data_BPY
#
_chem_comp.id BPY
_chem_comp.name BIPHENYL-2,3-DIOL
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C12 H10 O2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2000-03-01
_chem_comp.pdbx_modified_date 2011-06-04
_chem_comp.pdbx_ambiguous_flag N
_chem_comp.pdbx_release_status REL
_chem_comp.pdbx_replaced_by ?
_chem_comp.pdbx_replaces ?
_chem_comp.formula_weight 186.207
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code BPY
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details ?
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code ?
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
#
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.alt_atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.charge
_chem_comp_atom.pdbx_align
_chem_comp_atom.pdbx_aromatic_flag
_chem_comp_atom.pdbx_leaving_atom_flag
_chem_comp_atom.pdbx_stereo_config
_chem_comp_atom.pdbx_backbone_atom_flag
_chem_comp_atom.pdbx_n_terminal_atom_flag
_chem_comp_atom.pdbx_c_terminal_atom_flag
_chem_comp_atom.model_Cartn_x
_chem_comp_atom.model_Cartn_y
_chem_comp_atom.model_Cartn_z
_chem_comp_atom.pdbx_model_Cartn_x_ideal
_chem_comp_atom.pdbx_model_Cartn_y_ideal
_chem_comp_atom.pdbx_model_Cartn_z_ideal
_chem_comp_atom.pdbx_component_atom_id
_chem_comp_atom.pdbx_component_comp_id
_chem_comp_atom.pdbx_ordinal
BPY CK1 CK1 C 0 1 Y N N N N N 81.377 37.888 16.473 -1.737 -0.347 0.793 CK1 BPY 1
BPY CK2 CK2 C 0 1 Y N N N N N 82.791 38.329 16.417 -0.459 -0.091 0.299 CK2 BPY 2
BPY CK3 CK3 C 0 1 Y N N N N N 83.086 39.742 16.126 0.593 0.135 1.187 CK3 BPY 3
BPY CK4 CK4 C 0 1 Y N N N N N 82.012 40.700 15.900 0.361 0.094 2.557 CK4 BPY 4
BPY CK5 CK5 C 0 1 Y N N N N N 80.639 40.219 15.965 -0.914 -0.159 3.035 CK5 BPY 5
BPY CK6 CK6 C 0 1 Y N N N N N 80.290 38.846 16.243 -1.958 -0.379 2.155 CK6 BPY 6
BPY CK7 CK7 C 0 1 Y N N N N N 83.936 37.477 16.629 -0.220 -0.056 -1.164 CK7 BPY 7
BPY CK8 CK8 C 0 1 Y N N N N N 84.797 37.743 17.811 -0.897 0.864 -1.961 CK8 BPY 8
BPY CK9 CK9 C 0 1 Y N N N N N 85.972 36.871 18.046 -0.671 0.893 -3.322 CK9 BPY 9
BPY CKA CK10 C 0 1 Y N N N N N 86.273 35.758 17.118 0.226 0.010 -3.895 CKA BPY 10
BPY CKB CK11 C 0 1 Y N N N N N 85.423 35.481 15.938 0.901 -0.905 -3.109 CKB BPY 11
BPY CKC CK12 C 0 1 Y N N N N N 84.257 36.353 15.710 0.687 -0.939 -1.746 CKC BPY 12
BPY OK1 OK1 O 0 1 N N N N N N 82.282 42.013 15.630 1.383 0.310 3.427 OK1 BPY 13
BPY OK2 OK2 O 0 1 N N N N N N 84.346 40.202 16.058 1.843 0.385 0.714 OK2 BPY 14
BPY HCK1 HCK1 H 0 0 N N N N N N 81.130 36.834 16.688 -2.555 -0.520 0.109 HCK1 BPY 15
BPY HCK5 HCK5 H 0 0 N N N N N N 79.817 40.934 15.794 -1.094 -0.186 4.100 HCK5 BPY 16
BPY HCK6 HCK6 H 0 0 N N N N N N 79.230 38.539 16.278 -2.949 -0.577 2.534 HCK6 BPY 17
