375 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n 8.4417 -3.9750 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n -0.1583 0.9250 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 8.4417 1.7833 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 7.0125 -3.9750 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 9.1542 0.5500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1.2792 0.9250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 2.7042 1.7375 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 11.3042 0.9833 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 10.5792 -0.2542 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n 3.4292 0.5000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n 2.0000 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 9.8750 0.9708 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 9.1667 -4.4250 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 7.7167 -0.2875 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 1.2792 -0.7250 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n -1.5833 -4.0375 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n 7.7167 -5.2250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 7.0125 0.9583 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -0.1583 -0.7375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 8.4417 -3.1500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 4.1417 0.9250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 9.8750 -0.6542 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -1.5833 -3.2125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 6.2917 0.5333 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -0.1583 -1.5625 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 9.1542 -2.7292 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 4.8625 0.5208 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 9.8750 -1.4917 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -0.8625 -2.8000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 5.5792 0.9375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 9.1542 -1.9042 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -0.8625 -1.9750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 13.4750 -2.4292 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0\n 13.0667 -1.7125 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 13.8667 -3.1500 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 14.1917 -2.0250 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 12.7500 -2.8250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 2 13 1 0\n 3 8 1 0\n 4 19 1 0\n 5 17 1 0\n 6 2 1 0\n 7 1 1 0\n 8 27 1 0\n 9 2 2 0\n 10 1 2 0\n 11 3 2 0\n 12 1 1 0\n 13 18 1 0\n 14 5 2 0\n 15 4 2 0\n 16 4 1 0\n 17 28 1 0\n 18 5 1 0\n 19 12 1 0\n 20 8 1 0\n 21 7 1 0\n 22 6 1 0\n 23 30 1 0\n 24 3 1 0\n 25 7 1 0\n 26 6 1 0\n 27 33 1 0\n 28 34 1 0\n 29 16 1 0\n 30 36 1 0\n 31 25 1 0\n 32 26 1 0\n 33 38 1 0\n 34 37 1 0\n 35 29 1 0\n 36 39 1 0\n 37 31 1 0\n 38 35 1 0\n 39 32 1 0\n 41 40 2 0\n 42 40 2 0\n 43 40 1 0\n 44 40 1 0\nM END\n\n> <chembl_id>\nCHEMBL1234\n\n> <chembl_pref_name>\nDEFEROXAMINE MESYLATE\n\n',
'standard_inchi': 'InChI=1S/C25H48N6O8.CH4O3S/c1-21(32)29(37)18-9-3-6-16-27-22(33)12-14-25(36)31(39)20-10-4-7-17-28-23(34)11-13-24(35)30(38)19-8-2-5-15-26;1-5(2,3)4/h37-39H,2-20,26H2,1H3,(H,27,33)(H,28,34);1H3,(H,2,3,4)',
'standard_inchi_key': 'IDDIJAWJANBQLJ-UHFFFAOYSA-N'},
'molecule_synonyms': [{'molecule_synonym': 'BA-33112',
'syn_type': 'RESEARCH_CODE',
'synonyms': 'BA-33112'},
{'molecule_synonym': 'Deferoxamine mesilate',
'syn_type': 'JAN',
'synonyms': 'DEFEROXAMINE MESILATE'},
{'molecule_synonym': 'Deferoxamine mesilate',
'syn_type': 'OTHER',
'synonyms': 'DEFEROXAMINE MESILATE'},
{'molecule_synonym': 'Deferoxamine mesylate',
'syn_type': 'FDA',
'synonyms': 'DEFEROXAMINE MESYLATE'},
{'molecule_synonym': 'Deferoxamine mesylate',
'syn_type': 'OTHER',
'synonyms': 'DEFEROXAMINE MESYLATE'},
{'molecule_synonym': 'Deferoxamine mesylate',
'syn_type': 'TRADE_NAME',
'synonyms': 'DEFEROXAMINE MESYLATE'},
{'molecule_synonym': 'Deferoxamine mesylate',
'syn_type': 'USAN',
'synonyms': 'DEFEROXAMINE MESYLATE'},
{'molecule_synonym': 'Deferoxamine mesylate',
'syn_type': 'USP',
'synonyms': 'DEFEROXAMINE MESYLATE'},
{'molecule_synonym': 'Deferoxamine methanesulfonate',
'syn_type': 'MERCK_INDEX',
'synonyms': 'DEFEROXAMINE METHANESULFONATE'},
{'molecule_synonym': 'Deferoxamini mesilas',
'syn_type': 'OTHER',
'synonyms': 'DEFEROXAMINI MESILAS'},
{'molecule_synonym': 'Desferal',
'syn_type': 'TRADE_NAME',
'synonyms': 'Desferal'},
{'molecule_synonym': 'Desferal Mesylate',
'syn_type': 'TRADE_NAME',
'synonyms': 'Desferal Mesylate'},
{'molecule_synonym': 'Desferrioxamine mesilate',
'syn_type': 'BAN',
'synonyms': 'DESFERRIOXAMINE MESILATE'},
{'molecule_synonym': 'Desferrioxamine mesilate',
'syn_type': 'BNF',
'synonyms': 'DESFERRIOXAMINE MESILATE'},
{'molecule_synonym': 'Desferrioxamine Mesylate',
'syn_type': 'TRADE_NAME',
'synonyms': 'Desferrioxamine Mesylate'},
{'molecule_synonym': 'Desferrioxamine mesylate',
'syn_type': 'OTHER',
'synonyms': 'DESFERRIOXAMINE MESYLATE'},
{'molecule_synonym': 'NSC-756718',
'syn_type': 'RESEARCH_CODE',
'synonyms': 'NSC-756718'}],
'molecule_type': 'Small molecule',
'natural_product': 0,
'oral': False,
'parenteral': True,
'polymer_flag': 0,
'pref_name': 'DEFEROXAMINE MESYLATE',
'prodrug': 0,
'structure_type': 'MOL',
'therapeutic_flag': True,
'topical': False,
'usan_stem': None,
'usan_stem_definition': None,
'usan_substem': None,
'usan_year': 1966,
'withdrawn_class': None,
'withdrawn_country': None,
'withdrawn_flag': False,
'withdrawn_reason': None,
'withdrawn_year': None}