data_YKG
#
_chem_comp.id YKG
_chem_comp.name "[(5-bromo-7-methyl-2-oxo-2H-1-benzopyran-4-yl)methyl]phosphonic acid"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C11 H10 Br O5 P"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2018-04-17
_chem_comp.pdbx_modified_date 2019-04-12
_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 333.072
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code YKG
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details Corina
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 6D19
_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
YKG C01 C1 C 0 1 N N N N N N 24.289 15.401 5.223 5.274 -0.192 0.024 C01 YKG 1
YKG C02 C2 C 0 1 Y N N N N N 23.200 16.107 6.024 3.770 -0.291 0.013 C02 YKG 2
YKG C03 C3 C 0 1 Y N N N N N 23.332 16.178 7.379 3.006 0.866 0.011 C03 YKG 3
YKG C04 C4 C 0 1 Y N N N N N 22.402 16.792 8.162 1.630 0.792 0.002 C04 YKG 4
YKG C06 C5 C 0 1 Y N N N N N 21.262 17.373 7.564 1.006 -0.460 -0.006 C06 YKG 5
YKG C07 C6 C 0 1 N N N N N N 20.195 18.058 8.246 -0.455 -0.576 -0.016 C07 YKG 6
YKG C08 C7 C 0 1 N N N N N N 20.152 18.281 9.709 -1.329 0.652 -0.018 C08 YKG 7
YKG C13 C8 C 0 1 N N N N N N 19.175 18.573 7.458 -1.000 -1.819 -0.022 C13 YKG 8
YKG C14 C9 C 0 1 N N N N N N 19.187 18.388 6.127 -0.159 -2.953 -0.020 C14 YKG 9
YKG C17 C10 C 0 1 Y N N N N N 21.141 17.281 6.221 1.783 -1.632 -0.004 C17 YKG 10
YKG C18 C11 C 0 1 Y N N N N N 22.109 16.663 5.425 3.168 -1.532 -0.000 C18 YKG 11
YKG O10 O1 O 0 1 N N N N N N 17.654 17.440 10.063 -3.329 -0.753 -1.177 O10 YKG 12
YKG O11 O2 O 0 1 N N N N N N 19.046 17.398 11.912 -3.430 -0.617 1.342 O11 YKG 13
YKG O12 O3 O 0 1 N N N N N N 19.478 15.749 10.334 -4.013 1.457 -0.166 O12 YKG 14
YKG O15 O4 O 0 1 N N N N N N 18.203 18.849 5.321 -0.660 -4.063 -0.025 O15 YKG 15
YKG O16 O5 O 0 1 N N N N N N 20.135 17.766 5.574 1.178 -2.839 -0.012 O16 YKG 16
YKG P09 P1 P 0 1 N N N N N N 18.974 17.171 10.574 -3.082 0.150 -0.030 P09 YKG 17
YKG BR05 BR1 BR 0 0 N N N N N N 22.820 16.704 9.973 0.592 2.373 -0.000 BR05 YKG 18
YKG H1 H1 H 0 1 N N N N N N 25.062 16.128 4.933 5.629 -0.171 1.054 H1 YKG 19
YKG H2 H2 H 0 1 N N N N N N 24.742 14.610 5.839 5.698 -1.055 -0.490 H2 YKG 20
YKG H3 H3 H 0 1 N N N N N N 23.848 14.955 4.319 5.581 0.721 -0.486 H3 YKG 21
YKG H4 H4 H 0 1 N N N N N N 24.199 15.734 7.845 3.492 1.831 0.018 H4 YKG 22
YKG H5 H5 H 0 1 N N N N N N 21.159 18.110 10.119 -1.127 1.244 0.874 H5 YKG 23
YKG H6 H6 H 0 1 N N N N N N 19.852 19.323 9.895 -1.116 1.247 -0.906 H6 YKG 24
YKG H7 H7 H 0 1 N N N N N N 18.368 19.125 7.917 -2.073 -1.941 -0.029 H7 YKG 25
YKG H8 H8 H 0 1 N N N N N N 21.995 16.626 4.352 3.774 -2.426 -0.003 H8 YKG 26
YKG H9 H9 H 0 1 N N N N N N 18.200 17.690 12.230 -3.291 -0.084 2.136 H9 YKG 27
YKG H10 H10 H 0 1 N N N N N N 18.815 15.252 9.869 -4.961 1.264 -0.178 H10 YKG 28
#
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
YKG C01 C02 SING N N 1
YKG O15 C14 DOUB N N 2
YKG C18 C02 DOUB Y N 3
YKG C18 C17 SING Y N 4
YKG O16 C14 SING N N 5
YKG O16 C17 SING N N 6
YKG C02 C03 SING Y N 7
