data_W8C
#
_chem_comp.id W8C
_chem_comp.name 5-(benzyloxy)-4-(prop-2-en-1-yl)-4H-1,2,4-triazole-3-thiol
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C12 H13 N3 O S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2023-05-09
_chem_comp.pdbx_modified_date 2023-06-09
_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 247.316
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code W8C
_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 7FYK
_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
W8C C02 C1 C 0 1 Y N N N N N 4.899 6.945 18.104 -0.671 -0.712 -0.063 C02 W8C 1
W8C C10 C2 C 0 1 N N N N N N 8.826 7.789 19.065 -2.887 3.220 -0.279 C10 W8C 2
W8C C11 C3 C 0 1 N N N N N N 5.511 8.300 20.033 1.644 -1.148 -0.365 C11 W8C 3
W8C C13 C4 C 0 1 Y N N N N N 6.254 7.925 22.288 3.651 -0.650 1.045 C13 W8C 4
W8C C15 C5 C 0 1 Y N N N N N 4.201 6.106 22.700 4.761 0.897 -0.959 C15 W8C 5
W8C C16 C6 C 0 1 Y N N N N N 6.119 7.349 23.526 4.878 -0.043 1.240 C16 W8C 6
W8C C17 C7 C 0 1 Y N N N N N 5.110 6.414 23.737 5.433 0.730 0.237 C17 W8C 7
W8C N01 N1 N 0 1 Y N N N N N 5.957 6.905 17.240 -1.798 -0.023 0.280 N01 W8C 8
W8C C03 C8 C 0 1 Y N N N N N 5.896 5.768 16.490 -2.878 -0.810 -0.002 C03 W8C 9
W8C N04 N2 N 0 1 Y N N N N N 4.188 5.855 17.899 -1.036 -1.876 -0.537 N04 W8C 10
W8C N05 N3 N 0 1 Y N N N N N 4.789 5.147 16.864 -2.435 -1.940 -0.499 N05 W8C 11
W8C O06 O1 O 0 1 N N N N N N 4.572 7.989 19.001 0.604 -0.266 0.061 O06 W8C 12
W8C S07 S1 S 0 1 N N N N N N 6.961 5.317 15.256 -4.568 -0.384 0.256 S07 W8C 13
W8C C08 C9 C 0 1 N N N N N N 7.105 7.864 17.213 -1.842 1.326 0.852 C08 W8C 14
W8C C09 C10 C 0 1 N N N N N N 8.264 7.247 17.966 -1.917 2.340 -0.260 C09 W8C 15
W8C C12 C11 C 0 1 Y N N N N N 5.326 7.626 21.302 2.982 -0.487 -0.153 C12 W8C 16
W8C C14 C12 C 0 1 Y N N N N N 4.337 6.667 21.459 3.540 0.281 -1.158 C14 W8C 17
W8C H23 H1 H 0 1 N N N N N N 8.450 8.721 19.460 -3.633 3.219 0.502 H23 W8C 18
W8C H22 H2 H 0 1 N N N N N N 9.652 7.291 19.551 -2.941 3.948 -1.075 H22 W8C 19
W8C H25 H3 H 0 1 N N N N N N 6.514 8.042 19.661 1.599 -2.070 0.215 H25 W8C 20
W8C H24 H4 H 0 1 N N N N N N 5.456 9.383 20.219 1.516 -1.378 -1.423 H24 W8C 21
W8C H26 H5 H 0 1 N N N N N N 7.071 8.601 22.084 3.218 -1.254 1.828 H26 W8C 22
W8C H28 H6 H 0 1 N N N N N N 3.389 5.420 22.889 5.195 1.501 -1.742 H28 W8C 23
W8C H29 H7 H 0 1 N N N N N N 6.789 7.619 24.329 5.403 -0.174 2.174 H29 W8C 24
W8C H30 H8 H 0 1 N N N N N N 5.022 5.923 24.695 6.392 1.204 0.389 H30 W8C 25
W8C H18 H9 H 0 1 N N N N N N 6.404 4.234 14.801 -4.914 0.199 -0.906 H18 W8C 26
W8C H19 H10 H 0 1 N N N N N N 7.401 8.059 16.172 -2.720 1.421 1.491 H19 W8C 27
W8C H20 H11 H 0 1 N N N N N N 6.811 8.809 17.694 -0.943 1.499 1.442 H20 W8C 28
W8C H21 H12 H 0 1 N N N N N N 8.666 6.314 17.600 -1.171 2.342 -1.041 H21 W8C 29
W8C H27 H13 H 0 1 N N N N N N 3.701 6.375 20.637 3.017 0.408 -2.094 H27 W8C 30
#
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
W8C N01 C02 SING Y N 1
W8C N01 C03 SING Y N 2
W8C C02 N04 DOUB Y N 3
W8C C03 N05 DOUB Y N 4
