data_VAO
#
_chem_comp.id VAO
_chem_comp.name "2-(5-cyano-2-oxidanyl-phenyl)pyridine-4-carboxylic acid"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C13 H8 N2 O3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2015-07-09
_chem_comp.pdbx_modified_date 2016-01-08
_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 240.214
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code VAO
_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 5A7N
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site EBI
#
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
VAO N1 N1 N 0 1 N N N N N N -45.770 -57.334 7.740 -3.967 -3.327 -0.007 N1 VAO 1
VAO C C C 0 1 N N N N N N -44.766 -57.446 7.169 -3.535 -2.276 -0.003 C VAO 2
VAO C1 C1 C 0 1 Y N N N N N -43.546 -57.531 6.430 -2.991 -0.952 0.002 C1 VAO 3
VAO C6 C6 C 0 1 Y N N N N N -43.394 -56.659 5.365 -1.608 -0.765 0.002 C6 VAO 4
VAO C5 C5 C 0 1 Y N N N N N -42.203 -56.613 4.679 -1.086 0.523 0.007 C5 VAO 5
VAO C4 C4 C 0 1 Y N N N N N -41.125 -57.429 5.097 -1.950 1.625 0.012 C4 VAO 6
VAO O2 O2 O 0 1 N N N N N N -39.935 -57.270 4.477 -1.443 2.884 0.016 O2 VAO 7
VAO C3 C3 C 0 1 Y N N N N N -41.292 -58.340 6.159 -3.324 1.431 0.012 C3 VAO 8
VAO C2 C2 C 0 1 Y N N N N N -42.513 -58.397 6.812 -3.845 0.156 0.002 C2 VAO 9
VAO C7 C7 C 0 1 Y N N N N N -42.208 -55.776 3.478 0.382 0.729 0.006 C7 VAO 10
VAO N N N 0 1 Y N N N N N -41.103 -55.055 3.166 0.872 1.962 0.011 N VAO 11
VAO C11 C11 C 0 1 Y N N N N N -41.163 -54.313 2.058 2.168 2.197 0.011 C11 VAO 12
VAO C10 C10 C 0 1 Y N N N N N -42.287 -54.236 1.211 3.080 1.159 0.006 C10 VAO 13
VAO C9 C9 C 0 1 Y N N N N N -43.406 -54.989 1.568 2.613 -0.161 0.001 C9 VAO 14
VAO C8 C8 C 0 1 Y N N N N N -43.386 -55.772 2.704 1.234 -0.374 0.007 C8 VAO 15
VAO C12 C12 C 0 1 N N N N N N -44.633 -54.979 0.759 3.558 -1.301 -0.004 C12 VAO 16
VAO O1 O1 O 0 1 N N N N N N -45.761 -55.018 1.226 3.136 -2.440 -0.008 O1 VAO 17
VAO O O O 0 1 N N N N N N -44.525 -54.943 -0.603 4.886 -1.075 -0.005 O VAO 18
VAO H6 H6 H 0 1 N N N N N N -44.211 -56.015 5.073 -0.946 -1.618 -0.002 H6 VAO 19
VAO H2 H2 H 0 1 N N N N N N -42.668 -59.106 7.612 -4.915 0.011 -0.001 H2 VAO 20
VAO H3 H3 H 0 1 N N N N N N -40.480 -58.985 6.460 -3.988 2.283 0.017 H3 VAO 21
VAO H8 H8 H 0 1 N N N N N N -44.244 -56.362 2.990 0.833 -1.377 0.008 H8 VAO 22
VAO H11 H11 H 0 1 N N N N N N -40.292 -53.733 1.793 2.523 3.216 0.015 H11 VAO 23
VAO H10 H10 H 0 1 N N N N N N -42.282 -53.620 0.324 4.140 1.364 0.005 H10 VAO 24
VAO H H H 0 1 N N N N N N -45.392 -54.955 -0.990 5.463 -1.851 -0.008 H VAO 25
VAO H21 H21 H 0 1 N N N N N N -39.301 -57.873 4.848 -1.297 3.252 -0.866 H21 VAO 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
VAO N1 C TRIP N N 1
VAO C C1 SING N N 2
VAO C1 C6 SING Y N 3
VAO C1 C2 DOUB Y N 4
VAO C6 C5 DOUB Y N 5