YKG C14 C13 SING N N 8
YKG C17 C06 DOUB Y N 9
YKG C03 C04 DOUB Y N 10
YKG C13 C07 DOUB N N 11
YKG C06 C04 SING Y N 12
YKG C06 C07 SING N N 13
YKG C04 BR05 SING N N 14
YKG C07 C08 SING N N 15
YKG C08 P09 SING N N 16
YKG O10 P09 DOUB N N 17
YKG O12 P09 SING N N 18
YKG P09 O11 SING N N 19
YKG C01 H1 SING N N 20
YKG C01 H2 SING N N 21
YKG C01 H3 SING N N 22
YKG C03 H4 SING N N 23
YKG C08 H5 SING N N 24
YKG C08 H6 SING N N 25
YKG C13 H7 SING N N 26
YKG C18 H8 SING N N 27
YKG O11 H9 SING N N 28
YKG O12 H10 SING N N 29
#
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
YKG SMILES ACDLabs 12.01 Cc2cc(Br)c1C(CP(=O)(O)O)=CC(=O)Oc1c2
YKG InChI InChI 1.03 InChI=1S/C11H10BrO5P/c1-6-2-8(12)11-7(5-18(14,15)16)4-10(13)17-9(11)3-6/h2-4H,5H2,1H3,(H2,14,15,16)
YKG InChIKey InChI 1.03 AVDUOTYJUPESMO-UHFFFAOYSA-N
YKG SMILES_CANONICAL CACTVS 3.385 Cc1cc(Br)c2C(=CC(=O)Oc2c1)C[P](O)(O)=O
YKG SMILES CACTVS 3.385 Cc1cc(Br)c2C(=CC(=O)Oc2c1)C[P](O)(O)=O
YKG SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 Cc1cc2c(c(c1)Br)C(=CC(=O)O2)CP(=O)(O)O
YKG SMILES "OpenEye OEToolkits" 2.0.6 Cc1cc2c(c(c1)Br)C(=CC(=O)O2)CP(=O)(O)O
#
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
YKG "SYSTEMATIC NAME" ACDLabs 12.01 "[(5-bromo-7-methyl-2-oxo-2H-1-benzopyran-4-yl)methyl]phosphonic acid"
YKG "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "(5-bromanyl-7-methyl-2-oxidanylidene-chromen-4-yl)methylphosphonic acid"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
YKG 'Create component' 2018-04-17 RCSB
YKG 'Initial release' 2019-04-17 RCSB
#
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
YKG C01 C 3.000 -3.688 1
YKG C02 C 4.296 -2.933 2
YKG C03 C 4.296 -1.370 3
YKG C04 C 5.655 -0.599 4
YKG C06 C 6.996 -1.401 5
YKG C07 C 8.295 -0.651 6
YKG C08 C 8.295 0.849 7
YKG C13 C 9.594 -1.401 8
YKG C14 C 9.594 -2.901 9
YKG C17 C 6.996 -2.901 10
YKG C18 C 5.655 -3.703 11
YKG O10 O 10.893 2.349 12
YKG O11 O 10.344 0.300 13
YKG O12 O 8.844 2.898 14
YKG O15 O 10.893 -3.651 15
YKG O16 O 8.295 -3.651 16
YKG P09 P 9.594 1.599 17
YKG BR05 Br 5.673 0.901 18
#
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
YKG C01 C02 SINGLE NONE 1
YKG O15 C14 DOUBLE NONE 2
YKG C18 C02 DOUBLE NONE 3
YKG C18 C17 SINGLE NONE 4
YKG O16 C14 SINGLE NONE 5
YKG O16 C17 SINGLE NONE 6
YKG C02 C03 SINGLE NONE 7
YKG C14 C13 SINGLE NONE 8
YKG C17 C06 DOUBLE NONE 9
YKG C03 C04 DOUBLE NONE 10
YKG C13 C07 DOUBLE NONE 11
YKG C06 C04 SINGLE NONE 12
YKG C06 C07 SINGLE NONE 13
YKG C04 BR05 SINGLE NONE 14
YKG C07 C08 SINGLE NONE 15
YKG C08 P09 SINGLE NONE 16
YKG O10 P09 DOUBLE NONE 17
YKG O12 P09 SINGLE NONE 18
YKG P09 O11 SINGLE NONE 19
#
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
YKG MurckoScaffold S1 scaffold O=c1ccc2ccccc2o1 InChI=1S/C9H6O2/c10-9-6-5-7-3-1-2-4-8(7)11-9/h1-6H ZYGHJZDHTFUPRJ-UHFFFAOYSA-N
YKG 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
YKG C02 S1 1
YKG C03 S1 1
YKG C04 S1 1
YKG C06 S1 1
YKG C07 S1 1
YKG C13 S1 1
YKG C14 S1 1
YKG C17 S1 1
YKG C18 S1 1
YKG O15 S1 1
YKG O16 S1 1
YKG C02 F1 1
