data_WZ7
#
_chem_comp.id WZ7
_chem_comp.name 2-[(cyclopent-3-en-1-yl)amino]pyridine-4-carboxamide
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C11 H13 N3 O"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2020-11-18
_chem_comp.pdbx_modified_date 2021-06-25
_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 203.240
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code WZ7
_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 5S4W
_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
WZ7 C4 C1 C 0 1 Y N N N N N 16.396 66.356 36.939 -2.735 -1.154 0.151 C4 WZ7 1
WZ7 C5 C2 C 0 1 Y N N N N N 16.786 65.498 38.013 -2.071 0.067 -0.023 C5 WZ7 2
WZ7 C6 C3 C 0 1 N N N N N N 17.796 64.435 37.836 -2.827 1.339 -0.103 C6 WZ7 3
WZ7 C11 C4 C 0 1 N N N N N N 13.405 67.990 42.453 2.572 0.636 1.050 C11 WZ7 4
WZ7 C7 C5 C 0 1 N N N N N N 13.993 68.166 41.036 2.125 0.052 -0.310 C7 WZ7 5
WZ7 C8 C6 C 0 1 N N N N N N 15.057 69.272 41.200 3.488 -0.214 -0.991 C8 WZ7 6
WZ7 C9 C7 C 0 1 N N N N N N 14.410 70.099 42.268 4.445 0.746 -0.323 C9 WZ7 7
WZ7 C10 C8 C 0 1 N N N N N N 13.518 69.393 42.963 3.945 1.210 0.790 C10 WZ7 8
WZ7 N1 N1 N 0 1 Y N N N N N 14.861 67.509 38.380 -0.680 -2.292 0.129 N1 WZ7 9
WZ7 N2 N2 N 0 1 N N N N N N 18.380 64.237 36.596 -4.172 1.331 -0.009 N2 WZ7 10
WZ7 C3 C9 C 0 1 Y N N N N N 15.453 67.340 37.121 -1.996 -2.316 0.222 C3 WZ7 11
WZ7 N3 N3 N 0 1 N N N N N N 14.626 66.890 40.639 1.376 -1.193 -0.128 N3 WZ7 12
WZ7 C1 C10 C 0 1 Y N N N N N 16.196 65.675 39.249 -0.679 0.054 -0.117 C1 WZ7 13
WZ7 C2 C11 C 0 1 Y N N N N N 15.229 66.682 39.437 -0.011 -1.163 -0.036 C2 WZ7 14
WZ7 O1 O1 O 0 1 N N N N N N 18.147 63.688 38.768 -2.235 2.389 -0.254 O1 WZ7 15
WZ7 H3 H1 H 0 1 N N N N N N 16.850 66.229 35.967 -3.811 -1.184 0.233 H3 WZ7 16
WZ7 H12 H2 H 0 1 N N N N N N 12.359 67.651 42.421 1.887 1.421 1.370 H12 WZ7 17
WZ7 H13 H3 H 0 1 N N N N N N 13.999 67.288 43.056 2.625 -0.150 1.803 H13 WZ7 18
WZ7 H7 H4 H 0 1 N N N N N N 13.213 68.475 40.324 1.541 0.779 -0.875 H7 WZ7 19
WZ7 H9 H5 H 0 1 N N N N N N 16.023 68.863 41.530 3.803 -1.244 -0.821 H9 WZ7 20
WZ7 H8 H6 H 0 1 N N N N N N 15.198 69.843 40.271 3.426 -0.007 -2.059 H8 WZ7 21
WZ7 H10 H7 H 0 1 N N N N N N 14.638 71.138 42.452 5.415 1.013 -0.715 H10 WZ7 22
WZ7 H11 H8 H 0 1 N N N N N N 12.947 69.785 43.792 4.448 1.911 1.439 H11 WZ7 23
WZ7 H5 H9 H 0 1 N N N N N N 19.059 63.513 36.473 -4.644 0.492 0.111 H5 WZ7 24
WZ7 H4 H10 H 0 1 N N N N N N 18.123 64.818 35.824 -4.667 2.163 -0.062 H4 WZ7 25
WZ7 H2 H11 H 0 1 N N N N N N 15.170 67.979 36.298 -2.503 -3.261 0.356 H2 WZ7 26
WZ7 H6 H12 H 0 1 N N N N N N 13.907 66.198 40.705 1.848 -2.039 -0.072 H6 WZ7 27
WZ7 H1 H13 H 0 1 N N N N N N 16.477 65.039 40.075 -0.130 0.974 -0.252 H1 WZ7 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
WZ7 N2 C6 SING N N 1
WZ7 C4 C3 DOUB Y N 2
WZ7 C4 C5 SING Y N 3
WZ7 C3 N1 SING Y N 4
WZ7 C6 C5 SING N N 5
WZ7 C6 O1 DOUB N N 6
WZ7 C5 C1 DOUB Y N 7
WZ7 N1 C2 DOUB Y N 8
WZ7 C1 C2 SING Y N 9
WZ7 C2 N3 SING N N 10
WZ7 N3 C7 SING N N 11