BPY HCK8 HCK8 H 0 0 N N N N N N 84.568 38.572 18.501 -1.599 1.553 -1.515 HCK8 BPY 18
BPY HCK9 HCK9 H 0 0 N N N N N N 86.625 37.051 18.915 -1.196 1.605 -3.941 HCK9 BPY 19
BPY HC10 HC10 H 0 0 N N N N N N 87.151 35.119 17.310 0.400 0.036 -4.961 HC10 BPY 20
BPY HC11 HC11 H 0 0 N N N N N N 85.651 34.650 15.249 1.600 -1.593 -3.561 HC11 BPY 21
BPY HC12 HC12 H 0 0 N N N N N N 83.612 36.160 14.835 1.214 -1.655 -1.133 HC12 BPY 22
BPY H0K1 H0K1 H 0 0 N N N N N N 81.581 42.637 15.482 1.777 -0.552 3.614 H0K1 BPY 23
BPY HOK2 HOK2 H 0 0 N N N N N N 84.536 41.113 15.870 1.914 1.343 0.605 HOK2 BPY 24
#
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_aromatic_flag
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_ordinal
BPY CK1 CK2 DOUB Y N 1
BPY CK1 CK6 SING Y N 2
BPY CK1 HCK1 SING N N 3
BPY CK2 CK3 SING Y N 4
BPY CK2 CK7 SING Y N 5
BPY CK3 CK4 DOUB Y N 6
BPY CK3 OK2 SING N N 7
BPY CK4 CK5 SING Y N 8
BPY CK4 OK1 SING N N 9
BPY CK5 CK6 DOUB Y N 10
BPY CK5 HCK5 SING N N 11
BPY CK6 HCK6 SING N N 12
BPY CK7 CK8 DOUB Y N 13
BPY CK7 CKC SING Y N 14
BPY CK8 CK9 SING Y N 15
BPY CK8 HCK8 SING N N 16
BPY CK9 CKA DOUB Y N 17
BPY CK9 HCK9 SING N N 18
BPY CKA CKB SING Y N 19
BPY CKA HC10 SING N N 20
BPY CKB CKC DOUB Y N 21
BPY CKB HC11 SING N N 22
BPY CKC HC12 SING N N 23
BPY OK1 H0K1 SING N N 24
BPY OK2 HOK2 SING N N 25
#
loop_
_pdbx_chem_comp_descriptor.comp_id
_pdbx_chem_comp_descriptor.type
_pdbx_chem_comp_descriptor.program
_pdbx_chem_comp_descriptor.program_version
_pdbx_chem_comp_descriptor.descriptor
BPY SMILES ACDLabs 10.04 Oc2c(c1ccccc1)cccc2O
BPY SMILES_CANONICAL CACTVS 3.341 Oc1cccc(c2ccccc2)c1O
BPY SMILES CACTVS 3.341 Oc1cccc(c2ccccc2)c1O
BPY SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 c1ccc(cc1)c2cccc(c2O)O
BPY SMILES "OpenEye OEToolkits" 1.5.0 c1ccc(cc1)c2cccc(c2O)O
BPY InChI InChI 1.03 InChI=1S/C12H10O2/c13-11-8-4-7-10(12(11)14)9-5-2-1-3-6-9/h1-8,13-14H
BPY InChIKey InChI 1.03 YKOQAAJBYBTSBS-UHFFFAOYSA-N
#
loop_
_pdbx_chem_comp_identifier.comp_id
_pdbx_chem_comp_identifier.type
_pdbx_chem_comp_identifier.program
_pdbx_chem_comp_identifier.program_version
_pdbx_chem_comp_identifier.identifier
BPY "SYSTEMATIC NAME" ACDLabs 10.04 biphenyl-2,3-diol
BPY "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 3-phenylbenzene-1,2-diol
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
BPY 'Create component' 2000-03-01 RCSB
BPY 'Modify aromatic_flag' 2011-06-04 RCSB
BPY 'Modify descriptor' 2011-06-04 RCSB
#
_pdbe_chem_comp_drugbank_details.comp_id BPY
_pdbe_chem_comp_drugbank_details.drugbank_id DB02923
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name Biphenyl-2,3-Diol
_pdbe_chem_comp_drugbank_details.description ?
