data_7JR
#
_chem_comp.id 7JR
_chem_comp.name 1-methyl-3-oxidanyl-5-phenyl-pyridin-2-one
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C12 H11 N O2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms 3-hydroxy-1-methyl-5-phenylpyridin-2-one
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2016-11-02
_chem_comp.pdbx_modified_date 2020-06-17
_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 201.221
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 7JR
_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 5PA0
_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
7JR N1 N1 N 0 1 N N N N N N -0.007 12.881 26.109 1.878 -1.167 0.182 N1 7JR 1
7JR C4 C1 C 0 1 N N N N N N 2.139 14.492 25.535 0.543 1.218 -0.183 C4 7JR 2
7JR C5 C2 C 0 1 N N N N N N 0.869 14.823 25.077 -0.165 0.009 -0.000 C5 7JR 3
7JR C6 C3 C 0 1 N N N N N N -0.184 13.998 25.368 0.521 -1.156 0.179 C6 7JR 4
7JR C7 C4 C 0 1 N N N N N N -1.157 12.022 26.390 2.590 -2.433 0.375 C7 7JR 5
7JR C10 C5 C 0 1 Y N N N N N 0.683 16.076 24.281 -1.649 0.007 -0.002 C10 7JR 6
7JR C13 C6 C 0 1 Y N N N N N 0.355 18.424 22.797 -4.417 0.003 -0.004 C13 7JR 7
7JR C15 C7 C 0 1 Y N N N N N -0.284 16.145 23.295 -2.346 -0.667 -1.002 C15 7JR 8
7JR C2 C8 C 0 1 N N N N N N 1.196 12.562 26.575 2.579 -0.032 0.004 C2 7JR 9
7JR C3 C9 C 0 1 N N N N N N 2.317 13.339 26.289 1.907 1.195 -0.184 C3 7JR 10
7JR O8 O1 O 0 1 N N N N N N 1.348 11.465 27.352 3.799 -0.063 0.005 O8 7JR 11
7JR O9 O2 O 0 1 N N N N N N 3.516 12.935 26.776 2.612 2.345 -0.358 O9 7JR 12
7JR C11 C10 C 0 1 Y N N N N N 1.486 17.187 24.517 -2.350 0.675 1.000 C11 7JR 13
7JR C12 C11 C 0 1 Y N N N N N 1.339 18.358 23.779 -3.730 0.670 0.995 C12 7JR 14
7JR C14 C12 C 0 1 Y N N N N N -0.451 17.306 22.555 -3.727 -0.670 -0.995 C14 7JR 15
7JR H41 H1 H 0 1 N N N N N N 2.982 15.127 25.306 0.011 2.147 -0.325 H41 7JR 16
7JR H61 H2 H 0 1 N N N N N N -1.170 14.243 25.001 -0.022 -2.080 0.319 H61 7JR 17
7JR H71 H3 H 0 1 N N N N N N -0.835 11.165 27.000 3.665 -2.253 0.344 H71 7JR 18
7JR H72 H4 H 0 1 N N N N N N -1.918 12.597 26.938 2.321 -2.857 1.343 H72 7JR 19
7JR H73 H5 H 0 1 N N N N N N -1.583 11.658 25.443 2.315 -3.129 -0.416 H73 7JR 20
7JR H131 H6 H 0 0 N N N N N N 0.215 19.330 22.227 -5.497 0.002 -0.004 H131 7JR 21
7JR H151 H7 H 0 0 N N N N N N -0.913 15.289 23.100 -1.808 -1.186 -1.781 H151 7JR 22
7JR H91 H8 H 0 1 N N N N N N 3.401 12.139 27.282 3.572 2.224 -0.343 H91 7JR 23
7JR H111 H9 H 0 0 N N N N N N 2.240 17.140 25.289 -1.814 1.196 1.781 H111 7JR 24
7JR H121 H10 H 0 0 N N N N N N 1.981 19.206 23.966 -4.274 1.194 1.766 H121 7JR 25
7JR H141 H11 H 0 0 N N N N N N -1.209 17.348 21.786 -4.268 -1.189 -1.772 H141 7JR 26
#
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
7JR C14 C13 DOUB Y N 1
7JR C14 C15 SING Y N 2
7JR C13 C12 SING Y N 3
7JR C15 C10 DOUB Y N 4
7JR C12 C11 DOUB Y N 5
7JR C10 C11 SING Y N 6
7JR C10 C5 SING N N 7
7JR C5 C6 DOUB N N 8