WZ7 C7 C8 SING N N 12
WZ7 C7 C11 SING N N 13
WZ7 C8 C9 SING N N 14
WZ7 C9 C10 DOUB N N 15
WZ7 C11 C10 SING N N 16
WZ7 C4 H3 SING N N 17
WZ7 C11 H12 SING N N 18
WZ7 C11 H13 SING N N 19
WZ7 C7 H7 SING N N 20
WZ7 C8 H9 SING N N 21
WZ7 C8 H8 SING N N 22
WZ7 C9 H10 SING N N 23
WZ7 C10 H11 SING N N 24
WZ7 N2 H5 SING N N 25
WZ7 N2 H4 SING N N 26
WZ7 C3 H2 SING N N 27
WZ7 N3 H6 SING N N 28
WZ7 C1 H1 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
WZ7 SMILES ACDLabs 12.01 c2cnc(NC1CC=CC1)cc2C(=O)N
WZ7 InChI InChI 1.03 InChI=1S/C11H13N3O/c12-11(15)8-5-6-13-10(7-8)14-9-3-1-2-4-9/h1-2,5-7,9H,3-4H2,(H2,12,15)(H,13,14)
WZ7 InChIKey InChI 1.03 NDEZMUYBKJXUGJ-UHFFFAOYSA-N
WZ7 SMILES_CANONICAL CACTVS 3.385 NC(=O)c1ccnc(NC2CC=CC2)c1
WZ7 SMILES CACTVS 3.385 NC(=O)c1ccnc(NC2CC=CC2)c1
WZ7 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 c1cnc(cc1C(=O)N)NC2CC=CC2
WZ7 SMILES "OpenEye OEToolkits" 2.0.7 c1cnc(cc1C(=O)N)NC2CC=CC2
#
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
WZ7 "SYSTEMATIC NAME" ACDLabs 12.01 2-[(cyclopent-3-en-1-yl)amino]pyridine-4-carboxamide
WZ7 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 2-(cyclopent-3-en-1-ylamino)pyridine-4-carboxamide
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
WZ7 'Create component' 2020-11-18 RCSB
WZ7 'Initial release' 2021-06-30 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
WZ7 C4 C 6.897 2.544 1
WZ7 C5 C 5.598 1.794 2
WZ7 C6 C 4.299 2.544 3
WZ7 C11 C 9.566 -2.095 4
WZ7 C7 C 8.196 -2.706 5
WZ7 C8 C 8.353 -4.197 6
WZ7 C9 C 9.820 -4.509 7
WZ7 C10 C 10.570 -3.210 8
WZ7 N1 N 8.196 0.294 9
WZ7 N2 N 3.000 1.794 10
WZ7 C3 C 8.196 1.794 11
WZ7 N3 N 6.897 -1.956 12
WZ7 C1 C 5.598 0.294 13
WZ7 C2 C 6.897 -0.456 14
WZ7 O1 O 4.299 4.044 15
#
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
WZ7 N2 C6 SINGLE NONE 1
WZ7 C4 C3 DOUBLE NONE 2
WZ7 C4 C5 SINGLE NONE 3
WZ7 C3 N1 SINGLE NONE 4
WZ7 C6 C5 SINGLE NONE 5
WZ7 C6 O1 DOUBLE NONE 6
WZ7 C5 C1 DOUBLE NONE 7
WZ7 N1 C2 DOUBLE NONE 8
WZ7 C1 C2 SINGLE NONE 9
WZ7 C2 N3 SINGLE NONE 10
WZ7 N3 C7 SINGLE NONE 11
WZ7 C7 C8 SINGLE NONE 12
WZ7 C7 C11 SINGLE NONE 13
WZ7 C8 C9 SINGLE NONE 14
WZ7 C9 C10 DOUBLE NONE 15
WZ7 C11 C10 SINGLE NONE 16
#
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
WZ7 MurckoScaffold S1 scaffold C1=CCC(Nc2ccccn2)C1 InChI=1S/C10H12N2/c1-2-6-9(5-1)12-10-7-3-4-8-11-10/h1-4,7-9H,5-6H2,(H,11,12) HOLFVIVLBVFCPS-UHFFFAOYSA-N
WZ7 amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
WZ7 pyridine F2 fragment c1ccncc1 InChI=1S/C5H5N/c1-2-4-6-5-3-1/h1-5H JUJWROOIHBZHMG-UHFFFAOYSA-N
WZ7 Z1416571195 F3 fragment NC(=O)c1ccnc(NC2CC=CC2)c1 InChI=1S/C11H13N3O/c12-11(15)8-5-6-13-10(7-8)14-9-3-1-2-4-9/h1-2,5-7,9H,3-4H2,(H2,12,15)(H,13,14) NDEZMUYBKJXUGJ-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
WZ7 C4 S1 1
WZ7 C5 S1 1
WZ7 C11 S1 1
WZ7 C7 S1 1
WZ7 C8 S1 1
WZ7 C9 S1 1
WZ7 C10 S1 1
WZ7 N1 S1 1
WZ7 C3 S1 1
WZ7 N3 S1 1
WZ7 C1 S1 1
WZ7 C2 S1 1
WZ7 N2 F1 1
WZ7 C6 F1 1
WZ7 O1 F1 1
WZ7 C5 F1 1
WZ7 C3 F2 1
WZ7 C4 F2 1
WZ7 C5 F2 1
WZ7 C1 F2 1
WZ7 C2 F2 1
