data_AXV
#
_chem_comp.id AXV
_chem_comp.name 1~{H}-benzimidazol-2-ylcyanamide
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C8 H6 N4"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2017-07-28
_chem_comp.pdbx_modified_date 2018-08-03
_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 158.160
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code AXV
_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 5Q1W
_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
AXV N1 N1 N 0 1 Y N N N N N 16.525 2.676 26.120 0.617 0.726 0.004 N1 AXV 1
AXV N3 N2 N 0 1 N N N N N N 16.249 2.521 28.502 2.478 -0.849 -0.000 N3 AXV 2
AXV C4 C1 C 0 1 Y N N N N N 17.640 0.798 25.795 -1.038 -0.769 -0.001 C4 AXV 3
AXV C5 C2 C 0 1 Y N N N N N 17.109 1.910 25.131 -0.763 0.609 0.002 C5 AXV 4
AXV C6 C3 C 0 1 Y N N N N N 17.209 2.074 23.761 -1.806 1.523 0.002 C6 AXV 5
AXV C7 C4 C 0 1 Y N N N N N 16.718 2.023 27.287 1.130 -0.539 0.002 C7 AXV 6
AXV C8 C5 C 0 1 N N N N N N 16.300 1.779 29.686 3.401 0.143 -0.002 C8 AXV 7
AXV C1 C6 C 0 1 Y N N N N N 17.872 1.086 23.067 -3.111 1.075 -0.001 C1 AXV 8
AXV C2 C7 C 0 1 Y N N N N N 18.410 -0.030 23.715 -3.388 -0.284 -0.004 C2 AXV 9
AXV C3 C8 C 0 1 Y N N N N N 18.306 -0.191 25.077 -2.365 -1.205 -0.003 C3 AXV 10
AXV N2 N3 N 0 1 Y N N N N N 17.385 0.891 27.162 0.157 -1.415 0.005 N2 AXV 11
AXV N4 N4 N 0 1 N N N N N N 16.335 1.175 30.669 4.175 0.974 -0.004 N4 AXV 12
AXV H1 H1 H 0 1 N N N N N N 16.050 3.547 25.996 1.124 1.553 0.002 H1 AXV 13
AXV H2 H2 H 0 1 N N N N N N 15.862 3.443 28.528 2.762 -1.776 -0.001 H2 AXV 14
AXV H3 H3 H 0 1 N N N N N N 16.788 2.934 23.261 -1.597 2.582 0.004 H3 AXV 15
AXV H4 H4 H 0 1 N N N N N N 17.979 1.176 21.996 -3.922 1.788 -0.001 H4 AXV 16
AXV H5 H5 H 0 1 N N N N N N 18.919 -0.783 23.132 -4.414 -0.622 -0.005 H5 AXV 17
AXV H6 H6 H 0 1 N N N N N N 18.726 -1.054 25.572 -2.588 -2.262 -0.005 H6 AXV 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
AXV C1 C2 DOUB Y N 1
AXV C1 C6 SING Y N 2
AXV C2 C3 SING Y N 3
AXV C6 C5 DOUB Y N 4
AXV C3 C4 DOUB Y N 5
AXV C5 C4 SING Y N 6
AXV C5 N1 SING Y N 7
AXV C4 N2 SING Y N 8
AXV N1 C7 SING Y N 9
AXV N2 C7 DOUB Y N 10
AXV C7 N3 SING N N 11
AXV N3 C8 SING N N 12
AXV C8 N4 TRIP N N 13
AXV N1 H1 SING N N 14
AXV N3 H2 SING N N 15
AXV C6 H3 SING N N 16
AXV C1 H4 SING N N 17
AXV C2 H5 SING N N 18
AXV C3 H6 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
AXV InChI InChI 1.03 InChI=1S/C8H6N4/c9-5-10-8-11-6-3-1-2-4-7(6)12-8/h1-4H,(H2,10,11,12)
AXV InChIKey InChI 1.03 NYLIXUBOFQIMGV-UHFFFAOYSA-N
AXV SMILES_CANONICAL CACTVS 3.385 "N#CNc1[nH]c2ccccc2n1"
AXV SMILES CACTVS 3.385 "N#CNc1[nH]c2ccccc2n1"
AXV SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "c1ccc2c(c1)[nH]c(n2)NC#N"
AXV SMILES "OpenEye OEToolkits" 2.0.6 "c1ccc2c(c1)[nH]c(n2)NC#N"
#
_pdbx_chem_comp_identifier.comp_id AXV
_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~{H}-benzimidazol-2-ylcyanamide
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
AXV 'Create component' 2017-07-28 RCSB
AXV 'Initial release' 2018-08-08 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
AXV N1 N 7.018 1.461 1
AXV N3 N 9.393 0.254 2
AXV C4 C 5.598 -0.496 3
AXV C5 C 5.598 1.004 4
AXV C6 C 4.299 1.754 5
AXV C7 C 7.893 0.254 6
AXV C8 C 10.143 -1.046 7
AXV C1 C 3.000 1.004 8
AXV C2 C 3.000 -0.496 9
AXV C3 C 4.299 -1.246 10
AXV N2 N 7.018 -0.954 11
AXV N4 N 10.893 -2.345 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
AXV C1 C2 DOUBLE NONE 1
AXV C1 C6 SINGLE NONE 2
AXV C2 C3 SINGLE NONE 3
