data_W6M
#
_chem_comp.id W6M
_chem_comp.name "3-{[(3-methyl-1,2,4-oxadiazol-5-yl)methyl]carbamoyl}benzoic acid"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C12 H11 N3 O4"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2020-09-29
_chem_comp.pdbx_modified_date 2020-12-11
_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 261.233
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code W6M
_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 5RUW
_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
W6M C10 C1 C 0 1 Y N N N N N -49.524 -29.371 5.741 1.346 -0.028 0.016 C10 W6M 1
W6M C13 C2 C 0 1 Y N N N N N -46.788 -29.050 5.492 3.504 1.719 0.118 C13 W6M 2
W6M C15 C3 C 0 1 N N N N N N -46.996 -29.100 2.960 5.105 -0.178 -0.095 C15 W6M 3
W6M C01 C4 C 0 1 N N N N N N -54.000 -26.138 10.027 -6.330 1.275 -1.034 C01 W6M 4
W6M C02 C5 C 0 1 Y N N N N N -54.146 -27.186 8.922 -5.232 0.535 -0.316 C02 W6M 5
W6M C05 C6 C 0 1 Y N N N N N -53.719 -28.927 7.745 -3.487 -0.586 0.104 C05 W6M 6
W6M C06 C7 C 0 1 N N N N N N -53.036 -30.188 7.263 -2.208 -1.377 -0.008 C06 W6M 7
W6M C08 C8 C 0 1 N N N N N N -51.038 -29.562 5.874 0.191 -0.950 -0.037 C08 W6M 8
W6M C11 C9 C 0 1 Y N N N N N -48.741 -29.272 6.878 1.139 1.346 0.152 C11 W6M 9
W6M C12 C10 C 0 1 Y N N N N N -47.367 -29.109 6.749 2.216 2.208 0.201 C12 W6M 10
W6M C14 C11 C 0 1 Y N N N N N -47.588 -29.143 4.369 3.726 0.345 -0.012 C14 W6M 11
W6M C18 C12 C 0 1 Y N N N N N -48.943 -29.317 4.498 2.643 -0.530 -0.063 C18 W6M 12
W6M N03 N1 N 0 1 Y N N N N N -55.080 -27.243 7.969 -5.130 0.366 0.969 N03 W6M 13
W6M N07 N2 N 0 1 N N N N N N -51.599 -29.978 7.138 -1.064 -0.463 0.045 N07 W6M 14
W6M N19 N3 N 0 1 Y N N N N N -53.322 -28.208 8.769 -4.180 -0.078 -0.887 N19 W6M 15
W6M O04 O1 O 0 1 Y N N N N N -54.821 -28.364 7.232 -4.133 -0.273 1.230 O04 W6M 16
W6M O09 O2 O 0 1 N N N N N N -51.738 -29.384 4.949 0.372 -2.146 -0.155 O09 W6M 17
W6M O16 O3 O 0 1 N N N N N N -45.774 -29.266 2.795 6.151 0.670 -0.045 O16 W6M 18
W6M O17 O4 O 0 1 N N N N N N -47.761 -28.921 1.968 5.296 -1.372 -0.207 O17 W6M 19
W6M H131 H1 H 0 0 N N N N N N -45.719 -28.932 5.390 4.343 2.399 0.158 H131 W6M 20
W6M H011 H2 H 0 0 N N N N N N -54.805 -25.394 9.936 -6.054 2.325 -1.136 H011 W6M 21
W6M H012 H3 H 0 0 N N N N N N -54.065 -26.629 11.009 -6.476 0.840 -2.023 H012 W6M 22
W6M H013 H4 H 0 0 N N N N N N -53.025 -25.637 9.931 -7.255 1.197 -0.463 H013 W6M 23
W6M H061 H5 H 0 0 N N N N N N -53.447 -30.469 6.282 -2.146 -2.085 0.818 H061 W6M 24
W6M H062 H6 H 0 0 N N N N N N -53.222 -30.998 7.984 -2.197 -1.918 -0.954 H062 W6M 25
W6M H111 H7 H 0 0 N N N N N N -49.194 -29.321 7.857 0.134 1.736 0.217 H111 W6M 26
W6M H121 H8 H 0 0 N N N N N N -46.749 -29.028 7.631 2.051 3.271 0.305 H121 W6M 27
W6M H181 H9 H 0 0 N N N N N N -49.557 -29.412 3.615 2.809 -1.593 -0.163 H181 W6M 28
W6M H071 H10 H 0 0 N N N N N N -51.002 -30.122 7.927 -1.209 0.491 0.139 H071 W6M 29
W6M H1 H11 H 0 1 N N N N N N -45.572 -29.232 1.867 7.035 0.281 -0.103 H1 W6M 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
W6M O17 C15 DOUB N N 1
W6M O16 C15 SING N N 2
W6M C15 C14 SING N N 3
W6M C14 C18 DOUB Y N 4
W6M C14 C13 SING Y N 5
W6M C18 C10 SING Y N 6
