data_W9K
#
_chem_comp.id W9K
_chem_comp.name (5R)-7-(4-hydroxyphenyl)-1,8-dithia-3-azaspiro[4.5]dec-6-ene-2,4-dione
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C13 H11 N O3 S2"
_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 293.361
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code W9K
_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 7FYS
_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
W9K C01 C1 C 0 1 N N R N N N 6.738 7.411 17.604 1.734 -0.203 -0.281 C01 W9K 1
W9K C02 C2 C 0 1 N N N N N N 5.819 7.184 18.778 0.296 0.167 -0.166 C02 W9K 2
W9K C04 C3 C 0 1 N N N N N N 5.839 7.877 16.384 2.385 -0.232 1.084 C04 W9K 3
W9K C05 C4 C 0 1 N N N N N N 7.845 8.421 17.956 1.962 -1.528 -0.995 C05 W9K 4
W9K C06 C5 C 0 1 N N N N N N 5.916 7.586 20.094 -0.742 -0.639 -0.253 C06 W9K 5
W9K C07 C6 C 0 1 N N N N N N 6.452 5.723 15.678 3.700 1.475 0.237 C07 W9K 6
W9K C10 C7 C 0 1 N N N N N N 8.343 8.101 19.355 1.196 -2.639 -0.263 C10 W9K 7
W9K C11 C8 C 0 1 Y N N N N N 4.919 7.243 21.136 -2.100 -0.071 -0.092 C11 W9K 8
W9K C15 C9 C 0 1 Y N N N N N 5.316 7.192 22.523 -3.026 -0.699 0.740 C15 W9K 9
W9K C16 C10 C 0 1 Y N N N N N 2.694 6.594 21.814 -3.720 1.621 -0.620 C16 W9K 10
W9K C17 C11 C 0 1 Y N N N N N 4.423 6.826 23.525 -4.290 -0.167 0.888 C17 W9K 11
W9K C18 C12 C 0 1 Y N N N N N 3.085 6.544 23.173 -4.640 0.993 0.209 C18 W9K 12
W9K S03 S1 S 0 1 N N N N N N 7.493 5.823 17.106 2.648 1.118 -1.145 S03 W9K 13
W9K N08 N1 N 0 1 N N N N N N 5.737 6.853 15.331 3.357 0.652 1.230 N08 W9K 14
W9K O09 O1 O 0 1 N N N N N N 5.184 9.029 16.282 2.046 -0.995 1.963 O09 W9K 15
W9K S12 S2 S 0 1 N N N N N N 7.266 8.474 20.722 -0.578 -2.367 -0.554 S12 W9K 16
W9K O13 O2 O 0 1 N N N N N N 6.280 4.658 15.154 4.576 2.318 0.272 O13 W9K 17
W9K C14 C13 C 0 1 Y N N N N N 3.586 6.913 20.815 -2.453 1.098 -0.767 C14 W9K 18
W9K O19 O3 O 0 1 N N N N N N 2.209 6.241 24.217 -5.888 1.511 0.353 O19 W9K 19
W9K H21 H1 H 0 1 N N N N N N 4.934 6.609 18.549 0.080 1.210 0.008 H21 W9K 20
W9K H22 H2 H 0 1 N N N N N N 8.672 8.334 17.236 1.603 -1.454 -2.022 H22 W9K 21
W9K H23 H3 H 0 1 N N N N N N 7.440 9.443 17.928 3.027 -1.761 -0.997 H23 W9K 22
W9K H26 H4 H 0 1 N N N N N N 8.556 7.022 19.389 1.491 -3.612 -0.656 H26 W9K 23
W9K H25 H5 H 0 1 N N N N N N 9.276 8.664 19.508 1.407 -2.592 0.806 H25 W9K 24
W9K H28 H6 H 0 1 N N N N N N 6.332 7.444 22.789 -2.755 -1.601 1.268 H28 W9K 25
W9K H29 H7 H 0 1 N N N N N N 1.669 6.376 21.554 -3.996 2.523 -1.146 H29 W9K 26
W9K H30 H8 H 0 1 N N N N N N 4.747 6.759 24.553 -5.008 -0.653 1.532 H30 W9K 27
W9K H24 H9 H 0 1 N N N N N N 5.221 6.961 14.481 3.830 0.704 2.075 H24 W9K 28
W9K H27 H10 H 0 1 N N N N N N 3.264 6.911 19.784 -1.736 1.589 -1.408 H27 W9K 29
W9K H1 H11 H 0 1 N N N N N N 2.679 6.263 25.042 -6.530 1.174 -0.287 H1 W9K 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
W9K C01 C02 SING N N 1
W9K C01 S03 SING N N 2
W9K C01 C04 SING N N 3
W9K C01 C05 SING N N 4
W9K C02 C06 DOUB N N 5
W9K S03 C07 SING N N 6
W9K C04 N08 SING N N 7
W9K C04 O09 DOUB N N 8
W9K C05 C10 SING N N 9
W9K C06 C11 SING N N 10
W9K C06 S12 SING N N 11
W9K C07 N08 SING N N 12
W9K C07 O13 DOUB N N 13
W9K C10 S12 SING N N 14
W9K C11 C14 DOUB Y N 15
W9K C11 C15 SING Y N 16
W9K C14 C16 SING Y N 17
