data_VAJ
#
_chem_comp.id VAJ
_chem_comp.name "[1,1'-biphenyl]-3,4'-dicarboxylic acid"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C14 H10 O4"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2020-07-22
_chem_comp.pdbx_modified_date 2021-11-26
_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 242.227
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code VAJ
_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 7JHQ
_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
VAJ C1 C1 C 0 1 Y N N N N N 39.219 -41.581 11.183 3.266 0.111 0.001 C1 VAJ 1
VAJ C2 C2 C 0 1 Y N N N N N 38.680 -41.684 12.460 2.818 -1.213 0.003 C2 VAJ 2
VAJ C3 C3 C 0 1 Y N N N N N 38.161 -40.573 13.099 1.468 -1.482 0.003 C3 VAJ 3
VAJ C4 C4 C 0 1 Y N N N N N 38.160 -39.322 12.489 0.548 -0.434 0.001 C4 VAJ 4
VAJ C7 C5 C 0 1 Y N N N N N 37.581 -38.135 13.168 -0.906 -0.725 0.001 C7 VAJ 5
VAJ C9 C6 C 0 1 Y N N N N N 37.436 -35.739 13.453 -2.708 -2.321 -0.004 C9 VAJ 6
VAJ C10 C7 C 0 1 Y N N N N N 36.472 -35.903 14.431 -3.627 -1.291 -0.001 C10 VAJ 7
VAJ C13 C8 C 0 1 N N N N N N 34.981 -37.351 15.813 -4.175 1.139 0.001 C13 VAJ 8
VAJ C C9 C 0 1 N N N N N N 39.751 -42.783 10.485 4.714 0.401 0.001 C VAJ 9
VAJ O O1 O 0 1 N N N N N N 40.615 -42.531 9.544 5.516 -0.512 0.003 O VAJ 10
VAJ C11 C10 C 0 1 Y N N N N N 36.047 -37.176 14.789 -3.192 0.037 -0.002 C11 VAJ 11
VAJ C12 C11 C 0 1 Y N N N N N 36.609 -38.284 14.160 -1.826 0.319 -0.002 C12 VAJ 12
VAJ C5 C12 C 0 1 Y N N N N N 38.708 -39.226 11.210 0.993 0.888 -0.001 C5 VAJ 13
VAJ C6 C13 C 0 1 Y N N N N N 39.230 -40.334 10.567 2.343 1.160 -0.007 C6 VAJ 14
VAJ C8 C14 C 0 1 Y N N N N N 37.985 -36.844 12.824 -1.354 -2.046 -0.003 C8 VAJ 15
VAJ O1 O2 O 0 1 N N N N N N 39.390 -43.913 10.782 5.145 1.677 -0.001 O1 VAJ 16
VAJ O2 O3 O 0 1 N N N N N N 34.242 -36.428 16.126 -3.795 2.293 0.000 O2 VAJ 17
VAJ O3 O4 O 0 1 N N N N N N 34.902 -38.544 16.338 -5.494 0.865 0.005 O3 VAJ 18
VAJ H1 H1 H 0 1 N N N N N N 38.666 -42.642 12.958 3.531 -2.025 0.004 H1 VAJ 19
VAJ H2 H2 H 0 1 N N N N N N 37.748 -40.678 14.091 1.122 -2.505 0.004 H2 VAJ 20
VAJ H3 H3 H 0 1 N N N N N N 37.762 -34.746 13.179 -3.049 -3.345 -0.003 H3 VAJ 21
VAJ H4 H4 H 0 1 N N N N N N 36.048 -35.038 14.918 -4.684 -1.511 0.002 H4 VAJ 22
VAJ H5 H5 H 0 1 N N N N N N 36.288 -39.275 14.444 -1.484 1.343 -0.003 H5 VAJ 23
VAJ H6 H6 H 0 1 N N N N N N 38.725 -38.268 10.712 0.280 1.698 -0.002 H6 VAJ 24
VAJ H7 H7 H 0 1 N N N N N N 39.650 -40.230 9.577 2.688 2.183 -0.009 H7 VAJ 25
VAJ H8 H8 H 0 1 N N N N N N 38.734 -36.705 12.059 -0.641 -2.857 -0.005 H8 VAJ 26
VAJ H9 H9 H 0 1 N N N N N N 39.834 -44.544 10.227 6.102 1.817 -0.001 H9 VAJ 27
VAJ H10 H10 H 0 1 N N N N N N 34.199 -38.563 16.977 -6.100 1.619 0.007 H10 VAJ 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
VAJ O C DOUB N N 1
VAJ C O1 SING N N 2
VAJ C C1 SING N N 3
VAJ C6 C1 DOUB Y N 4
