data_W1B
#
_chem_comp.id W1B
_chem_comp.name "4-azanyl-~{N}-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2-oxidanyl-benzamide"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C12 H13 N3 O4"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2023-04-24
_chem_comp.pdbx_modified_date 2023-11-10
_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 263.249
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code W1B
_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 8OU9
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBE
#
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
W1B C4 C1 C 0 1 N N N N N N 22.502 16.839 -7.568 -4.629 0.268 -0.138 C4 W1B 1
W1B C5 C2 C 0 1 N N N N N N 24.842 16.970 -8.209 -2.469 -0.466 -0.712 C5 W1B 2
W1B C6 C3 C 0 1 N N N N N N 27.034 19.536 -7.646 0.503 -0.438 0.399 C6 W1B 3
W1B N1 N1 N 0 1 N N N N N N 23.632 16.369 -8.158 -3.777 -0.338 -0.978 N1 W1B 4
W1B N3 N2 N 0 1 N N N N N N 30.987 21.965 -10.892 5.828 1.166 -0.506 N3 W1B 5
W1B C2 C4 C 0 1 N N N N N N 23.718 19.036 -7.290 -2.694 1.265 1.041 C2 W1B 6
W1B C1 C5 C 0 1 N N S N N N 25.018 18.260 -7.459 -1.876 0.058 0.569 C1 W1B 7
W1B C3 C6 C 0 1 N N N N N N 22.674 18.069 -6.777 -4.160 0.840 1.174 C3 W1B 8
W1B O1 O1 O 0 1 N N N N N N 25.740 16.455 -8.841 -1.749 -1.016 -1.518 O1 W1B 9
W1B O2 O2 O 0 1 N N N N N N 21.534 16.125 -7.505 -5.799 0.360 -0.442 O2 W1B 10
W1B N2 N3 N 0 1 N N N N N N 25.921 19.089 -8.211 -0.490 0.471 0.335 N2 W1B 11
W1B C7 C7 C 0 1 Y N N N N N 27.970 20.210 -8.573 1.896 -0.023 0.163 C7 W1B 12
W1B O3 O3 O 0 1 N N N N N N 27.301 19.345 -6.449 0.249 -1.600 0.651 O3 W1B 13
W1B C8 C8 C 0 1 Y N N N N N 29.219 20.499 -8.041 2.191 1.313 -0.128 C8 W1B 14
W1B C9 C9 C 0 1 Y N N N N N 30.201 21.072 -8.794 3.482 1.697 -0.346 C9 W1B 15
W1B C10 C10 C 0 1 Y N N N N N 29.977 21.361 -10.149 4.516 0.764 -0.282 C10 W1B 16
W1B C11 C11 C 0 1 Y N N N N N 28.721 21.064 -10.702 4.239 -0.567 0.006 C11 W1B 17
W1B C12 C12 C 0 1 Y N N N N N 27.725 20.509 -9.916 2.934 -0.966 0.235 C12 W1B 18
W1B O4 O4 O 0 1 N N N N N N 26.524 20.215 -10.476 2.657 -2.264 0.516 O4 W1B 19
W1B H6 H1 H 0 1 N N N N N N 23.561 15.477 -8.605 -4.121 -0.696 -1.812 H6 W1B 20
W1B H12 H2 H 0 1 N N N N N N 31.796 22.089 -10.317 6.023 2.095 -0.708 H12 W1B 21
W1B H13 H3 H 0 1 N N N N N N 31.219 21.385 -11.673 6.548 0.518 -0.462 H13 W1B 22
W1B H3 H4 H 0 1 N N N N N N 23.860 19.853 -6.568 -2.322 1.604 2.008 H3 W1B 23
W1B H2 H5 H 0 1 N N N N N N 23.401 19.452 -8.257 -2.612 2.073 0.314 H2 W1B 24