_pdbe_chem_comp_drugbank_details.cas_number 1133-63-7
_pdbe_chem_comp_drugbank_details.mechanism_of_action ?
#
_pdbe_chem_comp_drugbank_classification.comp_id BPY
_pdbe_chem_comp_drugbank_classification.drugbank_id DB02923
_pdbe_chem_comp_drugbank_classification.parent 'Biphenyls and derivatives'
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class 'Benzene and substituted derivatives'
_pdbe_chem_comp_drugbank_classification.superclass Benzenoids
_pdbe_chem_comp_drugbank_classification.description
'This compound belongs to the class of organic compounds known as biphenyls and derivatives. These are organic compounds containing to benzene rings linked together by a C-C bond.'
#
loop_
_pdbe_chem_comp_drugbank_targets.comp_id
_pdbe_chem_comp_drugbank_targets.drugbank_id
_pdbe_chem_comp_drugbank_targets.name
_pdbe_chem_comp_drugbank_targets.organism
_pdbe_chem_comp_drugbank_targets.uniprot_id
_pdbe_chem_comp_drugbank_targets.pharmacologically_active
_pdbe_chem_comp_drugbank_targets.ordinal
BPY DB02923 '1,2-dihydroxynaphthalene dioxygenase' 'Pseudomonas sp. (strain C18)' P0A108 unknown 1
BPY DB02923 'Biphenyl-2,3-diol 1,2-dioxygenase' 'Burkholderia xenovorans (strain LB400)' P47228 unknown 2
BPY DB02923 'Biphenyl-2,3-diol 1,2-dioxygenase' 'Pseudomonas sp. (strain KKS102)' P17297 unknown 3
#
loop_
_software.name
_software.version
_software.description
rdkit 2023.03.3 'Core functionality.'
pdbeccdutils 0.8.4 'Wrapper to provide 2D templates and molecular fragments.'
#
loop_
_pdbe_chem_comp_atom_depiction.comp_id
_pdbe_chem_comp_atom_depiction.atom_id
_pdbe_chem_comp_atom_depiction.element
_pdbe_chem_comp_atom_depiction.model_Cartn_x
_pdbe_chem_comp_atom_depiction.model_Cartn_y
_pdbe_chem_comp_atom_depiction.pdbx_ordinal
BPY CK1 C 7.702 -1.035 1
BPY CK2 C 6.404 -0.285 2
BPY CK3 C 5.104 -1.035 3
BPY CK4 C 5.104 -2.535 4
BPY CK5 C 6.404 -3.285 5
BPY CK6 C 7.702 -2.535 6
BPY CK7 C 6.404 1.215 7
BPY CK8 C 7.702 1.965 8
BPY CK9 C 7.702 3.465 9
BPY CKA C 6.404 4.215 10
BPY CKB C 5.104 3.465 11
BPY CKC C 5.104 1.965 12
BPY OK1 O 3.805 -3.285 13
BPY OK2 O 3.805 -0.285 14
#
loop_
_pdbe_chem_comp_bond_depiction.comp_id
_pdbe_chem_comp_bond_depiction.atom_id_1
_pdbe_chem_comp_bond_depiction.atom_id_2
_pdbe_chem_comp_bond_depiction.value_order
_pdbe_chem_comp_bond_depiction.bond_dir
_pdbe_chem_comp_bond_depiction.pdbx_ordinal
BPY CK1 CK2 DOUBLE NONE 1
BPY CK1 CK6 SINGLE NONE 2
BPY CK2 CK3 SINGLE NONE 3
BPY CK2 CK7 SINGLE NONE 4
BPY CK3 CK4 DOUBLE NONE 5