W8C N04 N05 SING Y N 5
W8C C02 O06 SING N N 6
W8C C03 S07 SING N N 7
W8C N01 C08 SING N N 8
W8C C08 C09 SING N N 9
W8C C09 C10 DOUB N N 10
W8C O06 C11 SING N N 11
W8C C11 C12 SING N N 12
W8C C12 C13 DOUB Y N 13
W8C C12 C14 SING Y N 14
W8C C14 C15 DOUB Y N 15
W8C C13 C16 SING Y N 16
W8C C15 C17 SING Y N 17
W8C C16 C17 DOUB Y N 18
W8C C10 H23 SING N N 19
W8C C10 H22 SING N N 20
W8C C11 H25 SING N N 21
W8C C11 H24 SING N N 22
W8C C13 H26 SING N N 23
W8C C15 H28 SING N N 24
W8C C16 H29 SING N N 25
W8C C17 H30 SING N N 26
W8C S07 H18 SING N N 27
W8C C08 H19 SING N N 28
W8C C08 H20 SING N N 29
W8C C09 H21 SING N N 30
W8C C14 H27 SING N N 31
#
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
W8C SMILES ACDLabs 12.01 C=CCn1c(S)nnc1OCc1ccccc1
W8C InChI InChI 1.06 InChI=1S/C12H13N3OS/c1-2-8-15-11(13-14-12(15)17)16-9-10-6-4-3-5-7-10/h2-7H,1,8-9H2,(H,14,17)
W8C InChIKey InChI 1.06 HQHVIDWGWBKEJO-UHFFFAOYSA-N
W8C SMILES_CANONICAL CACTVS 3.385 Sc1nnc(OCc2ccccc2)n1CC=C
W8C SMILES CACTVS 3.385 Sc1nnc(OCc2ccccc2)n1CC=C
W8C SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 C=CCn1c(nnc1S)OCc2ccccc2
W8C SMILES "OpenEye OEToolkits" 2.0.7 C=CCn1c(nnc1S)OCc2ccccc2
#
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
W8C "SYSTEMATIC NAME" ACDLabs 12.01 5-(benzyloxy)-4-(prop-2-en-1-yl)-4H-1,2,4-triazole-3-thiol
W8C "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 5-phenylmethoxy-4-prop-2-enyl-1,2,4-triazole-3-thiol
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
W8C 'Create component' 2023-05-09 RCSB
W8C 'Initial release' 2023-06-14 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
W8C C02 C 5.598 1.614 1
W8C C10 C 10.780 2.572 2
W8C C11 C 4.299 -0.636 3
W8C C13 C 3.000 -2.886 4
W8C C15 C 5.598 -4.386 5
W8C C16 C 3.000 -4.386 6
W8C C17 C 4.299 -5.136 7
W8C N01 N 6.812 2.496 8
W8C C03 C 6.348 3.922 9
W8C N04 N 4.385 2.496 10
W8C N05 N 4.848 3.922 11
W8C O06 O 5.598 0.114 12
W8C S07 S 7.230 5.136 13
W8C C08 C 8.238 2.032 14
W8C C09 C 9.353 3.036 15
W8C C12 C 4.299 -2.136 16
W8C C14 C 5.598 -2.886 17
#
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
W8C N01 C02 SINGLE NONE 1
W8C N01 C03 SINGLE NONE 2
W8C C02 N04 DOUBLE NONE 3
W8C C03 N05 DOUBLE NONE 4
W8C N04 N05 SINGLE NONE 5
W8C C02 O06 SINGLE NONE 6
W8C C03 S07 SINGLE NONE 7
W8C N01 C08 SINGLE NONE 8
W8C C08 C09 SINGLE NONE 9
W8C C09 C10 DOUBLE NONE 10
W8C O06 C11 SINGLE NONE 11
W8C C11 C12 SINGLE NONE 12
W8C C12 C13 DOUBLE NONE 13
W8C C12 C14 SINGLE NONE 14
W8C C14 C15 DOUBLE NONE 15
W8C C13 C16 SINGLE NONE 16
W8C C15 C17 SINGLE NONE 17
W8C C16 C17 DOUBLE NONE 18
#
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
W8C MurckoScaffold S1 scaffold 'c1ccc(COc2nnc[nH]2)cc1' InChI=1S/C9H9N3O/c1-2-4-8(5-3-1)6-13-9-10-7-11-12-9/h1-5,7H,6H2,(H,10,11,12) IKVYKDIUYLIYNV-UHFFFAOYSA-N
W8C phenyl F1 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
W8C C02 S1 1
W8C C11 S1 1
W8C C13 S1 1
W8C C15 S1 1
W8C C16 S1 1
W8C C17 S1 1
W8C N01 S1 1
W8C C03 S1 1
W8C N04 S1 1
W8C N05 S1 1
W8C O06 S1 1
W8C C12 S1 1