VAO C5 C4 SING Y N 6
VAO C5 C7 SING N N 7
VAO C4 O2 SING N N 8
VAO C4 C3 DOUB Y N 9
VAO C3 C2 SING Y N 10
VAO C7 N DOUB Y N 11
VAO C7 C8 SING Y N 12
VAO N C11 SING Y N 13
VAO C11 C10 DOUB Y N 14
VAO C10 C9 SING Y N 15
VAO C9 C8 DOUB Y N 16
VAO C9 C12 SING N N 17
VAO C12 O1 DOUB N N 18
VAO C12 O SING N N 19
VAO C6 H6 SING N N 20
VAO C2 H2 SING N N 21
VAO C3 H3 SING N N 22
VAO C8 H8 SING N N 23
VAO C11 H11 SING N N 24
VAO C10 H10 SING N N 25
VAO O H SING N N 26
VAO O2 H21 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
VAO InChI InChI 1.03 InChI=1S/C13H8N2O3/c14-7-8-1-2-12(16)10(5-8)11-6-9(13(17)18)3-4-15-11/h1-6,16H,(H,17,18)
VAO InChIKey InChI 1.03 NARDFYYIAAFALG-UHFFFAOYSA-N
VAO SMILES_CANONICAL CACTVS 3.385 "OC(=O)c1ccnc(c1)c2cc(ccc2O)C#N"
VAO SMILES CACTVS 3.385 "OC(=O)c1ccnc(c1)c2cc(ccc2O)C#N"
VAO SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "c1cc(c(cc1C#N)c2cc(ccn2)C(=O)O)O"
VAO SMILES "OpenEye OEToolkits" 1.7.6 "c1cc(c(cc1C#N)c2cc(ccn2)C(=O)O)O"
#
_pdbx_chem_comp_identifier.comp_id VAO
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version 1.7.6
_pdbx_chem_comp_identifier.identifier "2-(5-cyano-2-oxidanyl-phenyl)pyridine-4-carboxylic 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
VAO 'Create component' 2015-07-09 EBI
VAO 'Initial release' 2016-01-13 RCSB
#
loop_
_software.name
_software.version
_software.description
rdkit 2025.03.3 'Core functionality.'
pdbeccdutils 1.0.0 '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
VAO N1 N 10.301 -5.107 1
VAO C C 9.002 -4.357 2
VAO C1 C 7.702 -3.607 3
VAO C6 C 7.702 -2.107 4
VAO C5 C 6.404 -1.357 5
VAO C4 C 5.104 -2.107 6
VAO O2 O 3.805 -1.357 7
VAO C3 C 5.104 -3.607 8
VAO C2 C 6.404 -4.357 9
VAO C7 C 6.404 0.142 10
VAO N N 5.104 0.892 11
VAO C11 C 5.104 2.393 12
VAO C10 C 6.404 3.143 13
VAO C9 C 7.702 2.393 14
VAO C8 C 7.702 0.892 15
VAO C12 C 9.002 3.143 16
VAO O1 O 9.002 4.643 17
VAO O O 10.301 2.393 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
VAO N1 C TRIPLE NONE 1
VAO C C1 SINGLE NONE 2
VAO C1 C6 DOUBLE NONE 3
VAO C1 C2 SINGLE NONE 4
VAO C6 C5 SINGLE NONE 5
VAO C5 C4 DOUBLE NONE 6
VAO C5 C7 SINGLE NONE 7
VAO C4 O2 SINGLE NONE 8
VAO C4 C3 SINGLE NONE 9
VAO C3 C2 DOUBLE NONE 10
VAO C7 N DOUBLE NONE 11
VAO C7 C8 SINGLE NONE 12
VAO N C11 SINGLE NONE 13
VAO C11 C10 DOUBLE NONE 14
VAO C10 C9 SINGLE NONE 15
VAO C9 C8 DOUBLE NONE 16
VAO C9 C12 SINGLE NONE 17
VAO C12 O1 DOUBLE NONE 18
VAO C12 O 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
VAO MurckoScaffold S1 scaffold c1ccc(-c2ccccn2)cc1 InChI=1S/C11H9N/c1-2-6-10(7-3-1)11-8-4-5-9-12-11/h1-9H VQGHOUODWALEFC-UHFFFAOYSA-N
VAO phenyl F1 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
VAO 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
VAO C1 S1 1
VAO C6 S1 1
VAO C5 S1 1
VAO C4 S1 1