W1B H1 H6 H 0 1 N N N N N N 25.439 18.047 -6.465 -1.901 -0.723 1.329 H1 W1B 25
W1B H5 H7 H 0 1 N N N N N N 21.708 18.595 -6.755 -4.769 1.706 1.432 H5 W1B 26
W1B H4 H8 H 0 1 N N N N N N 22.956 17.777 -5.755 -4.250 0.084 1.954 H4 W1B 27
W1B H7 H9 H 0 1 N N N N N N 25.710 19.328 -9.159 -0.287 1.398 0.133 H7 W1B 28
W1B H8 H10 H 0 1 N N N N N N 29.418 20.264 -7.006 1.396 2.042 -0.180 H8 W1B 29
W1B H9 H11 H 0 1 N N N N N N 31.156 21.305 -8.346 3.705 2.730 -0.571 H9 W1B 30
W1B H10 H12 H 0 1 N N N N N N 28.531 21.269 -11.745 5.042 -1.288 0.055 H10 W1B 31
W1B H11 H13 H 0 1 N N N N N N 25.949 19.844 -9.817 2.677 -2.475 1.460 H11 W1B 32
#
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
W1B N3 C10 SING N N 1
W1B C11 C10 DOUB Y N 2
W1B C11 C12 SING Y N 3
W1B O4 C12 SING N N 4
W1B C10 C9 SING Y N 5
W1B C12 C7 DOUB Y N 6
W1B O1 C5 DOUB N N 7
W1B C9 C8 DOUB Y N 8
W1B C7 C8 SING Y N 9
W1B C7 C6 SING N N 10
W1B N2 C6 SING N N 11
W1B N2 C1 SING N N 12
W1B C5 N1 SING N N 13
W1B C5 C1 SING N N 14
W1B N1 C4 SING N N 15
W1B C6 O3 DOUB N N 16
W1B C4 O2 DOUB N N 17
W1B C4 C3 SING N N 18
W1B C1 C2 SING N N 19
W1B C2 C3 SING N N 20
W1B N1 H6 SING N N 21
W1B N3 H12 SING N N 22
W1B N3 H13 SING N N 23
W1B C2 H3 SING N N 24
W1B C2 H2 SING N N 25
W1B C1 H1 SING N N 26
W1B C3 H5 SING N N 27
W1B C3 H4 SING N N 28
W1B N2 H7 SING N N 29
W1B C8 H8 SING N N 30
W1B C9 H9 SING N N 31
W1B C11 H10 SING N N 32
W1B O4 H11 SING N N 33
#
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
W1B InChI InChI 1.06 "InChI=1S/C12H13N3O4/c13-6-1-2-7(9(16)5-6)11(18)14-8-3-4-10(17)15-12(8)19/h1-2,5,8,16H,3-4,13H2,(H,14,18)(H,15,17,19)/t8-/m0/s1"
W1B InChIKey InChI 1.06 IPUAAMOPTISHEC-QMMMGPOBSA-N
W1B SMILES_CANONICAL CACTVS 3.385 "Nc1ccc(c(O)c1)C(=O)N[C@H]2CCC(=O)NC2=O"
W1B SMILES CACTVS 3.385 "Nc1ccc(c(O)c1)C(=O)N[CH]2CCC(=O)NC2=O"
W1B SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1cc(c(cc1N)O)C(=O)N[C@H]2CCC(=O)NC2=O"
W1B SMILES "OpenEye OEToolkits" 2.0.7 "c1cc(c(cc1N)O)C(=O)NC2CCC(=O)NC2=O"
#
_pdbx_chem_comp_identifier.comp_id W1B
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version 2.0.7
_pdbx_chem_comp_identifier.identifier "4-azanyl-~{N}-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2-oxidanyl-benzamide"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
W1B 'Create component' 2023-04-24 PDBE
W1B 'Initial release' 2023-11-15 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
W1B C4 C 7.702 5.107 1
W1B C5 C 6.404 2.857 2
W1B C6 C 6.404 -0.142 3
W1B N1 N 6.404 4.357 4
W1B N3 N 6.404 -6.143 5
