data_7R4
#
_chem_comp.id 7R4
_chem_comp.name (5R)-5-benzyl-2-sulfanylidene-1,3-thiazolidin-4-one
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C10 H9 N O S2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2016-11-30
_chem_comp.pdbx_modified_date 2017-08-25
_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 223.315
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 7R4
_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 5U0E
_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
7R4 C9 C1 C 0 1 Y N N N N N -3.108 6.885 14.064 4.427 0.968 0.283 C9 7R4 1
7R4 C8 C2 C 0 1 Y N N N N N -4.422 6.518 14.212 3.443 1.652 -0.407 C8 7R4 2
7R4 C10 C3 C 0 1 Y N N N N N -2.194 5.919 13.764 4.237 -0.358 0.623 C10 7R4 3
7R4 C7 C4 C 0 1 Y N N N N N -4.842 5.214 14.084 2.268 1.011 -0.752 C7 7R4 4
7R4 C11 C5 C 0 1 Y N N N N N -2.625 4.609 13.632 3.065 -1.001 0.272 C11 7R4 5
7R4 C6 C6 C 0 1 Y N N N N N -3.943 4.233 13.791 2.076 -0.314 -0.407 C6 7R4 6
7R4 C2 C7 C 0 1 N N N N N N -4.631 0.640 14.764 -1.476 -1.656 0.036 C2 7R4 7
7R4 C13 C8 C 0 1 N N N N N N -5.722 1.298 16.598 -2.522 0.409 0.083 C13 7R4 8
7R4 C3 C9 C 0 1 N N R N N N -3.996 2.008 14.883 -0.225 -0.861 0.337 C3 7R4 9
7R4 C5 C10 C 0 1 N N N N N N -4.440 2.829 13.671 0.799 -1.015 -0.790 C5 7R4 10
7R4 N12 N1 N 0 1 N N N N N N -5.558 0.336 15.676 -2.567 -0.916 -0.070 N12 7R4 11
7R4 O1 O1 O 0 1 N N N N N N -4.318 -0.151 13.891 -1.478 -2.861 -0.102 O1 7R4 12
7R4 S14 S1 S 0 1 N N N N N N -6.766 1.290 17.876 -3.850 1.484 -0.026 S14 7R4 13
7R4 S4 S2 S 0 1 N N N N N N -4.659 2.650 16.418 -0.840 0.855 0.420 S4 7R4 14
7R4 H1 H1 H 0 1 N N N N N N -2.805 7.915 14.182 5.344 1.469 0.553 H1 7R4 15
7R4 H2 H2 H 0 1 N N N N N N -5.153 7.280 14.437 3.593 2.687 -0.676 H2 7R4 16
7R4 H3 H3 H 0 1 N N N N N N -1.152 6.171 13.632 5.006 -0.892 1.162 H3 7R4 17
7R4 H4 H4 H 0 1 N N N N N N -5.885 4.968 14.216 1.500 1.545 -1.291 H4 7R4 18
7R4 H5 H5 H 0 1 N N N N N N -1.897 3.848 13.394 2.918 -2.038 0.537 H5 7R4 19
7R4 H6 H6 H 0 1 N N N N N N -2.901 1.954 14.967 0.204 -1.163 1.292 H6 7R4 20
7R4 H7 H7 H 0 1 N N N N N N -5.539 2.835 13.619 0.402 -0.573 -1.704 H7 7R4 21
7R4 H8 H8 H 0 1 N N N N N N -4.032 2.376 12.755 1.000 -2.073 -0.956 H8 7R4 22
7R4 H9 H9 H 0 1 N N N N N N -6.076 -0.519 15.673 -3.416 -1.344 -0.262 H9 7R4 23
#
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
7R4 C11 C10 DOUB Y N 1
7R4 C11 C6 SING Y N 2
7R4 C5 C6 SING N N 3
7R4 C5 C3 SING N N 4
7R4 C10 C9 SING Y N 5
7R4 C6 C7 DOUB Y N 6
7R4 O1 C2 DOUB N N 7
7R4 C9 C8 DOUB Y N 8
7R4 C7 C8 SING Y N 9
7R4 C2 C3 SING N N 10
7R4 C2 N12 SING N N 11
7R4 C3 S4 SING N N 12
7R4 N12 C13 SING N N 13
7R4 S4 C13 SING N N 14