VAJ C6 C5 SING Y N 5
VAJ C1 C2 SING Y N 6
VAJ C5 C4 DOUB Y N 7
VAJ C2 C3 DOUB Y N 8
VAJ C4 C3 SING Y N 9
VAJ C4 C7 SING N N 10
VAJ C8 C7 DOUB Y N 11
VAJ C8 C9 SING Y N 12
VAJ C7 C12 SING Y N 13
VAJ C9 C10 DOUB Y N 14
VAJ C12 C11 DOUB Y N 15
VAJ C10 C11 SING Y N 16
VAJ C11 C13 SING N N 17
VAJ C13 O2 DOUB N N 18
VAJ C13 O3 SING N N 19
VAJ C2 H1 SING N N 20
VAJ C3 H2 SING N N 21
VAJ C9 H3 SING N N 22
VAJ C10 H4 SING N N 23
VAJ C12 H5 SING N N 24
VAJ C5 H6 SING N N 25
VAJ C6 H7 SING N N 26
VAJ C8 H8 SING N N 27
VAJ O1 H9 SING N N 28
VAJ O3 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
VAJ SMILES ACDLabs 12.01 c2(ccc(c1cc(ccc1)C(=O)O)cc2)C(O)=O
VAJ InChI InChI 1.03 InChI=1S/C14H10O4/c15-13(16)10-6-4-9(5-7-10)11-2-1-3-12(8-11)14(17)18/h1-8H,(H,15,16)(H,17,18)
VAJ InChIKey InChI 1.03 GSYIVQLTSZFJRV-UHFFFAOYSA-N
VAJ SMILES_CANONICAL CACTVS 3.385 OC(=O)c1ccc(cc1)c2cccc(c2)C(O)=O
VAJ SMILES CACTVS 3.385 OC(=O)c1ccc(cc1)c2cccc(c2)C(O)=O
VAJ SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 c1cc(cc(c1)C(=O)O)c2ccc(cc2)C(=O)O
VAJ SMILES "OpenEye OEToolkits" 2.0.7 c1cc(cc(c1)C(=O)O)c2ccc(cc2)C(=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
VAJ "SYSTEMATIC NAME" ACDLabs 12.01 "[1,1'-biphenyl]-3,4'-dicarboxylic acid"
VAJ "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "3-(4-carboxyphenyl)benzoic 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
VAJ 'Create component' 2020-07-22 RCSB
VAJ 'Initial release' 2021-12-01 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
VAJ C1 C 4.299 -3.143 1
VAJ C2 C 3.000 -2.393 2
VAJ C3 C 3.000 -0.892 3
VAJ C4 C 4.299 -0.142 4
VAJ C7 C 4.299 1.357 5
VAJ C9 C 3.000 3.607 6
VAJ C10 C 4.299 4.357 7
VAJ C13 C 6.897 4.357 8
VAJ C C 4.299 -4.643 9
VAJ O O 3.000 -5.393 10
VAJ C11 C 5.598 3.607 11
VAJ C12 C 5.598 2.107 12
VAJ C5 C 5.598 -0.892 13
VAJ C6 C 5.598 -2.393 14
VAJ C8 C 3.000 2.107 15
VAJ O1 O 5.598 -5.393 16
VAJ O2 O 6.897 5.857 17
VAJ O3 O 8.196 3.607 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
VAJ O C DOUBLE NONE 1
VAJ C O1 SINGLE NONE 2
VAJ C C1 SINGLE NONE 3
VAJ C6 C1 DOUBLE NONE 4
VAJ C6 C5 SINGLE NONE 5
VAJ C1 C2 SINGLE NONE 6
VAJ C5 C4 DOUBLE NONE 7
VAJ C2 C3 DOUBLE NONE 8
VAJ C4 C3 SINGLE NONE 9
VAJ C4 C7 SINGLE NONE 10
VAJ C8 C7 SINGLE NONE 11
VAJ C8 C9 DOUBLE NONE 12
VAJ C7 C12 DOUBLE NONE 13
VAJ C9 C10 SINGLE NONE 14
VAJ C12 C11 SINGLE NONE 15
VAJ C10 C11 DOUBLE NONE 16
VAJ C11 C13 SINGLE NONE 17
VAJ C13 O2 DOUBLE NONE 18
VAJ C13 O3 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
VAJ 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
VAJ 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
VAJ C1 S1 1
VAJ C2 S1 1
VAJ C3 S1 1
VAJ C4 S1 1
VAJ C7 S1 1
VAJ C9 S1 1
VAJ C10 S1 1
VAJ C11 S1 1
VAJ C12 S1 1
VAJ C5 S1 1
VAJ C6 S1 1
VAJ C8 S1 1
VAJ C1 F1 1
VAJ C6 F1 1
VAJ C5 F1 1
VAJ C4 F1 1
VAJ C3 F1 1
VAJ C2 F1 1
VAJ C7 F1 2
VAJ C8 F1 2