W1B C2 C 9.002 2.857 6
W1B C1 C 7.702 2.107 7
W1B C3 C 9.002 4.357 8
W1B O1 O 5.104 2.107 9
W1B O2 O 7.702 6.607 10
W1B N2 N 7.702 0.608 11
W1B C7 C 6.404 -1.643 12
W1B O3 O 5.104 0.608 13
W1B C8 C 7.702 -2.393 14
W1B C9 C 7.702 -3.893 15
W1B C10 C 6.404 -4.643 16
W1B C11 C 5.104 -3.893 17
W1B C12 C 5.104 -2.393 18
W1B O4 O 3.805 -1.643 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
W1B N3 C10 SINGLE NONE 1
W1B C11 C10 DOUBLE NONE 2
W1B C11 C12 SINGLE NONE 3
W1B O4 C12 SINGLE NONE 4
W1B C10 C9 SINGLE NONE 5
W1B C12 C7 DOUBLE NONE 6
W1B O1 C5 DOUBLE NONE 7
W1B C9 C8 DOUBLE NONE 8
W1B C7 C8 SINGLE NONE 9
W1B C7 C6 SINGLE NONE 10
W1B N2 C6 SINGLE NONE 11
W1B C1 N2 SINGLE BEGINDASH 12
W1B C5 N1 SINGLE NONE 13
W1B C5 C1 SINGLE NONE 14
W1B N1 C4 SINGLE NONE 15
W1B C6 O3 DOUBLE NONE 16
W1B C4 O2 DOUBLE NONE 17
W1B C4 C3 SINGLE NONE 18
W1B C1 C2 SINGLE NONE 19
W1B C2 C3 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
W1B MurckoScaffold S1 scaffold 'O=C1CC[C@H](NC(=O)c2ccccc2)C(=O)N1' InChI=1S/C12H12N2O3/c15-10-7-6-9(12(17)14-10)13-11(16)8-4-2-1-3-5-8/h1-5,9H,6-7H2,(H,13,16)(H,14,15,17)/t9-/m0/s1 QDCDITVKCKBZTO-VIFPVBQESA-N
W1B amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
W1B peptide F2 fragment NCC=O InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2 LYIIBVSRGJSHAV-UHFFFAOYSA-N
W1B 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
W1B C4 S1 1
W1B C5 S1 1
W1B C6 S1 1
W1B N1 S1 1
W1B C2 S1 1
W1B C1 S1 1
W1B C3 S1 1
W1B O1 S1 1
W1B O2 S1 1
W1B N2 S1 1
W1B C7 S1 1
W1B O3 S1 1
W1B C8 S1 1
W1B C9 S1 1
W1B C10 S1 1
W1B C11 S1 1
W1B C12 S1 1
W1B N1 F1 1
W1B C5 F1 1
W1B O1 F1 1
W1B C1 F1 1
W1B N1 F1 2
W1B C4 F1 2
W1B O2 F1 2
W1B C3 F1 2
W1B N2 F1 3
W1B C6 F1 3
W1B O3 F1 3
W1B C7 F1 3
W1B O1 F2 1
W1B C5 F2 1
W1B C1 F2 1
W1B N2 F2 1
W1B C7 F3 1
W1B C12 F3 1
W1B C11 F3 1
W1B C10 F3 1
W1B C9 F3 1
W1B C8 F3 1
#
_pdbe_chem_comp_rdkit_properties.comp_id W1B
_pdbe_chem_comp_rdkit_properties.exactmw 263.091
_pdbe_chem_comp_rdkit_properties.amw 263.253
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 7
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 5
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 4
_pdbe_chem_comp_rdkit_properties.NumHBD 4
_pdbe_chem_comp_rdkit_properties.NumHBA 5
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 19
_pdbe_chem_comp_rdkit_properties.NumAtoms 32
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 7
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 3
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.250