7R4 C13 S14 DOUB N N 15
7R4 C9 H1 SING N N 16
7R4 C8 H2 SING N N 17
7R4 C10 H3 SING N N 18
7R4 C7 H4 SING N N 19
7R4 C11 H5 SING N N 20
7R4 C3 H6 SING N N 21
7R4 C5 H7 SING N N 22
7R4 C5 H8 SING N N 23
7R4 N12 H9 SING N N 24
#
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
7R4 SMILES ACDLabs 12.01 c1ccc(cc1)CC2C(NC(=S)S2)=O
7R4 InChI InChI 1.03 InChI=1S/C10H9NOS2/c12-9-8(14-10(13)11-9)6-7-4-2-1-3-5-7/h1-5,8H,6H2,(H,11,12,13)/t8-/m1/s1
7R4 InChIKey InChI 1.03 HEFVAMUJRPNDFW-MRVPVSSYSA-N
7R4 SMILES_CANONICAL CACTVS 3.385 O=C1NC(=S)S[C@@H]1Cc2ccccc2
7R4 SMILES CACTVS 3.385 O=C1NC(=S)S[CH]1Cc2ccccc2
7R4 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 c1ccc(cc1)C[C@@H]2C(=O)NC(=S)S2
7R4 SMILES "OpenEye OEToolkits" 2.0.6 c1ccc(cc1)CC2C(=O)NC(=S)S2
#
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
7R4 "SYSTEMATIC NAME" ACDLabs 12.01 (5R)-5-benzyl-2-sulfanylidene-1,3-thiazolidin-4-one
7R4 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 (5~{R})-5-(phenylmethyl)-2-sulfanylidene-1,3-thiazolidin-4-one
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
7R4 'Create component' 2016-11-30 RCSB
7R4 'Initial release' 2017-08-30 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
7R4 C9 C 4.299 -3.952 1
7R4 C8 C 5.598 -3.202 2
7R4 C10 C 3.000 -3.202 3
7R4 C7 C 5.598 -1.702 4
7R4 C11 C 3.000 -1.702 5
7R4 C6 C 4.299 -0.952 6
7R4 C2 C 5.755 2.790 7
7R4 C13 C 7.972 1.803 8
7R4 C3 C 5.598 1.298 9
7R4 C5 C 4.299 0.548 10
7R4 N12 N 7.222 3.102 11
7R4 O1 O 4.640 3.794 12
7R4 S14 S 9.464 1.646 13
7R4 S4 S 6.968 0.688 14
#
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
7R4 C11 C10 SINGLE NONE 1
7R4 C11 C6 DOUBLE NONE 2
7R4 C5 C6 SINGLE NONE 3
7R4 C3 C5 SINGLE BEGINDASH 4
7R4 C10 C9 DOUBLE NONE 5
7R4 C6 C7 SINGLE NONE 6
7R4 O1 C2 DOUBLE NONE 7
7R4 C9 C8 SINGLE NONE 8
7R4 C7 C8 DOUBLE NONE 9
7R4 C2 C3 SINGLE NONE 10
7R4 C2 N12 SINGLE NONE 11
7R4 C3 S4 SINGLE NONE 12
7R4 N12 C13 SINGLE NONE 13
7R4 S4 C13 SINGLE NONE 14
7R4 C13 S14 DOUBLE NONE 15
#
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
7R4 MurckoScaffold S1 scaffold 'O=C1NC(=S)S[C@@H]1Cc1ccccc1' InChI=1S/C10H9NOS2/c12-9-8(14-10(13)11-9)6-7-4-2-1-3-5-7/h1-5,8H,6H2,(H,11,12,13)/t8-/m1/s1 HEFVAMUJRPNDFW-MRVPVSSYSA-N
7R4 amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
7R4 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
7R4 C9 S1 1
7R4 C8 S1 1
7R4 C10 S1 1
7R4 C7 S1 1
7R4 C11 S1 1
7R4 C6 S1 1
7R4 C2 S1 1
7R4 C13 S1 1
7R4 C3 S1 1
7R4 C5 S1 1
7R4 N12 S1 1
7R4 O1 S1 1
7R4 S14 S1 1
7R4 S4 S1 1
7R4 N12 F1 1
7R4 C2 F1 1
7R4 O1 F1 1
7R4 C3 F1 1
7R4 C9 F2 1
7R4 C10 F2 1
7R4 C11 F2 1
7R4 C6 F2 1
7R4 C7 F2 1