WZ7 N1 F2 1
WZ7 N2 F3 1
WZ7 C6 F3 1
WZ7 O1 F3 1
WZ7 C5 F3 1
WZ7 C4 F3 1
WZ7 C3 F3 1
WZ7 N1 F3 1
WZ7 C2 F3 1
WZ7 N3 F3 1
WZ7 C7 F3 1
WZ7 C8 F3 1
WZ7 C9 F3 1
WZ7 C10 F3 1
WZ7 C11 F3 1
WZ7 C1 F3 1
#
_pdbe_chem_comp_rdkit_properties.comp_id WZ7
_pdbe_chem_comp_rdkit_properties.exactmw 203.106
_pdbe_chem_comp_rdkit_properties.amw 203.245
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 4
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 3
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 15
_pdbe_chem_comp_rdkit_properties.NumAtoms 28
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 4
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 1
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.273
_pdbe_chem_comp_rdkit_properties.NumRings 2
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 1
_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 106.635
_pdbe_chem_comp_rdkit_properties.tpsa 68.010
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.876
_pdbe_chem_comp_rdkit_properties.CrippenMR 57.450
_pdbe_chem_comp_rdkit_properties.chi0v 7.250
_pdbe_chem_comp_rdkit_properties.chi1v 3.822
_pdbe_chem_comp_rdkit_properties.chi2v 1.435
_pdbe_chem_comp_rdkit_properties.chi3v 1.435
_pdbe_chem_comp_rdkit_properties.chi4v 0.842
_pdbe_chem_comp_rdkit_properties.chi0n 20.250
_pdbe_chem_comp_rdkit_properties.chi1n 10.164
_pdbe_chem_comp_rdkit_properties.chi2n 1.435
_pdbe_chem_comp_rdkit_properties.chi3n 1.435
_pdbe_chem_comp_rdkit_properties.chi4n 0.842
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.840
_pdbe_chem_comp_rdkit_properties.kappa1 2.638
_pdbe_chem_comp_rdkit_properties.kappa2 4.125
_pdbe_chem_comp_rdkit_properties.kappa3 2.340
_pdbe_chem_comp_rdkit_properties.Phi 0.726
#
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
WZ7 UniChem PDBe WZ7
WZ7 UniChem ZINC ZINC000095413916
WZ7 UniChem PubChem 75380155
WZ7 UniChem Mcule MCULE-8686332069
#
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
WZ7 C4 2.784 1.346 0.058 ETKDGv3 1
WZ7 C5 2.789 -0.136 -0.052 ETKDGv3 2
WZ7 C6 4.048 -0.877 -0.310 ETKDGv3 3
WZ7 C11 -3.289 -1.033 1.036 ETKDGv3 4
WZ7 C7 -2.139 -0.056 0.727 ETKDGv3 5
WZ7 C8 -2.597 0.742 -0.504 ETKDGv3 6
WZ7 C9 -4.041 0.417 -0.631 ETKDGv3 7
WZ7 C10 -4.415 -0.539 0.202 ETKDGv3 8
WZ7 N1 0.410 1.254 0.433 ETKDGv3 9
WZ7 N2 5.324 -0.303 -0.013 ETKDGv3 10
WZ7 C3 1.636 1.990 0.292 ETKDGv3 11
WZ7 N3 -0.870 -0.750 0.474 ETKDGv3 12
WZ7 C1 1.622 -0.795 0.070 ETKDGv3 13
WZ7 C2 0.372 -0.045 0.331 ETKDGv3 14
WZ7 O1 4.003 -2.041 -0.792 ETKDGv3 15
WZ7 H3 3.690 1.920 -0.075 ETKDGv3 16
WZ7 H12 -3.564 -0.999 2.112 ETKDGv3 17
WZ7 H13 -3.058 -2.078 0.741 ETKDGv3 18
WZ7 H7 -2.018 0.634 1.593 ETKDGv3 19
WZ7 H9 -2.458 1.833 -0.349 ETKDGv3 20
WZ7 H8 -2.068 0.418 -1.427 ETKDGv3 21
WZ7 H10 -4.709 0.877 -1.352 ETKDGv3 22
WZ7 H11 -5.421 -0.944 0.234 ETKDGv3 23
WZ7 H5 6.197 -0.821 -0.258 ETKDGv3 24
WZ7 H4 5.415 0.587 0.522 ETKDGv3 25
WZ7 H2 1.623 3.069 0.366 ETKDGv3 26
WZ7 H6 -0.847 -1.794 0.429 ETKDGv3 27
WZ7 H1 1.581 -1.875 -0.007 ETKDGv3 28
#