W9K C15 C17 DOUB Y N 18
W9K C16 C18 DOUB Y N 19
W9K C17 C18 SING Y N 20
W9K C18 O19 SING N N 21
W9K C02 H21 SING N N 22
W9K C05 H22 SING N N 23
W9K C05 H23 SING N N 24
W9K C10 H26 SING N N 25
W9K C10 H25 SING N N 26
W9K C15 H28 SING N N 27
W9K C16 H29 SING N N 28
W9K C17 H30 SING N N 29
W9K N08 H24 SING N N 30
W9K C14 H27 SING N N 31
W9K O19 H1 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
W9K SMILES ACDLabs 12.01 Oc1ccc(cc1)C1=CC2(CCS1)SC(=O)NC2=O
W9K InChI InChI 1.06 InChI=1S/C13H11NO3S2/c15-9-3-1-8(2-4-9)10-7-13(5-6-18-10)11(16)14-12(17)19-13/h1-4,7,15H,5-6H2,(H,14,16,17)/t13-/m1/s1
W9K InChIKey InChI 1.06 VJAVMIFSWYAVBZ-CYBMUJFWSA-N
W9K SMILES_CANONICAL CACTVS 3.385 Oc1ccc(cc1)C2=C[C@@]3(CCS2)SC(=O)NC3=O
W9K SMILES CACTVS 3.385 Oc1ccc(cc1)C2=C[C]3(CCS2)SC(=O)NC3=O
W9K SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 c1cc(ccc1C2=C[C@]3(CCS2)C(=O)NC(=O)S3)O
W9K SMILES "OpenEye OEToolkits" 2.0.7 c1cc(ccc1C2=CC3(CCS2)C(=O)NC(=O)S3)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
W9K "SYSTEMATIC NAME" ACDLabs 12.01 (5R)-7-(4-hydroxyphenyl)-1,8-dithia-3-azaspiro[4.5]dec-6-ene-2,4-dione
W9K "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 (5~{R})-7-(4-hydroxyphenyl)-1,8-dithia-3-azaspiro[4.5]dec-6-ene-2,4-dione
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
W9K 'Create component' 2023-05-09 RCSB
W9K 'Initial release' 2023-06-14 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
W9K C01 C 9.180 1.927 1
W9K C02 C 8.430 0.628 2
W9K C04 C 10.062 3.141 3
W9K C05 C 8.430 3.227 4
W9K C06 C 6.930 0.628 5
W9K C07 C 11.488 1.177 6
W9K C10 C 6.930 3.227 7
W9K C11 C 6.180 -0.670 8
W9K C15 C 6.930 -1.970 9
W9K C16 C 3.930 -1.970 10
W9K C17 C 6.180 -3.269 11
W9K C18 C 4.680 -3.269 12
W9K S03 S 10.062 0.714 13
W9K N08 N 11.488 2.678 14
W9K O09 O 9.598 4.568 15
W9K S12 S 6.180 1.927 16
W9K O13 O 12.702 0.296 17
W9K C14 C 4.680 -0.670 18
W9K O19 O 3.930 -4.568 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
W9K C01 C02 SINGLE NONE 1
W9K C01 S03 SINGLE NONE 2
W9K C01 C04 SINGLE NONE 3
W9K C01 C05 SINGLE BEGINWEDGE 4
W9K C02 C06 DOUBLE NONE 5
W9K S03 C07 SINGLE NONE 6
W9K C04 N08 SINGLE NONE 7
W9K C04 O09 DOUBLE NONE 8
W9K C05 C10 SINGLE NONE 9
W9K C06 C11 SINGLE NONE 10
W9K C06 S12 SINGLE NONE 11
W9K C07 N08 SINGLE NONE 12
W9K C07 O13 DOUBLE NONE 13
W9K C10 S12 SINGLE NONE 14
W9K C11 C14 SINGLE NONE 15
W9K C11 C15 DOUBLE NONE 16
W9K C14 C16 DOUBLE NONE 17
W9K C15 C17 SINGLE NONE 18
W9K C16 C18 SINGLE NONE 19
W9K C17 C18 DOUBLE NONE 20
W9K C18 O19 SINGLE NONE 21
#
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
W9K MurckoScaffold S1 scaffold 'O=C1NC(=O)[C@@]2(C=C(c3ccccc3)SCC2)S1' InChI=1S/C13H11NO2S2/c15-11-13(18-12(16)14-11)6-7-17-10(8-13)9-4-2-1-3-5-9/h1-5,8H,6-7H2,(H,14,15,16)/t13-/m1/s1 DQILIPNSKGBOGP-CYBMUJFWSA-N
W9K amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
W9K phenyl F2 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
W9K C01 S1 1
W9K C02 S1 1
W9K C04 S1 1
W9K C05 S1 1
W9K C06 S1 1
W9K C07 S1 1
W9K C10 S1 1
W9K C11 S1 1
W9K C15 S1 1
W9K C16 S1 1
W9K C17 S1 1
W9K C18 S1 1
W9K S03 S1 1
W9K N08 S1 1
W9K O09 S1 1
W9K S12 S1 1
W9K O13 S1 1
W9K C14 S1 1
W9K N08 F1 1
W9K C04 F1 1
W9K O09 F1 1
W9K C01 F1 1
W9K C11 F2 1
