data_KDV
#
_chem_comp.id KDV
_chem_comp.name quinoline-3-carbonitrile
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C10 H6 N2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2018-11-27
_chem_comp.pdbx_modified_date 2019-03-22
_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 154.168
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code KDV
_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 6N69
_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
KDV C2 C1 C 0 1 N N N N N N 16.106 -5.123 3.848 -3.146 -0.322 0.002 C2 KDV 1
KDV C3 C2 C 0 1 Y N N N N N 14.785 -4.547 3.830 -1.754 0.013 0.001 C3 KDV 2
KDV C6 C3 C 0 1 Y N N N N N 12.258 -3.458 3.898 0.887 0.773 0.001 C6 KDV 3
KDV C7 C4 C 0 1 Y N N N N N 10.959 -2.900 3.939 2.240 1.153 0.000 C7 KDV 4
KDV C8 C5 C 0 1 Y N N N N N 10.342 -2.476 2.784 3.211 0.199 0.002 C8 KDV 5
KDV C10 C6 C 0 1 Y N N N N N 12.257 -3.132 1.486 1.589 -1.565 -0.005 C10 KDV 6
KDV C11 C7 C 0 1 Y N N N N N 12.920 -3.578 2.654 0.560 -0.607 -0.002 C11 KDV 7
KDV C12 C8 C 0 1 Y N N N N N 14.206 -4.134 2.634 -0.791 -0.991 -0.002 C12 KDV 8
KDV N1 N1 N 0 1 N N N N N N 17.155 -5.580 3.848 -4.251 -0.588 0.002 N1 KDV 9
KDV C4 C9 C 0 1 Y N N N N N 14.068 -4.396 5.015 -1.349 1.359 -0.001 C4 KDV 10
KDV N5 N2 N 0 1 Y N N N N N 12.842 -3.870 5.069 -0.084 1.693 -0.002 N5 KDV 11
KDV C9 C10 C 0 1 Y N N N N N 10.989 -2.591 1.560 2.888 -1.157 0.005 C9 KDV 12
KDV H14 H1 H 0 1 N N N N N N 10.447 -2.806 4.885 2.508 2.199 -0.002 H14 KDV 13
KDV H15 H2 H 0 1 N N N N N N 9.350 -2.052 2.829 4.249 0.498 0.002 H15 KDV 14
KDV H17 H3 H 0 1 N N N N N N 12.748 -3.216 0.528 1.351 -2.618 -0.002 H17 KDV 15
KDV H18 H4 H 0 1 N N N N N N 14.741 -4.241 1.702 -1.074 -2.033 -0.004 H18 KDV 16
KDV H13 H5 H 0 1 N N N N N N 14.527 -4.721 5.937 -2.099 2.136 -0.003 H13 KDV 17
KDV H16 H6 H 0 1 N N N N N N 10.496 -2.255 0.660 3.678 -1.893 0.002 H16 KDV 18
#
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
KDV C10 C9 DOUB Y N 1
KDV C10 C11 SING Y N 2
KDV C9 C8 SING Y N 3
KDV C12 C11 DOUB Y N 4
KDV C12 C3 SING Y N 5
KDV C11 C6 SING Y N 6
KDV C8 C7 DOUB Y N 7
KDV C3 C2 SING N N 8
KDV C3 C4 DOUB Y N 9
KDV N1 C2 TRIP N N 10
KDV C6 C7 SING Y N 11
KDV C6 N5 DOUB Y N 12
KDV C4 N5 SING Y N 13
KDV C7 H14 SING N N 14
KDV C8 H15 SING N N 15
KDV C10 H17 SING N N 16
KDV C12 H18 SING N N 17
KDV C4 H13 SING N N 18
KDV C9 H16 SING N N 19
#
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
KDV SMILES ACDLabs 12.01 "C(c2cnc1ccccc1c2)#N"
KDV InChI InChI 1.03 InChI=1S/C10H6N2/c11-6-8-5-9-3-1-2-4-10(9)12-7-8/h1-5,7H
KDV InChIKey InChI 1.03 QZZYYBQGTSGDPP-UHFFFAOYSA-N
KDV SMILES_CANONICAL CACTVS 3.385 "N#Cc1cnc2ccccc2c1"
KDV SMILES CACTVS 3.385 "N#Cc1cnc2ccccc2c1"
KDV SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "c1ccc2c(c1)cc(cn2)C#N"
KDV SMILES "OpenEye OEToolkits" 2.0.6 "c1ccc2c(c1)cc(cn2)C#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
KDV "SYSTEMATIC NAME" ACDLabs 12.01 quinoline-3-carbonitrile
KDV "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 quinoline-3-carbonitrile
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
KDV 'Create component' 2018-11-27 RCSB
KDV 'Initial release' 2019-03-27 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
KDV C2 C 9.597 1.151 1
KDV C3 C 8.298 0.401 2
KDV C6 C 5.700 -1.099 3
KDV C7 C 4.359 -1.901 4
KDV C8 C 3.000 -1.130 5
KDV C10 C 4.359 1.203 6
KDV C11 C 5.700 0.401 7
KDV C12 C 6.999 1.151 8
KDV N1 N 10.896 1.901 9
KDV C4 C 8.298 -1.099 10
KDV N5 N 6.999 -1.849 11
KDV C9 C 3.000 0.432 12
#
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
KDV C10 C9 SINGLE NONE 1
KDV C10 C11 DOUBLE NONE 2
KDV C9 C8 DOUBLE NONE 3
KDV C12 C11 SINGLE NONE 4
KDV C12 C3 DOUBLE NONE 5
KDV C11 C6 SINGLE NONE 6