_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 1
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 1
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 126.917
_pdbe_chem_comp_rdkit_properties.tpsa 121.520
_pdbe_chem_comp_rdkit_properties.CrippenClogP -1.388
_pdbe_chem_comp_rdkit_properties.CrippenMR 64.457
_pdbe_chem_comp_rdkit_properties.chi0v 8.975
_pdbe_chem_comp_rdkit_properties.chi1v 4.685
_pdbe_chem_comp_rdkit_properties.chi2v 1.886
_pdbe_chem_comp_rdkit_properties.chi3v 1.886
_pdbe_chem_comp_rdkit_properties.chi4v 1.103
_pdbe_chem_comp_rdkit_properties.chi0n 21.975
_pdbe_chem_comp_rdkit_properties.chi1n 10.882
_pdbe_chem_comp_rdkit_properties.chi2n 1.886
_pdbe_chem_comp_rdkit_properties.chi3n 1.886
_pdbe_chem_comp_rdkit_properties.chi4n 1.103
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.570
_pdbe_chem_comp_rdkit_properties.kappa1 4.224
_pdbe_chem_comp_rdkit_properties.kappa2 4.968
_pdbe_chem_comp_rdkit_properties.kappa3 2.817
_pdbe_chem_comp_rdkit_properties.Phi 1.105
#
_pdbe_chem_comp_external_mappings.comp_id W1B
_pdbe_chem_comp_external_mappings.source UniChem
_pdbe_chem_comp_external_mappings.resource PubChem
_pdbe_chem_comp_external_mappings.resource_id 169409275
#
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
W1B C4 -4.874 0.942 -0.551 ETKDGv3 1
W1B C5 -2.588 1.157 -1.522 ETKDGv3 2
W1B C6 0.250 -0.796 -0.072 ETKDGv3 3
W1B N1 -3.961 1.562 -1.462 ETKDGv3 4
W1B N3 5.811 0.140 1.047 ETKDGv3 5
W1B C2 -2.928 -0.057 0.644 ETKDGv3 6
W1B C1 -2.081 0.045 -0.636 ETKDGv3 7
W1B C3 -4.419 -0.191 0.321 ETKDGv3 8
W1B O1 -1.820 1.690 -2.368 ETKDGv3 9
W1B O2 -6.076 1.315 -0.516 ETKDGv3 10
W1B N2 -0.680 0.280 -0.278 ETKDGv3 11
W1B C7 1.682 -0.526 0.191 ETKDGv3 12
W1B O3 -0.159 -1.989 -0.073 ETKDGv3 13
W1B C8 2.415 -1.412 1.132 ETKDGv3 14
W1B C9 3.708 -1.201 1.398 ETKDGv3 15
W1B C10 4.430 -0.083 0.752 ETKDGv3 16
W1B C11 3.780 0.712 -0.111 ETKDGv3 17
W1B C12 2.349 0.479 -0.420 ETKDGv3 18
W1B O4 1.716 1.287 -1.364 ETKDGv3 19
W1B H6 -4.300 2.326 -2.089 ETKDGv3 20
W1B H12 6.339 0.923 0.600 ETKDGv3 21
W1B H13 6.316 -0.481 1.718 ETKDGv3 22
W1B H3 -2.603 -0.943 1.233 ETKDGv3 23
W1B H2 -2.769 0.847 1.274 ETKDGv3 24
W1B H1 -2.172 -0.903 -1.210 ETKDGv3 25
W1B H5 -4.999 -0.194 1.270 ETKDGv3 26
W1B H4 -4.605 -1.152 -0.206 ETKDGv3 27
W1B H7 -0.401 1.244 0.015 ETKDGv3 28
W1B H8 1.901 -2.231 1.619 ETKDGv3 29
W1B H9 4.227 -1.851 2.091 ETKDGv3 30
W1B H10 4.300 1.529 -0.595 ETKDGv3 31
W1B H11 2.211 2.037 -1.832 ETKDGv3 32
#