W6M O09 C08 DOUB N N 7
W6M C13 C12 DOUB Y N 8
W6M C10 C08 SING N N 9
W6M C10 C11 DOUB Y N 10
W6M C08 N07 SING N N 11
W6M C12 C11 SING Y N 12
W6M N07 C06 SING N N 13
W6M O04 C05 SING Y N 14
W6M O04 N03 SING Y N 15
W6M C06 C05 SING N N 16
W6M C05 N19 DOUB Y N 17
W6M N03 C02 DOUB Y N 18
W6M N19 C02 SING Y N 19
W6M C02 C01 SING N N 20
W6M C13 H131 SING N N 21
W6M C01 H011 SING N N 22
W6M C01 H012 SING N N 23
W6M C01 H013 SING N N 24
W6M C06 H061 SING N N 25
W6M C06 H062 SING N N 26
W6M C11 H111 SING N N 27
W6M C12 H121 SING N N 28
W6M C18 H181 SING N N 29
W6M N07 H071 SING N N 30
W6M O16 H1 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
W6M SMILES ACDLabs 12.01 c2(C(NCc1nc(C)no1)=O)cccc(C(O)=O)c2
W6M InChI InChI 1.03 InChI=1S/C12H11N3O4/c1-7-14-10(19-15-7)6-13-11(16)8-3-2-4-9(5-8)12(17)18/h2-5H,6H2,1H3,(H,13,16)(H,17,18)
W6M InChIKey InChI 1.03 MSLQEHYKFTUMQL-UHFFFAOYSA-N
W6M SMILES_CANONICAL CACTVS 3.385 Cc1noc(CNC(=O)c2cccc(c2)C(O)=O)n1
W6M SMILES CACTVS 3.385 Cc1noc(CNC(=O)c2cccc(c2)C(O)=O)n1
W6M SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 Cc1nc(on1)CNC(=O)c2cccc(c2)C(=O)O
W6M SMILES "OpenEye OEToolkits" 2.0.7 Cc1nc(on1)CNC(=O)c2cccc(c2)C(=O)O
#
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
W6M "SYSTEMATIC NAME" ACDLabs 12.01 "3-{[(3-methyl-1,2,4-oxadiazol-5-yl)methyl]carbamoyl}benzoic acid"
W6M "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "3-[(3-methyl-1,2,4-oxadiazol-5-yl)methylcarbamoyl]benzoic acid"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
W6M 'Create component' 2020-09-29 RCSB
W6M 'Initial release' 2020-12-16 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
W6M C10 C 6.897 -1.355 1
W6M C13 C 6.897 -4.354 2
W6M C15 C 4.299 -4.354 3
W6M C01 C 11.729 6.319 4
W6M C02 C 11.119 4.949 5
W6M C05 C 9.495 3.146 6
W6M C06 C 8.196 2.396 7
W6M C08 C 6.897 0.145 8
W6M C11 C 8.196 -2.104 9
W6M C12 C 8.196 -3.604 10
W6M C14 C 5.598 -3.604 11
W6M C18 C 5.598 -2.104 12
W6M N03 N 11.869 3.650 13
W6M N07 N 8.196 0.895 14
W6M N19 N 9.652 4.637 15
W6M O04 O 10.866 2.535 16
W6M O09 O 5.598 0.895 17
W6M O16 O 3.000 -3.604 18
W6M O17 O 4.299 -5.854 19
#
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
W6M O17 C15 DOUBLE NONE 1
W6M O16 C15 SINGLE NONE 2
W6M C15 C14 SINGLE NONE 3
W6M C14 C18 SINGLE NONE 4
W6M C14 C13 DOUBLE NONE 5
W6M C18 C10 DOUBLE NONE 6
W6M O09 C08 DOUBLE NONE 7
W6M C13 C12 SINGLE NONE 8
W6M C10 C08 SINGLE NONE 9
W6M C10 C11 SINGLE NONE 10
W6M C08 N07 SINGLE NONE 11
W6M C12 C11 DOUBLE NONE 12
W6M N07 C06 SINGLE NONE 13
W6M O04 C05 SINGLE NONE 14
W6M O04 N03 SINGLE NONE 15
W6M C06 C05 SINGLE NONE 16
W6M C05 N19 DOUBLE NONE 17
W6M N03 C02 DOUBLE NONE 18
W6M N19 C02 SINGLE NONE 19
W6M C02 C01 SINGLE NONE 20
#
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
W6M MurckoScaffold S1 scaffold O=C(NCc1ncno1)c1ccccc1 InChI=1S/C10H9N3O2/c14-10(8-4-2-1-3-5-8)11-6-9-12-7-13-15-9/h1-5,7H,6H2,(H,11,14) DYMZLNOXOGCIDZ-UHFFFAOYSA-N
W6M amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
W6M isoxadiazole F2 fragment c1ncon1 InChI=1S/C2H2N2O/c1-3-2-5-4-1/h1-2H BBVIDBNAYOIXOE-UHFFFAOYSA-N
W6M 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
W6M C10 S1 1