7JR C5 C4 SING N N 9
7JR C6 N1 SING N N 10
7JR C4 C3 DOUB N N 11
7JR N1 C7 SING N N 12
7JR N1 C2 SING N N 13
7JR C3 C2 SING N N 14
7JR C3 O9 SING N N 15
7JR C2 O8 DOUB N N 16
7JR C4 H41 SING N N 17
7JR C6 H61 SING N N 18
7JR C7 H71 SING N N 19
7JR C7 H72 SING N N 20
7JR C7 H73 SING N N 21
7JR C13 H131 SING N N 22
7JR C15 H151 SING N N 23
7JR O9 H91 SING N N 24
7JR C11 H111 SING N N 25
7JR C12 H121 SING N N 26
7JR C14 H141 SING N N 27
#
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
7JR InChI InChI 1.03 InChI=1S/C12H11NO2/c1-13-8-10(7-11(14)12(13)15)9-5-3-2-4-6-9/h2-8,14H,1H3
7JR InChIKey InChI 1.03 NDVZUSAEFIBAFV-UHFFFAOYSA-N
7JR SMILES_CANONICAL CACTVS 3.385 CN1C=C(C=C(O)C1=O)c2ccccc2
7JR SMILES CACTVS 3.385 CN1C=C(C=C(O)C1=O)c2ccccc2
7JR SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 CN1C=C(C=C(C1=O)O)c2ccccc2
7JR SMILES "OpenEye OEToolkits" 2.0.6 CN1C=C(C=C(C1=O)O)c2ccccc2
#
_pdbx_chem_comp_identifier.comp_id 7JR
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version 2.0.6
_pdbx_chem_comp_identifier.identifier 1-methyl-3-oxidanyl-5-phenyl-pyridin-2-one
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
7JR 'Create component' 2016-11-02 RCSB
7JR 'Initial release' 2017-11-22 RCSB
7JR 'Modify synonyms' 2020-06-05 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id 7JR
_pdbx_chem_comp_synonyms.name 3-hydroxy-1-methyl-5-phenylpyridin-2-one
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_synonyms.comp_id 7JR
_pdbe_chem_comp_synonyms.name 3-hydroxy-1-methyl-5-phenylpyridin-2-one
_pdbe_chem_comp_synonyms.provenance wwPDB
_pdbe_chem_comp_synonyms.type ?
#
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
7JR N1 N 4.299 0.375 1
7JR C4 C 6.897 -1.125 2
7JR C5 C 6.897 0.375 3
7JR C6 C 5.598 1.125 4
7JR C7 C 3.000 1.125 5
7JR C10 C 8.196 1.125 6
7JR C13 C 10.794 2.625 7
7JR C15 C 8.196 2.625 8
7JR C2 C 4.299 -1.125 9
7JR C3 C 5.598 -1.875 10
7JR O8 O 3.000 -1.875 11
7JR O9 O 5.598 -3.375 12
7JR C11 C 9.495 0.375 13
7JR C12 C 10.794 1.125 14
7JR C14 C 9.495 3.375 15
#
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
7JR C14 C13 DOUBLE NONE 1
7JR C14 C15 SINGLE NONE 2
7JR C13 C12 SINGLE NONE 3
7JR C15 C10 DOUBLE NONE 4
7JR C12 C11 DOUBLE NONE 5
7JR C10 C11 SINGLE NONE 6
7JR C10 C5 SINGLE NONE 7
7JR C5 C6 DOUBLE NONE 8
7JR C5 C4 SINGLE NONE 9
7JR C6 N1 SINGLE NONE 10
7JR C4 C3 DOUBLE NONE 11
7JR N1 C7 SINGLE NONE 12
7JR N1 C2 SINGLE NONE 13
7JR C3 C2 SINGLE NONE 14
7JR C3 O9 SINGLE NONE 15
7JR C2 O8 DOUBLE NONE 16
#
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
7JR MurckoScaffold S1 scaffold 'O=c1ccc(-c2ccccc2)c[nH]1' InChI=1S/C11H9NO/c13-11-7-6-10(8-12-11)9-4-2-1-3-5-9/h1-8H,(H,12,13) RWFAQYWIBBVEBY-UHFFFAOYSA-N
7JR phenyl F1 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
7JR pyridine F2 fragment c1ccncc1 InChI=1S/C5H5N/c1-2-4-6-5-3-1/h1-5H JUJWROOIHBZHMG-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
