data_W0V
#
_chem_comp.id W0V
_chem_comp.name N-[(1H-benzimidazol-2-yl)methyl]-2-methylpropanamide
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C12 H15 N3 O"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2020-09-24
_chem_comp.pdbx_modified_date 2021-01-08
_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 217.267
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code W0V
_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 5RQP
_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
W0V N1 N1 N 0 1 Y N N N N N -7.086 14.878 -0.178 -1.358 1.236 0.437 N1 W0V 1
W0V C4 C1 C 0 1 N N N N N N -8.712 14.403 1.669 0.874 0.987 -0.758 C4 W0V 2
W0V C5 C2 C 0 1 Y N N N N N -7.336 14.669 1.102 -0.556 0.610 -0.466 C5 W0V 3
W0V C6 C3 C 0 1 Y N N N N N -5.706 15.070 -0.246 -2.581 0.595 0.413 C6 W0V 4
W0V C7 C4 C 0 1 Y N N N N N -4.877 15.318 -1.335 -3.777 0.771 1.094 C7 W0V 5
W0V C8 C5 C 0 1 Y N N N N N -3.520 15.492 -1.107 -4.842 -0.064 0.831 C8 W0V 6
W0V C10 C6 C 0 1 Y N N N N N -3.806 15.156 1.270 -3.555 -1.266 -0.790 C10 W0V 7
W0V O O1 O 0 1 N N N N N N -9.053 16.166 3.770 3.564 1.150 -0.802 O W0V 8
W0V C3 C7 C 0 1 N N N N N N -8.805 14.988 4.030 3.107 0.316 -0.049 C3 W0V 9
W0V C1 C8 C 0 1 N N N N N N -8.701 14.481 5.489 4.030 -0.540 0.778 C1 W0V 10
W0V C2 C9 C 0 1 N N N N N N -8.406 15.643 6.405 3.810 -2.013 0.430 C2 W0V 11
W0V C C10 C 0 1 N N N N N N -9.976 13.741 5.912 5.482 -0.157 0.482 C W0V 12
W0V N N2 N 0 1 N N N N N N -8.622 14.071 3.077 1.772 0.155 0.047 N W0V 13
W0V N2 N3 N 0 1 Y N N N N N -6.223 14.717 1.872 -1.203 -0.362 -1.041 N2 W0V 14
W0V C11 C11 C 0 1 Y N N N N N -5.161 14.981 1.034 -2.463 -0.431 -0.539 C11 W0V 15
W0V C9 C12 C 0 1 Y N N N N N -2.991 15.415 0.180 -4.725 -1.078 -0.110 C9 W0V 16
W0V H1 H1 H 0 1 N N N N N N -7.742 14.895 -0.933 -1.115 1.990 0.996 H1 W0V 17
W0V H2 H2 H 0 1 N N N N N N -9.334 15.302 1.547 1.083 0.828 -1.816 H2 W0V 18
W0V H3 H3 H 0 1 N N N N N N -9.171 13.563 1.127 1.031 2.036 -0.510 H3 W0V 19
W0V H4 H4 H 0 1 N N N N N N -5.281 15.374 -2.335 -3.874 1.558 1.828 H4 W0V 20
W0V H5 H5 H 0 1 N N N N N N -2.863 15.690 -1.941 -5.774 0.071 1.360 H5 W0V 21
W0V H6 H6 H 0 1 N N N N N N -3.400 15.093 2.269 -3.475 -2.058 -1.520 H6 W0V 22
W0V H7 H7 H 0 1 N N N N N N -7.861 13.773 5.543 3.822 -0.382 1.837 H7 W0V 23
W0V H8 H8 H 0 1 N N N N N N -8.332 15.284 7.442 4.019 -2.171 -0.628 H8 W0V 24
W0V H9 H9 H 0 1 N N N N N N -7.455 16.110 6.110 4.478 -2.632 1.029 H9 W0V 25
W0V H10 H10 H 0 1 N N N N N N -9.216 16.383 6.331 2.776 -2.286 0.641 H10 W0V 26