W8C C14 S1 1
W8C C13 F1 1
W8C C12 F1 1
W8C C14 F1 1
W8C C15 F1 1
W8C C17 F1 1
W8C C16 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id W8C
_pdbe_chem_comp_rdkit_properties.exactmw 247.078
_pdbe_chem_comp_rdkit_properties.amw 247.323
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 4
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 0
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 6
_pdbe_chem_comp_rdkit_properties.NumHBD 1
_pdbe_chem_comp_rdkit_properties.NumHBA 5
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 17
_pdbe_chem_comp_rdkit_properties.NumAtoms 30
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 5
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.167
_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 123.300
_pdbe_chem_comp_rdkit_properties.tpsa 39.940
_pdbe_chem_comp_rdkit_properties.CrippenClogP 1.707
_pdbe_chem_comp_rdkit_properties.CrippenMR 67.939
_pdbe_chem_comp_rdkit_properties.chi0v 8.975
_pdbe_chem_comp_rdkit_properties.chi1v 4.589
_pdbe_chem_comp_rdkit_properties.chi2v 1.780
_pdbe_chem_comp_rdkit_properties.chi3v 1.780
_pdbe_chem_comp_rdkit_properties.chi4v 1.037
_pdbe_chem_comp_rdkit_properties.chi0n 21.158
_pdbe_chem_comp_rdkit_properties.chi1n 10.589
_pdbe_chem_comp_rdkit_properties.chi2n 1.516
_pdbe_chem_comp_rdkit_properties.chi3n 1.516
_pdbe_chem_comp_rdkit_properties.chi4n 0.872
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.750
_pdbe_chem_comp_rdkit_properties.kappa1 3.619
_pdbe_chem_comp_rdkit_properties.kappa2 5.540
_pdbe_chem_comp_rdkit_properties.kappa3 2.880
_pdbe_chem_comp_rdkit_properties.Phi 1.180
#
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
W8C UniChem ZINC ZINC000006492917
W8C UniChem BindingDb 80314
W8C UniChem eMolecules 2183572
W8C UniChem PubChem 802794
W8C UniChem Mcule MCULE-9192087393
#
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
W8C C02 -1.341 -1.137 -0.608 ETKDGv3 1
W8C C10 -2.076 1.491 1.463 ETKDGv3 2
W8C C11 1.009 -1.505 0.067 ETKDGv3 3
W8C C13 3.154 -0.636 -0.812 ETKDGv3 4
W8C C15 3.577 0.897 1.515 ETKDGv3 5
W8C C16 4.362 0.207 -0.689 ETKDGv3 6
W8C C17 4.564 0.934 0.416 ETKDGv3 7
W8C N01 -2.408 -0.311 -1.056 ETKDGv3 8
W8C C03 -3.485 -1.240 -0.992 ETKDGv3 9
W8C N04 -1.721 -2.349 -0.367 ETKDGv3 10
W8C N05 -3.099 -2.414 -0.614 ETKDGv3 11
W8C O06 -0.033 -0.679 -0.436 ETKDGv3 12
W8C S07 -5.188 -0.843 -1.368 ETKDGv3 13
W8C C08 -2.489 1.144 -0.959 ETKDGv3 14
W8C C09 -2.910 1.562 0.422 ETKDGv3 15
W8C C12 2.263 -0.691 0.194 ETKDGv3 16
W8C C14 2.485 0.130 1.410 ETKDGv3 17
W8C H23 -1.059 1.132 1.344 ETKDGv3 18
W8C H22 -2.411 1.802 2.448 ETKDGv3 19
W8C H25 1.168 -2.369 -0.617 ETKDGv3 20
W8C H24 0.722 -1.904 1.064 ETKDGv3 21
W8C H26 2.998 -1.203 -1.722 ETKDGv3 22
W8C H28 3.738 1.494 2.404 ETKDGv3 23
W8C H29 5.081 0.237 -1.498 ETKDGv3 24
W8C H30 5.447 1.553 0.506 ETKDGv3 25
W8C H18 -5.447 -0.466 -0.037 ETKDGv3 26
W8C H19 -1.508 1.598 -1.217 ETKDGv3 27
W8C H20 -3.236 1.514 -1.693 ETKDGv3 28
W8C H21 -3.918 1.938 0.575 ETKDGv3 29
W8C H27 1.762 0.113 2.217 ETKDGv3 30
#