BPY CK3 OK2 SINGLE NONE 6
BPY CK4 CK5 SINGLE NONE 7
BPY CK4 OK1 SINGLE NONE 8
BPY CK5 CK6 DOUBLE NONE 9
BPY CK7 CK8 DOUBLE NONE 10
BPY CK7 CKC SINGLE NONE 11
BPY CK8 CK9 SINGLE NONE 12
BPY CK9 CKA DOUBLE NONE 13
BPY CKA CKB SINGLE NONE 14
BPY CKB CKC DOUBLE NONE 15
#
loop_
_pdbe_chem_comp_substructure.comp_id
_pdbe_chem_comp_substructure.substructure_name
_pdbe_chem_comp_substructure.id
_pdbe_chem_comp_substructure.substructure_type
_pdbe_chem_comp_substructure.substructure_smiles
_pdbe_chem_comp_substructure.substructure_inchis
_pdbe_chem_comp_substructure.substructure_inchikeys
BPY MurckoScaffold S1 scaffold c1ccc(-c2ccccc2)cc1 InChI=1S/C12H10/c1-3-7-11(8-4-1)12-9-5-2-6-10-12/h1-10H ZUOUZKKEUPVFJK-UHFFFAOYSA-N
BPY phenyl F1 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
#
loop_
_pdbe_chem_comp_substructure_mapping.comp_id
_pdbe_chem_comp_substructure_mapping.atom_id
_pdbe_chem_comp_substructure_mapping.substructure_id
_pdbe_chem_comp_substructure_mapping.substructure_ordinal
BPY CK1 S1 1
BPY CK2 S1 1
BPY CK3 S1 1
BPY CK4 S1 1
BPY CK5 S1 1
BPY CK6 S1 1
BPY CK7 S1 1
BPY CK8 S1 1
BPY CK9 S1 1
BPY CKA S1 1
BPY CKB S1 1
BPY CKC S1 1
BPY CK1 F1 1
BPY CK2 F1 1
BPY CK3 F1 1
BPY CK4 F1 1
BPY CK5 F1 1
BPY CK6 F1 1
BPY CK7 F1 2
BPY CK8 F1 2
BPY CK9 F1 2
BPY CKA F1 2
BPY CKB F1 2
BPY CKC F1 2
#
_pdbe_chem_comp_rdkit_properties.comp_id BPY
_pdbe_chem_comp_rdkit_properties.exactmw 186.068
_pdbe_chem_comp_rdkit_properties.amw 186.210
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 2
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 2
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 3
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 2
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 14
_pdbe_chem_comp_rdkit_properties.NumAtoms 24
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 2
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0
_pdbe_chem_comp_rdkit_properties.NumRings 2
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 2
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 96.300
_pdbe_chem_comp_rdkit_properties.tpsa 40.460
_pdbe_chem_comp_rdkit_properties.CrippenClogP 1.460
_pdbe_chem_comp_rdkit_properties.CrippenMR 52.666
_pdbe_chem_comp_rdkit_properties.chi0v 6.816
_pdbe_chem_comp_rdkit_properties.chi1v 3.658
_pdbe_chem_comp_rdkit_properties.chi2v 1.547
_pdbe_chem_comp_rdkit_properties.chi3v 1.547
_pdbe_chem_comp_rdkit_properties.chi4v 0.929
_pdbe_chem_comp_rdkit_properties.chi0n 16.816