AXV C6 C5 DOUBLE NONE 4
AXV C3 C4 DOUBLE NONE 5
AXV C5 C4 SINGLE NONE 6
AXV C5 N1 SINGLE NONE 7
AXV C4 N2 SINGLE NONE 8
AXV N1 C7 SINGLE NONE 9
AXV N2 C7 DOUBLE NONE 10
AXV C7 N3 SINGLE NONE 11
AXV N3 C8 SINGLE NONE 12
AXV C8 N4 TRIPLE 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
AXV MurckoScaffold S1 scaffold 'c1ccc2[nH]cnc2c1' InChI=1S/C7H6N2/c1-2-4-7-6(3-1)8-5-9-7/h1-5H,(H,8,9) HYZJCKYKOHLVJF-UHFFFAOYSA-N
AXV benzimidazole F1 fragment 'c1ccc2[nH]cnc2c1' InChI=1S/C7H6N2/c1-2-4-7-6(3-1)8-5-9-7/h1-5H,(H,8,9) HYZJCKYKOHLVJF-UHFFFAOYSA-N
AXV imidazole F2 fragment 'c1c[nH]cn1' InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5) RAXXELZNTBOGNW-UHFFFAOYSA-N
AXV phenyl F3 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
AXV N1 S1 1
AXV C4 S1 1
AXV C5 S1 1
AXV C6 S1 1
AXV C7 S1 1
AXV C1 S1 1
AXV C2 S1 1
AXV C3 S1 1
AXV N2 S1 1
AXV C4 F1 1
AXV N2 F1 1
AXV C7 F1 1
AXV N1 F1 1
AXV C5 F1 1
AXV C6 F1 1
AXV C1 F1 1
AXV C2 F1 1
AXV C3 F1 1
AXV C4 F2 1
AXV C5 F2 1
AXV N1 F2 1
AXV C7 F2 1
AXV N2 F2 1
AXV C4 F3 1
AXV C3 F3 1
AXV C2 F3 1
AXV C1 F3 1
AXV C6 F3 1
AXV C5 F3 1
#
_pdbe_chem_comp_rdkit_properties.comp_id AXV
_pdbe_chem_comp_rdkit_properties.exactmw 158.059
_pdbe_chem_comp_rdkit_properties.amw 158.164
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 4
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 2
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 1
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 12
_pdbe_chem_comp_rdkit_properties.NumAtoms 18
_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 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 77.395
_pdbe_chem_comp_rdkit_properties.tpsa 64.500
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.647
_pdbe_chem_comp_rdkit_properties.CrippenMR 42.299
_pdbe_chem_comp_rdkit_properties.chi0v 5.789
_pdbe_chem_comp_rdkit_properties.chi1v 3.065
_pdbe_chem_comp_rdkit_properties.chi2v 1.222
_pdbe_chem_comp_rdkit_properties.chi3v 1.222
_pdbe_chem_comp_rdkit_properties.chi4v 0.781
_pdbe_chem_comp_rdkit_properties.chi0n 11.789
_pdbe_chem_comp_rdkit_properties.chi1n 5.960
_pdbe_chem_comp_rdkit_properties.chi2n 1.222
_pdbe_chem_comp_rdkit_properties.chi3n 1.222
_pdbe_chem_comp_rdkit_properties.chi4n 0.781
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.020
_pdbe_chem_comp_rdkit_properties.kappa1 2.791
_pdbe_chem_comp_rdkit_properties.kappa2 2.548
_pdbe_chem_comp_rdkit_properties.kappa3 0.974
_pdbe_chem_comp_rdkit_properties.Phi 0.593
#
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
AXV UniChem PDBe AXV
AXV UniChem ZINC ZINC000000394716
AXV UniChem eMolecules 1063713
AXV UniChem SureChEMBL SCHEMBL9247170
AXV UniChem ACTor 55864-37-4
AXV UniChem 'EPA CompTox Dashboard' DTXSID60204461
AXV UniChem PubChem 96685
AXV UniChem Mcule MCULE-6156135630
#
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
AXV N1 1.153 0.637 0.040 ETKDGv3 1
AXV N3 2.901 -1.160 -0.251 ETKDGv3 2
AXV C4 -0.626 -0.768 -0.310 ETKDGv3 3
AXV C5 -0.256 0.582 -0.026 ETKDGv3 4
AXV C6 -1.151 1.557 0.134 ETKDGv3 5
AXV C7 1.538 -0.728 -0.218 ETKDGv3 6
AXV C8 3.957 -0.266 -0.031 ETKDGv3 7
AXV C1 -2.588 1.185 0.004 ETKDGv3 8
AXV C2 -2.942 -0.094 -0.266 ETKDGv3 9
AXV C3 -1.899 -1.146 -0.436 ETKDGv3 10
AXV N2 0.550 -1.558 -0.423 ETKDGv3 11
AXV N4 4.830 0.473 0.150 ETKDGv3 12
AXV H1 1.759 1.465 0.229 ETKDGv3 13
AXV H2 3.122 -2.163 -0.443 ETKDGv3 14
AXV H3 -0.847 2.573 0.349 ETKDGv3 15
AXV H4 -3.351 1.943 0.126 ETKDGv3 16
AXV H5 -3.987 -0.358 -0.359 ETKDGv3 17
AXV H6 -2.163 -2.173 -0.651 ETKDGv3 18
#