W6M C13 S1 1
W6M C02 S1 1
W6M C05 S1 1
W6M C06 S1 1
W6M C08 S1 1
W6M C11 S1 1
W6M C12 S1 1
W6M C14 S1 1
W6M C18 S1 1
W6M N03 S1 1
W6M N07 S1 1
W6M N19 S1 1
W6M O04 S1 1
W6M O09 S1 1
W6M N07 F1 1
W6M C08 F1 1
W6M O09 F1 1
W6M C10 F1 1
W6M N03 F2 1
W6M C02 F2 1
W6M N19 F2 1
W6M C05 F2 1
W6M O04 F2 1
W6M C10 F3 1
W6M C18 F3 1
W6M C14 F3 1
W6M C13 F3 1
W6M C12 F3 1
W6M C11 F3 1
#
_pdbe_chem_comp_rdkit_properties.comp_id W6M
_pdbe_chem_comp_rdkit_properties.exactmw 261.075
_pdbe_chem_comp_rdkit_properties.amw 261.237
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 7
_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 6
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 19
_pdbe_chem_comp_rdkit_properties.NumAtoms 30
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 7
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 1
_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 123.400
_pdbe_chem_comp_rdkit_properties.tpsa 105.320
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.787
_pdbe_chem_comp_rdkit_properties.CrippenMR 62.543
_pdbe_chem_comp_rdkit_properties.chi0v 8.975
_pdbe_chem_comp_rdkit_properties.chi1v 4.617
_pdbe_chem_comp_rdkit_properties.chi2v 1.722
_pdbe_chem_comp_rdkit_properties.chi3v 1.722
_pdbe_chem_comp_rdkit_properties.chi4v 0.976
_pdbe_chem_comp_rdkit_properties.chi0n 19.975
_pdbe_chem_comp_rdkit_properties.chi1n 9.973
_pdbe_chem_comp_rdkit_properties.chi2n 1.722
_pdbe_chem_comp_rdkit_properties.chi3n 1.722
_pdbe_chem_comp_rdkit_properties.chi4n 0.976
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.700
_pdbe_chem_comp_rdkit_properties.kappa1 4.764
_pdbe_chem_comp_rdkit_properties.kappa2 5.298
_pdbe_chem_comp_rdkit_properties.kappa3 3.153
_pdbe_chem_comp_rdkit_properties.Phi 1.329
#
_pdbe_chem_comp_external_mappings.comp_id W6M
_pdbe_chem_comp_external_mappings.source UniChem
_pdbe_chem_comp_external_mappings.resource PubChem
_pdbe_chem_comp_external_mappings.resource_id 61865966
#
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
W6M C10 -1.642 0.055 -0.477 ETKDGv3 1
W6M C13 -3.970 0.567 1.056 ETKDGv3 2
W6M C15 -5.412 -0.424 -0.667 ETKDGv3 3
W6M C01 5.971 0.629 1.449 ETKDGv3 4
W6M C02 4.925 -0.143 0.717 ETKDGv3 5
W6M C05 3.282 -0.554 -0.563 ETKDGv3 6
W6M C06 2.083 -0.452 -1.450 ETKDGv3 7
W6M C08 -0.424 -0.212 -1.281 ETKDGv3 8
W6M C11 -1.544 0.727 0.846 ETKDGv3 9
W6M C12 -2.644 0.964 1.567 ETKDGv3 10
W6M C14 -4.085 -0.028 -0.145 ETKDGv3 11
W6M C18 -2.858 -0.288 -0.944 ETKDGv3 12
W6M N03 4.898 -1.435 0.677 ETKDGv3 13
W6M N07 0.861 -0.343 -0.655 ETKDGv3 14
W6M N19 3.904 0.468 -0.075 ETKDGv3 15
W6M O04 3.837 -1.746 -0.133 ETKDGv3 16
W6M O09 -0.521 -0.336 -2.533 ETKDGv3 17
W6M O16 -6.564 -0.185 0.078 ETKDGv3 18
W6M O17 -5.509 -0.981 -1.794 ETKDGv3 19
W6M H131 -4.840 0.771 1.666 ETKDGv3 20
W6M H011 5.587 1.639 1.700 ETKDGv3 21
W6M H012 6.872 0.729 0.808 ETKDGv3 22
W6M H013 6.245 0.103 2.388 ETKDGv3 23
W6M H061 2.029 -1.356 -2.093 ETKDGv3 24
W6M H062 2.184 0.442 -2.102 ETKDGv3 25
W6M H111 -0.588 1.057 1.229 ETKDGv3 26
W6M H121 -2.567 1.460 2.526 ETKDGv3 27
W6M H181 -2.952 -0.775 -1.907 ETKDGv3 28
W6M H071 0.919 -0.416 0.386 ETKDGv3 29
W6M H1 -7.476 -0.454 -0.274 ETKDGv3 30
#