_pdbe_chem_comp_rdkit_properties.chi1n 8.475
_pdbe_chem_comp_rdkit_properties.chi2n 1.547
_pdbe_chem_comp_rdkit_properties.chi3n 1.547
_pdbe_chem_comp_rdkit_properties.chi4n 0.929
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.960
_pdbe_chem_comp_rdkit_properties.kappa1 2.764
_pdbe_chem_comp_rdkit_properties.kappa2 3.420
_pdbe_chem_comp_rdkit_properties.kappa3 1.420
_pdbe_chem_comp_rdkit_properties.Phi 0.675
#
loop_
_pdbe_chem_comp_external_mappings.comp_id
_pdbe_chem_comp_external_mappings.source
_pdbe_chem_comp_external_mappings.resource
_pdbe_chem_comp_external_mappings.resource_id
BPY UniChem DrugBank DB02923
BPY UniChem PDBe BPY
BPY UniChem 'KEGG LIGAND' C02526
BPY UniChem ChEBI 16205
BPY UniChem ZINC ZINC000000901387
BPY UniChem eMolecules 485368
BPY UniChem 'PubChem TPHARMA' 15195255
BPY UniChem Nikkaji J631.139C
BPY UniChem 'EPA CompTox Dashboard' DTXSID60150353
BPY UniChem BRENDA 105703
BPY UniChem BRENDA 1584
BPY UniChem BRENDA 3990
BPY UniChem BRENDA 57325
BPY UniChem BRENDA 91536
BPY UniChem Rhea 16205
BPY UniChem 'Probes And Drugs' PD007953
BPY UniChem ACTor 1133-63-7
BPY UniChem SureChEMBL SCHEMBL94298
BPY UniChem PubChem 254
BPY UniChem Mcule MCULE-4795494875
#
loop_
_pdbe_chem_comp_rdkit_conformer.comp_id
_pdbe_chem_comp_rdkit_conformer.atom_id
_pdbe_chem_comp_rdkit_conformer.Cartn_x_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_y_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_z_rdkit
_pdbe_chem_comp_rdkit_conformer.rdkit_method
_pdbe_chem_comp_rdkit_conformer.rdkit_ordinal
BPY CK1 0.891 -1.336 -0.916 ETKDGv3 1
BPY CK2 0.442 -0.285 -0.206 ETKDGv3 2
BPY CK3 1.425 0.599 0.490 ETKDGv3 3
BPY CK4 2.745 0.354 0.376 ETKDGv3 4
BPY CK5 3.217 -0.798 -0.426 ETKDGv3 5
BPY CK6 2.338 -1.601 -1.032 ETKDGv3 6
BPY CK7 -1.014 -0.021 -0.118 ETKDGv3 7
BPY CK8 -1.507 1.212 -0.341 ETKDGv3 8
BPY CK9 -2.962 1.461 -0.264 ETKDGv3 9
BPY CKA -3.800 0.458 0.023 ETKDGv3 10
BPY CKB -3.272 -0.900 0.262 ETKDGv3 11
BPY CKC -1.955 -1.129 0.195 ETKDGv3 12
BPY OK1 3.673 1.174 1.016 ETKDGv3 13
BPY OK2 0.961 1.660 1.271 ETKDGv3 14
BPY HCK1 0.202 -1.990 -1.436 ETKDGv3 15
BPY HCK5 4.277 -0.995 -0.517 ETKDGv3 16
BPY HCK6 2.685 -2.444 -1.614 ETKDGv3 17
BPY HCK8 -0.852 2.034 -0.600 ETKDGv3 18
BPY HCK9 -3.348 2.456 -0.442 ETKDGv3 19
BPY HC10 -4.866 0.639 0.078 ETKDGv3 20
BPY HC11 -3.953 -1.708 0.495 ETKDGv3 21
BPY HC12 -1.578 -2.127 0.382 ETKDGv3 22
BPY H0K1 4.668 1.000 0.942 ETKDGv3 23
BPY HOK2 1.584 2.285 1.769 ETKDGv3 24
#