VAJ C9 F1 2
VAJ C10 F1 2
VAJ C11 F1 2
VAJ C12 F1 2
#
_pdbe_chem_comp_rdkit_properties.comp_id VAJ
_pdbe_chem_comp_rdkit_properties.exactmw 242.058
_pdbe_chem_comp_rdkit_properties.amw 242.230
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 4
_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 4
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 18
_pdbe_chem_comp_rdkit_properties.NumAtoms 28
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 4
_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 117.353
_pdbe_chem_comp_rdkit_properties.tpsa 74.600
_pdbe_chem_comp_rdkit_properties.CrippenClogP 2.261
_pdbe_chem_comp_rdkit_properties.CrippenMR 63.943
_pdbe_chem_comp_rdkit_properties.chi0v 8.633
_pdbe_chem_comp_rdkit_properties.chi1v 4.566
_pdbe_chem_comp_rdkit_properties.chi2v 1.908
_pdbe_chem_comp_rdkit_properties.chi3v 1.908
_pdbe_chem_comp_rdkit_properties.chi4v 1.110
_pdbe_chem_comp_rdkit_properties.chi0n 18.633
_pdbe_chem_comp_rdkit_properties.chi1n 9.383
_pdbe_chem_comp_rdkit_properties.chi2n 1.908
_pdbe_chem_comp_rdkit_properties.chi3n 1.908
_pdbe_chem_comp_rdkit_properties.chi4n 1.110
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.620
_pdbe_chem_comp_rdkit_properties.kappa1 4.570
_pdbe_chem_comp_rdkit_properties.kappa2 4.710
_pdbe_chem_comp_rdkit_properties.kappa3 2.376
_pdbe_chem_comp_rdkit_properties.Phi 1.196
#
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
VAJ UniChem PDBe VAJ
VAJ UniChem ZINC ZINC000035785283
VAJ UniChem eMolecules 32273628
VAJ UniChem Nikkaji J802.791I
VAJ UniChem ChemicalBook CB11455417
VAJ UniChem 'EPA CompTox Dashboard' DTXSID00468424
VAJ UniChem SureChEMBL SCHEMBL69066
VAJ UniChem 'PubChem TPHARMA' 16652651
VAJ UniChem PubChem 11550488
VAJ UniChem Mcule MCULE-2480569439
#
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
VAJ C1 -3.412 0.437 -0.028 ETKDGv3 1
VAJ C2 -2.728 0.375 1.287 ETKDGv3 2
VAJ C3 -1.411 0.149 1.358 ETKDGv3 3
VAJ C4 -0.610 -0.041 0.122 ETKDGv3 4
VAJ C7 0.849 -0.305 0.218 ETKDGv3 5
VAJ C9 2.680 -1.431 1.394 ETKDGv3 6
VAJ C10 3.627 -0.808 0.449 ETKDGv3 7
VAJ C13 4.124 0.630 -1.478 ETKDGv3 8
VAJ C -4.869 0.685 -0.089 ETKDGv3 9
VAJ O -5.466 0.742 -1.199 ETKDGv3 10
VAJ C11 3.180 0.002 -0.527 ETKDGv3 11
VAJ C12 1.721 0.263 -0.640 ETKDGv3 12
VAJ C5 -1.233 0.015 -1.071 ETKDGv3 13
VAJ C6 -2.687 0.265 -1.149 ETKDGv3 14
VAJ C8 1.368 -1.195 1.287 ETKDGv3 15
VAJ O1 -5.596 0.859 1.085 ETKDGv3 16
VAJ O2 3.695 1.386 -2.391 ETKDGv3 17
VAJ O3 5.493 0.394 -1.375 ETKDGv3 18
VAJ H1 -3.289 0.516 2.202 ETKDGv3 19
VAJ H2 -0.930 0.125 2.328 ETKDGv3 20
VAJ H3 3.051 -2.086 2.171 ETKDGv3 21
VAJ H4 4.682 -1.021 0.563 ETKDGv3 22
VAJ H5 1.364 0.936 -1.410 ETKDGv3 23
VAJ H6 -0.687 -0.144 -1.993 ETKDGv3 24
VAJ H7 -3.151 0.302 -2.127 ETKDGv3 25
VAJ H8 0.687 -1.674 1.978 ETKDGv3 26
VAJ H9 -6.595 1.030 1.059 ETKDGv3 27
VAJ H10 6.144 0.820 -2.023 ETKDGv3 28
#