W0V H11 H11 H 0 1 N N N N N N -9.872 13.394 6.951 5.639 0.892 0.731 H11 W0V 27
W0V H12 H12 H 0 1 N N N N N N -10.837 14.422 5.838 6.150 -0.776 1.081 H12 W0V 28
W0V H13 H13 H 0 1 N N N N N N -10.134 12.876 5.251 5.691 -0.316 -0.576 H13 W0V 29
W0V H14 H14 H 0 1 N N N N N N -8.417 13.129 3.342 1.406 -0.512 0.649 H14 W0V 30
W0V H16 H16 H 0 1 N N N N N N -1.931 15.559 0.330 -5.567 -1.725 -0.306 H16 W0V 31
#
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
W0V C7 C8 DOUB Y N 1
W0V C7 C6 SING Y N 2
W0V C8 C9 SING Y N 3
W0V C6 N1 SING Y N 4
W0V C6 C11 DOUB Y N 5
W0V N1 C5 SING Y N 6
W0V C9 C10 DOUB Y N 7
W0V C11 C10 SING Y N 8
W0V C11 N2 SING Y N 9
W0V C5 C4 SING N N 10
W0V C5 N2 DOUB Y N 11
W0V C4 N SING N N 12
W0V N C3 SING N N 13
W0V O C3 DOUB N N 14
W0V C3 C1 SING N N 15
W0V C1 C SING N N 16
W0V C1 C2 SING N N 17
W0V N1 H1 SING N N 18
W0V C4 H2 SING N N 19
W0V C4 H3 SING N N 20
W0V C7 H4 SING N N 21
W0V C8 H5 SING N N 22
W0V C10 H6 SING N N 23
W0V C1 H7 SING N N 24
W0V C2 H8 SING N N 25
W0V C2 H9 SING N N 26
W0V C2 H10 SING N N 27
W0V C H11 SING N N 28
W0V C H12 SING N N 29
W0V C H13 SING N N 30
W0V N H14 SING N N 31
W0V C9 H16 SING N N 32
#
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
W0V SMILES ACDLabs 12.01 n1c(CNC(=O)C(C)C)nc2c1cccc2
W0V InChI InChI 1.03 InChI=1S/C12H15N3O/c1-8(2)12(16)13-7-11-14-9-5-3-4-6-10(9)15-11/h3-6,8H,7H2,1-2H3,(H,13,16)(H,14,15)
W0V InChIKey InChI 1.03 KBFKODIOYYFXAF-UHFFFAOYSA-N
W0V SMILES_CANONICAL CACTVS 3.385 CC(C)C(=O)NCc1[nH]c2ccccc2n1
W0V SMILES CACTVS 3.385 CC(C)C(=O)NCc1[nH]c2ccccc2n1
W0V SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 CC(C)C(=O)NCc1[nH]c2ccccc2n1
W0V SMILES "OpenEye OEToolkits" 2.0.7 CC(C)C(=O)NCc1[nH]c2ccccc2n1
#
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
W0V "SYSTEMATIC NAME" ACDLabs 12.01 N-[(1H-benzimidazol-2-yl)methyl]-2-methylpropanamide
W0V "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 ~{N}-(1~{H}-benzimidazol-2-ylmethyl)-2-methyl-propanamide
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
W0V 'Create component' 2020-09-24 RCSB
W0V 'Initial release' 2021-01-13 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
W0V N1 N 7.018 2.110 1
W0V C4 C 9.393 0.903 2
W0V C5 C 7.893 0.903 3
W0V C6 C 5.598 1.653 4
W0V C7 C 4.299 2.403 5
W0V C8 C 3.000 1.653 6
W0V C10 C 4.299 -0.597 7
W0V O O 12.393 0.903 8
W0V C3 C 11.643 -0.396 9
W0V C1 C 12.393 -1.695 10
W0V C2 C 11.643 -2.994 11
W0V C C 13.893 -1.695 12
W0V N N 10.143 -0.396 13
W0V N2 N 7.018 -0.304 14
W0V C11 C 5.598 0.153 15