KDV C8 C7 SINGLE NONE 7
KDV C3 C2 SINGLE NONE 8
KDV C3 C4 SINGLE NONE 9
KDV N1 C2 TRIPLE NONE 10
KDV C6 C7 DOUBLE NONE 11
KDV C6 N5 SINGLE NONE 12
KDV C4 N5 DOUBLE NONE 13
#
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
KDV MurckoScaffold S1 scaffold c1ccc2ncccc2c1 InChI=1S/C9H7N/c1-2-6-9-8(4-1)5-3-7-10-9/h1-7H SMWDFEZZVXVKRB-UHFFFAOYSA-N
KDV phenyl F1 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
KDV pyridine F2 fragment c1ccncc1 InChI=1S/C5H5N/c1-2-4-6-5-3-1/h1-5H JUJWROOIHBZHMG-UHFFFAOYSA-N
KDV quinoline F3 fragment c1ccc2ncccc2c1 InChI=1S/C9H7N/c1-2-6-9-8(4-1)5-3-7-10-9/h1-7H SMWDFEZZVXVKRB-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
KDV C3 S1 1
KDV C6 S1 1
KDV C7 S1 1
KDV C8 S1 1
KDV C10 S1 1
KDV C11 S1 1
KDV C12 S1 1
KDV C4 S1 1
KDV N5 S1 1
KDV C9 S1 1
KDV C6 F1 1
KDV C11 F1 1
KDV C10 F1 1
KDV C9 F1 1
KDV C8 F1 1
KDV C7 F1 1
KDV C6 F2 1
KDV C11 F2 1
KDV C12 F2 1
KDV C3 F2 1
KDV C4 F2 1
KDV N5 F2 1
KDV C9 F3 1
KDV C10 F3 1
KDV C11 F3 1
KDV C6 F3 1
KDV C7 F3 1
KDV C8 F3 1
KDV N5 F3 1
KDV C4 F3 1
KDV C3 F3 1
KDV C12 F3 1
#
_pdbe_chem_comp_rdkit_properties.comp_id KDV
_pdbe_chem_comp_rdkit_properties.exactmw 154.053
_pdbe_chem_comp_rdkit_properties.amw 154.172
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 2
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 0
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 0
_pdbe_chem_comp_rdkit_properties.NumHBD 0
_pdbe_chem_comp_rdkit_properties.NumHBA 2
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 12
_pdbe_chem_comp_rdkit_properties.NumAtoms 18
_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 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 78.520
_pdbe_chem_comp_rdkit_properties.tpsa 36.680
_pdbe_chem_comp_rdkit_properties.CrippenClogP 1.623
_pdbe_chem_comp_rdkit_properties.CrippenMR 43.986
_pdbe_chem_comp_rdkit_properties.chi0v 5.894
_pdbe_chem_comp_rdkit_properties.chi1v 3.171
_pdbe_chem_comp_rdkit_properties.chi2v 1.309
_pdbe_chem_comp_rdkit_properties.chi3v 1.309
_pdbe_chem_comp_rdkit_properties.chi4v 0.798
_pdbe_chem_comp_rdkit_properties.chi0n 11.894
_pdbe_chem_comp_rdkit_properties.chi1n 6.171
_pdbe_chem_comp_rdkit_properties.chi2n 1.309
_pdbe_chem_comp_rdkit_properties.chi3n 1.309
_pdbe_chem_comp_rdkit_properties.chi4n 0.798
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.880
_pdbe_chem_comp_rdkit_properties.kappa1 2.872
_pdbe_chem_comp_rdkit_properties.kappa2 2.630
_pdbe_chem_comp_rdkit_properties.kappa3 1.017
_pdbe_chem_comp_rdkit_properties.Phi 0.629
#
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
KDV UniChem ZINC ZINC000000388450
KDV UniChem eMolecules 485583
KDV UniChem BindingDb 50526481
KDV UniChem 'EPA CompTox Dashboard' DTXSID70188400
KDV UniChem BRENDA 275366
KDV UniChem ChemicalBook CB2751261
KDV UniChem Nikkaji J289.851I
KDV UniChem SureChEMBL SCHEMBL63442
KDV UniChem 'PubChem TPHARMA' 14916157
KDV UniChem PubChem 93177
KDV UniChem Mcule MCULE-5436675713
KDV UniChem ACTor 34846-64-5
#
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
KDV C2 3.648 -0.239 0.024 ETKDGv3 1
KDV C3 2.246 0.055 -0.113 ETKDGv3 2
KDV C6 -0.472 0.759 -0.464 ETKDGv3 3
KDV C7 -1.761 1.085 -0.626 ETKDGv3 4
KDV C8 -2.814 0.224 -0.044 ETKDGv3 5
KDV C10 -1.056 -1.239 0.822 ETKDGv3 6
KDV C11 -0.101 -0.458 0.294 ETKDGv3 7
KDV C12 1.333 -0.762 0.436 ETKDGv3 8
KDV N1 4.776 -0.475 0.135 ETKDGv3 9
KDV C4 1.828 1.266 -0.866 ETKDGv3 10
KDV N5 0.571 1.572 -1.016 ETKDGv3 11
KDV C9 -2.480 -0.878 0.642 ETKDGv3 12
KDV H14 -2.038 1.973 -1.179 ETKDGv3 13
KDV H15 -3.856 0.487 -0.175 ETKDGv3 14
KDV H17 -0.799 -2.132 1.378 ETKDGv3 15
KDV H18 1.645 -1.644 0.984 ETKDGv3 16
KDV H13 2.581 1.911 -1.300 ETKDGv3 17
KDV H16 -3.251 -1.507 1.068 ETKDGv3 18
#