7R4 C8 F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 7R4
_pdbe_chem_comp_rdkit_properties.exactmw 223.013
_pdbe_chem_comp_rdkit_properties.amw 223.322
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 2
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 1
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 2
_pdbe_chem_comp_rdkit_properties.NumHBD 1
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 14
_pdbe_chem_comp_rdkit_properties.NumAtoms 23
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 4
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 1
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.200
_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 104.781
_pdbe_chem_comp_rdkit_properties.tpsa 29.100
_pdbe_chem_comp_rdkit_properties.CrippenClogP 1.691
_pdbe_chem_comp_rdkit_properties.CrippenMR 62.000
_pdbe_chem_comp_rdkit_properties.chi0v 8.305
_pdbe_chem_comp_rdkit_properties.chi1v 4.738
_pdbe_chem_comp_rdkit_properties.chi2v 2.403
_pdbe_chem_comp_rdkit_properties.chi3v 2.403
_pdbe_chem_comp_rdkit_properties.chi4v 1.715
_pdbe_chem_comp_rdkit_properties.chi0n 15.672
_pdbe_chem_comp_rdkit_properties.chi1n 7.961
_pdbe_chem_comp_rdkit_properties.chi2n 1.315
_pdbe_chem_comp_rdkit_properties.chi3n 1.315
_pdbe_chem_comp_rdkit_properties.chi4n 0.792
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.870
_pdbe_chem_comp_rdkit_properties.kappa1 3.611
_pdbe_chem_comp_rdkit_properties.kappa2 4.106
_pdbe_chem_comp_rdkit_properties.kappa3 2.135
_pdbe_chem_comp_rdkit_properties.Phi 1.059
#
_pdbe_chem_comp_external_mappings.comp_id 7R4
_pdbe_chem_comp_external_mappings.source UniChem
_pdbe_chem_comp_external_mappings.resource PubChem
_pdbe_chem_comp_external_mappings.resource_id 129900144
#
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
7R4 C9 -3.443 0.978 -0.739 ETKDGv3 1
7R4 C8 -3.029 0.564 0.617 ETKDGv3 2
7R4 C10 -2.653 0.722 -1.788 ETKDGv3 3
7R4 C7 -1.864 -0.071 0.798 ETKDGv3 4
7R4 C11 -1.365 0.024 -1.593 ETKDGv3 5
7R4 C6 -0.983 -0.364 -0.362 ETKDGv3 6
7R4 C2 2.819 -0.767 -0.057 ETKDGv3 7
7R4 C13 3.000 0.522 1.879 ETKDGv3 8
7R4 C3 1.506 -0.052 -0.150 ETKDGv3 9
7R4 C5 0.340 -1.053 -0.150 ETKDGv3 10
7R4 N12 3.623 -0.450 1.063 ETKDGv3 11
7R4 O1 3.211 -1.578 -0.937 ETKDGv3 12
7R4 S14 3.849 1.374 2.985 ETKDGv3 13
7R4 S4 1.402 1.076 1.304 ETKDGv3 14
7R4 H1 -4.386 1.490 -0.881 ETKDGv3 15
7R4 H2 -3.669 0.776 1.463 ETKDGv3 16
7R4 H3 -2.954 1.026 -2.782 ETKDGv3 17
7R4 H4 -1.566 -0.368 1.795 ETKDGv3 18
7R4 H5 -0.734 -0.167 -2.452 ETKDGv3 19
7R4 H6 1.494 0.555 -1.081 ETKDGv3 20
7R4 H7 0.328 -1.614 0.810 ETKDGv3 21
7R4 H8 0.489 -1.801 -0.960 ETKDGv3 22
7R4 H9 4.586 -0.822 1.218 ETKDGv3 23
#