W9K C14 F2 1
W9K C16 F2 1
W9K C18 F2 1
W9K C17 F2 1
W9K C15 F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id W9K
_pdbe_chem_comp_rdkit_properties.exactmw 293.018
_pdbe_chem_comp_rdkit_properties.amw 293.369
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 4
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 2
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 2
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 5
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 19
_pdbe_chem_comp_rdkit_properties.NumAtoms 30
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 6
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 2
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.231
_pdbe_chem_comp_rdkit_properties.NumRings 3
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 2
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 1
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 1
_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 133.797
_pdbe_chem_comp_rdkit_properties.tpsa 66.400
_pdbe_chem_comp_rdkit_properties.CrippenClogP 2.075
_pdbe_chem_comp_rdkit_properties.CrippenMR 76.144
_pdbe_chem_comp_rdkit_properties.chi0v 10.621
_pdbe_chem_comp_rdkit_properties.chi1v 6.509
_pdbe_chem_comp_rdkit_properties.chi2v 3.899
_pdbe_chem_comp_rdkit_properties.chi3v 3.899
_pdbe_chem_comp_rdkit_properties.chi4v 3.032
_pdbe_chem_comp_rdkit_properties.chi0n 19.988
_pdbe_chem_comp_rdkit_properties.chi1n 10.232
_pdbe_chem_comp_rdkit_properties.chi2n 2.233
_pdbe_chem_comp_rdkit_properties.chi3n 2.233
_pdbe_chem_comp_rdkit_properties.chi4n 1.410
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.400
_pdbe_chem_comp_rdkit_properties.kappa1 5.179
_pdbe_chem_comp_rdkit_properties.kappa2 4.611
_pdbe_chem_comp_rdkit_properties.kappa3 2.256
_pdbe_chem_comp_rdkit_properties.Phi 1.257
#
_pdbe_chem_comp_external_mappings.comp_id W9K
_pdbe_chem_comp_external_mappings.source UniChem
_pdbe_chem_comp_external_mappings.resource PDBe
_pdbe_chem_comp_external_mappings.resource_id W9K
#
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
W9K C01 -2.224 0.146 0.355 ETKDGv3 1
W9K C02 -0.727 0.400 0.376 ETKDGv3 2
W9K C04 -2.750 0.531 -1.006 ETKDGv3 3
W9K C05 -2.660 -1.302 0.695 ETKDGv3 4
W9K C06 0.227 -0.531 0.574 ETKDGv3 5
W9K C07 -3.933 2.082 0.261 ETKDGv3 6
W9K C10 -1.673 -2.348 0.189 ETKDGv3 7
W9K C11 1.653 -0.196 0.339 ETKDGv3 8
W9K C15 2.474 -1.084 -0.252 ETKDGv3 9
W9K C16 3.491 1.417 0.549 ETKDGv3 10
W9K C17 3.894 -0.752 -0.489 ETKDGv3 11
W9K C18 4.381 0.440 -0.110 ETKDGv3 12
W9K S03 -3.008 1.298 1.567 ETKDGv3 13
W9K N08 -3.692 1.586 -1.037 ETKDGv3 14
W9K O09 -2.378 -0.041 -2.065 ETKDGv3 15
W9K S12 -0.162 -2.190 1.171 ETKDGv3 16
W9K O13 -4.750 3.015 0.476 ETKDGv3 17
W9K C14 2.204 1.120 0.764 ETKDGv3 18
W9K O19 5.717 0.769 -0.328 ETKDGv3 19
W9K H21 -0.423 1.393 0.067 ETKDGv3 20
W9K H22 -3.666 -1.513 0.268 ETKDGv3 21
W9K H23 -2.759 -1.421 1.797 ETKDGv3 22
W9K H26 -1.456 -2.221 -0.892 ETKDGv3 23
W9K H25 -2.094 -3.362 0.349 ETKDGv3 24
W9K H28 2.107 -2.048 -0.583 ETKDGv3 25
W9K H29 3.885 2.374 0.867 ETKDGv3 26
W9K H30 4.535 -1.478 -0.972 ETKDGv3 27
W9K H24 -4.147 1.949 -1.905 ETKDGv3 28
W9K H27 1.573 1.841 1.269 ETKDGv3 29
W9K H1 6.359 0.126 -0.776 ETKDGv3 30
#