YKG C18 F1 1
YKG C17 F1 1
YKG C06 F1 1
YKG C04 F1 1
YKG C03 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id YKG
_pdbe_chem_comp_rdkit_properties.exactmw 331.945
_pdbe_chem_comp_rdkit_properties.amw 333.074
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 5
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 2
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 5
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 5
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 18
_pdbe_chem_comp_rdkit_properties.NumAtoms 28
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 7
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.182
_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 1
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 1
_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 124.951
_pdbe_chem_comp_rdkit_properties.tpsa 87.740
_pdbe_chem_comp_rdkit_properties.CrippenClogP 2.904
_pdbe_chem_comp_rdkit_properties.CrippenMR 68.039
_pdbe_chem_comp_rdkit_properties.chi0v 10.847
_pdbe_chem_comp_rdkit_properties.chi1v 6.658
_pdbe_chem_comp_rdkit_properties.chi2v 2.933
_pdbe_chem_comp_rdkit_properties.chi3v 2.933
_pdbe_chem_comp_rdkit_properties.chi4v 2.301
_pdbe_chem_comp_rdkit_properties.chi0n 18.366
_pdbe_chem_comp_rdkit_properties.chi1n 9.139
_pdbe_chem_comp_rdkit_properties.chi2n 1.840
_pdbe_chem_comp_rdkit_properties.chi3n 1.840
_pdbe_chem_comp_rdkit_properties.chi4n 1.283
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.940
_pdbe_chem_comp_rdkit_properties.kappa1 5.588
_pdbe_chem_comp_rdkit_properties.kappa2 4.626
_pdbe_chem_comp_rdkit_properties.kappa3 2.896
_pdbe_chem_comp_rdkit_properties.Phi 1.436
#
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
YKG UniChem ChEMBL CHEMBL4519591
YKG UniChem PDBe YKG
YKG UniChem ZINC ZINC000621485606
YKG UniChem SureChEMBL SCHEMBL19353896
YKG UniChem BindingDb 426626
YKG UniChem PubChem 130427303
#
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
YKG C01 4.589 0.418 0.413 ETKDGv3 1
YKG C02 3.104 0.207 0.393 ETKDGv3 2
YKG C03 2.196 1.366 0.307 ETKDGv3 3
YKG C04 0.865 1.205 0.248 ETKDGv3 4
YKG C06 0.272 -0.182 0.334 ETKDGv3 5
YKG C07 -1.206 -0.479 0.477 ETKDGv3 6
YKG C08 -2.229 0.555 0.882 ETKDGv3 7
YKG C13 -1.644 -1.747 0.360 ETKDGv3 8
YKG C14 -0.690 -2.838 0.189 ETKDGv3 9
YKG C17 1.135 -1.236 0.291 ETKDGv3 10
YKG C18 2.595 -1.027 0.328 ETKDGv3 11
YKG O10 -3.989 2.325 -0.211 ETKDGv3 12
YKG O11 -2.321 1.245 -1.920 ETKDGv3 13
YKG O12 -4.412 -0.183 -0.823 ETKDGv3 14
YKG O15 -1.088 -4.025 0.056 ETKDGv3 15
YKG O16 0.670 -2.553 0.213 ETKDGv3 16
YKG P09 -3.272 1.034 -0.536 ETKDGv3 17
YKG BR05 -0.114 2.796 -0.198 ETKDGv3 18
YKG H1 5.090 -0.369 1.016 ETKDGv3 19
YKG H2 4.835 1.404 0.862 ETKDGv3 20
YKG H3 4.981 0.387 -0.625 ETKDGv3 21
YKG H4 2.624 2.358 0.218 ETKDGv3 22
YKG H5 -2.894 0.137 1.668 ETKDGv3 23
YKG H6 -1.761 1.435 1.355 ETKDGv3 24
YKG H7 -2.697 -1.986 0.463 ETKDGv3 25
YKG H8 3.249 -1.891 0.324 ETKDGv3 26
YKG H9 -2.959 1.510 -2.630 ETKDGv3 27
YKG H10 -4.929 0.132 -1.607 ETKDGv3 28
#