W0V C9 C 3.000 0.153 16
#
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
W0V C7 C8 SINGLE NONE 1
W0V C7 C6 DOUBLE NONE 2
W0V C8 C9 DOUBLE NONE 3
W0V C6 N1 SINGLE NONE 4
W0V C6 C11 SINGLE NONE 5
W0V N1 C5 SINGLE NONE 6
W0V C9 C10 SINGLE NONE 7
W0V C11 C10 DOUBLE NONE 8
W0V C11 N2 SINGLE NONE 9
W0V C5 C4 SINGLE NONE 10
W0V C5 N2 DOUBLE NONE 11
W0V C4 N SINGLE NONE 12
W0V N C3 SINGLE NONE 13
W0V O C3 DOUBLE NONE 14
W0V C3 C1 SINGLE NONE 15
W0V C1 C SINGLE NONE 16
W0V C1 C2 SINGLE NONE 17
#
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
W0V 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
W0V amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
W0V benzimidazole F2 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
W0V imidazole F3 fragment 'c1c[nH]cn1' InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5) RAXXELZNTBOGNW-UHFFFAOYSA-N
W0V phenyl F4 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
W0V Z1203191681 F5 fragment 'CC(=O)NCc1ncc[nH]1' InChI=1S/C6H9N3O/c1-5(10)9-4-6-7-2-3-8-6/h2-3H,4H2,1H3,(H,7,8)(H,9,10) SXKAQLCLHGQXHB-UHFFFAOYSA-N
W0V Z26781943 F6 fragment 'CC(C)C(=O)NCc1nc2ccccc2[nH]1' InChI=1S/C12H15N3O/c1-8(2)12(16)13-7-11-14-9-5-3-4-6-10(9)15-11/h3-6,8H,7H2,1-2H3,(H,13,16)(H,14,15) KBFKODIOYYFXAF-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
W0V N1 S1 1
W0V C5 S1 1
W0V C6 S1 1
W0V C7 S1 1
W0V C8 S1 1
W0V C10 S1 1
W0V N2 S1 1
W0V C11 S1 1
W0V C9 S1 1
W0V N F1 1
W0V C3 F1 1
W0V O F1 1
W0V C1 F1 1
W0V C6 F2 1
W0V N1 F2 1
W0V C5 F2 1
W0V N2 F2 1
W0V C11 F2 1
W0V C10 F2 1
W0V C9 F2 1
W0V C8 F2 1
W0V C7 F2 1
W0V C6 F3 1
W0V C11 F3 1
W0V N2 F3 1
W0V C5 F3 1
W0V N1 F3 1
W0V C6 F4 1
W0V C7 F4 1
W0V C8 F4 1
W0V C9 F4 1
W0V C10 F4 1
W0V C11 F4 1
W0V C1 F5 1
W0V C3 F5 1
W0V O F5 1
W0V N F5 1
W0V C4 F5 1
W0V C5 F5 1
W0V N1 F5 1
W0V C6 F5 1
W0V C11 F5 1
W0V N2 F5 1
W0V C2 F6 1
W0V C1 F6 1
W0V C F6 1
W0V C3 F6 1
W0V O F6 1
W0V N F6 1
W0V C4 F6 1
W0V C5 F6 1
W0V N1 F6 1
W0V C6 F6 1
W0V C7 F6 1
W0V C8 F6 1
W0V C9 F6 1
W0V C10 F6 1
W0V C11 F6 1
W0V N2 F6 1
#
_pdbe_chem_comp_rdkit_properties.comp_id W0V
_pdbe_chem_comp_rdkit_properties.exactmw 217.122
_pdbe_chem_comp_rdkit_properties.amw 217.272
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 4
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 2
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 5
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 2
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 16
_pdbe_chem_comp_rdkit_properties.NumAtoms 31