VAO C3 S1 1
VAO C2 S1 1
VAO C7 S1 1
VAO N S1 1
VAO C11 S1 1
VAO C10 S1 1
VAO C9 S1 1
VAO C8 S1 1
VAO C1 F1 1
VAO C6 F1 1
VAO C5 F1 1
VAO C4 F1 1
VAO C3 F1 1
VAO C2 F1 1
VAO C7 F2 1
VAO C8 F2 1
VAO C9 F2 1
VAO C10 F2 1
VAO C11 F2 1
VAO N F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id VAO
_pdbe_chem_comp_rdkit_properties.exactmw 240.053
_pdbe_chem_comp_rdkit_properties.amw 240.218
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 5
_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 5
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 18
_pdbe_chem_comp_rdkit_properties.NumAtoms 26
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 5
_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 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 113.994
_pdbe_chem_comp_rdkit_properties.tpsa 94.210
_pdbe_chem_comp_rdkit_properties.CrippenClogP 1.072
_pdbe_chem_comp_rdkit_properties.CrippenMR 60.548
_pdbe_chem_comp_rdkit_properties.chi0v 8.619
_pdbe_chem_comp_rdkit_properties.chi1v 4.533
_pdbe_chem_comp_rdkit_properties.chi2v 1.923
_pdbe_chem_comp_rdkit_properties.chi3v 1.923
_pdbe_chem_comp_rdkit_properties.chi4v 1.155
_pdbe_chem_comp_rdkit_properties.chi0n 16.619
_pdbe_chem_comp_rdkit_properties.chi1n 8.350
_pdbe_chem_comp_rdkit_properties.chi2n 1.923
_pdbe_chem_comp_rdkit_properties.chi3n 1.923
_pdbe_chem_comp_rdkit_properties.chi4n 1.155
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.870
_pdbe_chem_comp_rdkit_properties.kappa1 5.188
_pdbe_chem_comp_rdkit_properties.kappa2 4.553
_pdbe_chem_comp_rdkit_properties.kappa3 2.128
_pdbe_chem_comp_rdkit_properties.Phi 1.312
#
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
VAO UniChem ZINC ZINC000263620778
VAO UniChem PubChem 135567036
VAO UniChem BindingDb 50151400
#
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
VAO N1 -3.511 3.710 -1.416 ETKDGv3 1
VAO C -3.178 2.687 -0.990 ETKDGv3 2
VAO C1 -2.765 1.414 -0.461 ETKDGv3 3
VAO C6 -1.465 1.154 -0.256 ETKDGv3 4
VAO C5 -1.032 -0.158 0.299 ETKDGv3 5
VAO C4 -1.972 -1.084 0.599 ETKDGv3 6
VAO O2 -1.609 -2.333 1.103 ETKDGv3 7
VAO C3 -3.405 -0.785 0.374 ETKDGv3 8
VAO C2 -3.780 0.394 -0.131 ETKDGv3 9
VAO C7 0.413 -0.415 0.519 ETKDGv3 10
VAO N 0.803 -1.100 1.558 ETKDGv3 11
VAO C11 2.190 -1.362 1.824 ETKDGv3 12
VAO C10 3.132 -0.896 0.999 ETKDGv3 13
VAO C9 2.737 -0.113 -0.198 ETKDGv3 14
VAO C8 1.431 0.114 -0.424 ETKDGv3 15
VAO C12 3.769 0.398 -1.126 ETKDGv3 16
VAO O1 4.989 0.171 -0.905 ETKDGv3 17
VAO O 3.405 1.135 -2.251 ETKDGv3 18
VAO H6 -0.725 1.915 -0.477 ETKDGv3 19
VAO H2 -4.831 0.600 -0.293 ETKDGv3 20
VAO H3 -4.156 -1.528 0.614 ETKDGv3 21
VAO H8 1.112 0.662 -1.302 ETKDGv3 22
VAO H11 2.469 -1.936 2.698 ETKDGv3 23
VAO H10 4.175 -1.097 1.210 ETKDGv3 24
VAO H 4.107 1.488 -2.891 ETKDGv3 25
VAO H21 -2.305 -3.035 1.325 ETKDGv3 26
#