7JR N1 S1 1
7JR C4 S1 1
7JR C5 S1 1
7JR C6 S1 1
7JR C10 S1 1
7JR C13 S1 1
7JR C15 S1 1
7JR C2 S1 1
7JR C3 S1 1
7JR O8 S1 1
7JR C11 S1 1
7JR C12 S1 1
7JR C14 S1 1
7JR C10 F1 1
7JR C15 F1 1
7JR C14 F1 1
7JR C13 F1 1
7JR C12 F1 1
7JR C11 F1 1
7JR C6 F2 1
7JR C5 F2 1
7JR C4 F2 1
7JR C3 F2 1
7JR C2 F2 1
7JR N1 F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 7JR
_pdbe_chem_comp_rdkit_properties.exactmw 201.079
_pdbe_chem_comp_rdkit_properties.amw 201.225
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 1
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 3
_pdbe_chem_comp_rdkit_properties.NumHBD 1
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 15
_pdbe_chem_comp_rdkit_properties.NumAtoms 26
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 3
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.083
_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 102.780
_pdbe_chem_comp_rdkit_properties.tpsa 42.230
_pdbe_chem_comp_rdkit_properties.CrippenClogP 1.815
_pdbe_chem_comp_rdkit_properties.CrippenMR 56.960
_pdbe_chem_comp_rdkit_properties.chi0v 7.264
_pdbe_chem_comp_rdkit_properties.chi1v 3.829
_pdbe_chem_comp_rdkit_properties.chi2v 1.609
_pdbe_chem_comp_rdkit_properties.chi3v 1.609
_pdbe_chem_comp_rdkit_properties.chi4v 0.952
_pdbe_chem_comp_rdkit_properties.chi0n 18.264
_pdbe_chem_comp_rdkit_properties.chi1n 9.237
_pdbe_chem_comp_rdkit_properties.chi2n 1.609
_pdbe_chem_comp_rdkit_properties.chi3n 1.609
_pdbe_chem_comp_rdkit_properties.chi4n 0.952
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.030
_pdbe_chem_comp_rdkit_properties.kappa1 2.981
_pdbe_chem_comp_rdkit_properties.kappa2 3.612
_pdbe_chem_comp_rdkit_properties.kappa3 1.764
_pdbe_chem_comp_rdkit_properties.Phi 0.718
#
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
7JR UniChem PDBe 7JR
7JR UniChem PubChem 131801421
#
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
7JR N1 -2.326 -0.966 -0.236 ETKDGv3 1
7JR C4 -0.878 1.440 0.097 ETKDGv3 2
7JR C5 -0.176 0.134 -0.002 ETKDGv3 3
7JR C6 -0.888 -0.998 -0.164 ETKDGv3 4
7JR C7 -3.074 -2.200 -0.477 ETKDGv3 5
7JR C10 1.306 0.095 0.091 ETKDGv3 6
7JR C13 4.133 0.066 0.274 ETKDGv3 7
7JR C15 2.038 -0.693 -0.722 ETKDGv3 8
7JR C2 -3.002 0.302 -0.174 ETKDGv3 9
7JR C3 -2.212 1.526 0.012 ETKDGv3 10
7JR O8 -4.257 0.370 -0.279 ETKDGv3 11
7JR O9 -2.856 2.761 0.094 ETKDGv3 12
7JR C11 2.009 0.950 1.085 ETKDGv3 13
7JR C12 3.345 0.934 1.170 ETKDGv3 14
7JR C14 3.513 -0.708 -0.624 ETKDGv3 15
7JR H41 -0.298 2.346 0.217 ETKDGv3 16
7JR H61 -0.379 -1.953 -0.218 ETKDGv3 17
7JR H71 -2.469 -3.091 -0.205 ETKDGv3 18
7JR H72 -3.349 -2.264 -1.550 ETKDGv3 19
7JR H73 -3.997 -2.216 0.141 ETKDGv3 20
7JR H131 5.213 0.057 0.346 ETKDGv3 21
7JR H151 1.564 -1.311 -1.475 ETKDGv3 22
7JR H91 -2.341 3.625 0.221 ETKDGv3 23
7JR H111 1.443 1.581 1.760 ETKDGv3 24
7JR H121 3.850 1.554 1.899 ETKDGv3 25
7JR H141 4.089 -1.344 -1.283 ETKDGv3 26
#