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 4
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 1
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.333
_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 115.269
_pdbe_chem_comp_rdkit_properties.tpsa 57.780
_pdbe_chem_comp_rdkit_properties.CrippenClogP 1.352
_pdbe_chem_comp_rdkit_properties.CrippenMR 60.306
_pdbe_chem_comp_rdkit_properties.chi0v 7.750
_pdbe_chem_comp_rdkit_properties.chi1v 4.046
_pdbe_chem_comp_rdkit_properties.chi2v 1.555
_pdbe_chem_comp_rdkit_properties.chi3v 1.555
_pdbe_chem_comp_rdkit_properties.chi4v 0.905
_pdbe_chem_comp_rdkit_properties.chi0n 22.750
_pdbe_chem_comp_rdkit_properties.chi1n 11.440
_pdbe_chem_comp_rdkit_properties.chi2n 1.555
_pdbe_chem_comp_rdkit_properties.chi3n 1.555
_pdbe_chem_comp_rdkit_properties.chi4n 0.905
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.840
_pdbe_chem_comp_rdkit_properties.kappa1 2.696
_pdbe_chem_comp_rdkit_properties.kappa2 4.346
_pdbe_chem_comp_rdkit_properties.kappa3 2.213
_pdbe_chem_comp_rdkit_properties.Phi 0.732
#
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
W0V UniChem PDBe W0V
W0V UniChem ZINC ZINC000000549915
W0V UniChem eMolecules 4484887
W0V UniChem SureChEMBL SCHEMBL13396939
W0V UniChem PubChem 949147
W0V UniChem Mcule MCULE-2821300626
#
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
W0V N1 1.802 -1.301 0.225 ETKDGv3 1
W0V C4 -0.169 -0.901 -1.382 ETKDGv3 2
W0V C5 1.212 -0.604 -0.888 ETKDGv3 3
W0V C6 3.050 -0.658 0.375 ETKDGv3 4
W0V C7 4.020 -0.885 1.261 ETKDGv3 5
W0V C8 5.231 -0.021 1.174 ETKDGv3 6
W0V C10 4.196 1.162 -0.730 ETKDGv3 7
W0V O -2.963 -1.041 -1.808 ETKDGv3 8
W0V C3 -2.565 -0.281 -0.883 ETKDGv3 9
W0V C1 -3.570 0.494 -0.068 ETKDGv3 10
W0V C2 -4.369 1.444 -0.966 ETKDGv3 11
W0V C -4.501 -0.462 0.683 ETKDGv3 12
W0V N -1.163 -0.158 -0.608 ETKDGv3 13
W0V N2 1.939 0.361 -1.388 ETKDGv3 14
W0V C11 3.134 0.363 -0.620 ETKDGv3 15
W0V C9 5.314 0.947 0.232 ETKDGv3 16
W0V H1 1.396 -2.074 0.797 ETKDGv3 17
W0V H2 -0.362 -1.990 -1.286 ETKDGv3 18
W0V H3 -0.249 -0.621 -2.455 ETKDGv3 19
W0V H4 3.931 -1.662 2.010 ETKDGv3 20
W0V H5 6.046 -0.171 1.870 ETKDGv3 21
W0V H6 4.242 1.936 -1.486 ETKDGv3 22
W0V H7 -3.035 1.111 0.687 ETKDGv3 23
W0V H8 -4.954 0.876 -1.721 ETKDGv3 24
W0V H9 -3.681 2.139 -1.493 ETKDGv3 25
W0V H10 -5.070 2.049 -0.353 ETKDGv3 26
W0V H11 -3.908 -1.133 1.341 ETKDGv3 27
W0V H12 -5.205 0.114 1.321 ETKDGv3 28
W0V H13 -5.089 -1.082 -0.027 ETKDGv3 29
W0V H14 -0.852 0.476 0.163 ETKDGv3 30
W0V H16 6.196 1.572 0.175 ETKDGv3 31
#