data_GDY
#
_chem_comp.id GDY
_chem_comp.name (5Z)-5-({4-[2-(thiophen-2-yl)ethoxy]phenyl}methylidene)-1,3-thiazolidine-2,4-dione
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C16 H13 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 2018-05-18
_chem_comp.pdbx_modified_date 2019-05-17
_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 331.409
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code GDY
_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 6DGR
_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
GDY C10 C1 C 0 1 Y N N N N N 18.650 61.569 13.079 -0.379 1.135 -0.837 C10 GDY 1
GDY C13 C2 C 0 1 Y N N N N N 16.673 61.955 14.972 -0.468 -1.486 0.090 C13 GDY 2
GDY C15 C3 C 0 1 N N N N N N 18.281 61.644 16.924 -2.950 -1.476 -0.056 C15 GDY 3
GDY C17 C4 C 0 1 N N N N N N 18.821 63.038 19.137 -5.471 -1.218 0.085 C17 GDY 4
GDY C20 C5 C 0 1 N N N N N N 20.519 64.539 18.799 -6.000 1.004 0.339 C20 GDY 5
GDY C01 C6 C 0 1 Y N N N N N 18.228 66.995 8.518 7.419 -1.032 -0.527 C01 GDY 6
GDY C02 C7 C 0 1 Y N N N N N 18.194 65.587 8.817 6.320 -0.396 -1.079 C02 GDY 7
GDY C03 C8 C 0 1 Y N N N N N 16.987 65.161 9.401 5.637 0.379 -0.235 C03 GDY 8
GDY C05 C9 C 0 1 Y N N N N N 17.065 67.714 8.834 7.628 -0.774 0.765 C05 GDY 9
GDY C06 C10 C 0 1 N N N N N N 16.583 63.741 9.850 4.406 1.174 -0.589 C06 GDY 10
GDY C07 C11 C 0 1 N N N N N N 17.655 62.827 10.463 3.160 0.319 -0.349 C07 GDY 11
GDY C09 C12 C 0 1 Y N N N N N 17.350 61.812 12.647 0.795 0.457 -0.528 C09 GDY 12
GDY C11 C13 C 0 1 Y N N N N N 18.969 61.517 14.445 -1.597 0.515 -0.680 C11 GDY 13
GDY C12 C14 C 0 1 Y N N N N N 17.983 61.736 15.406 -1.653 -0.805 -0.214 C12 GDY 14
GDY C14 C15 C 0 1 Y N N N N N 16.362 62.002 13.609 0.745 -0.851 -0.060 C14 GDY 15
GDY C16 C16 C 0 1 N N N N N N 19.013 62.726 17.755 -4.084 -0.741 0.069 C16 GDY 16
GDY N19 N1 N 0 1 N N N N N N 19.638 64.003 19.649 -6.385 -0.272 0.222 N19 GDY 17
GDY O08 O1 O 0 1 N N N N N N 17.015 61.859 11.272 1.994 1.074 -0.685 O08 GDY 18
GDY O18 O2 O 0 1 N N N N N N 17.876 62.438 19.984 -5.760 -2.395 -0.025 O18 GDY 19
GDY O21 O3 O 0 1 N N N N N N 21.436 65.551 19.099 -6.726 1.971 0.470 O21 GDY 20
GDY S04 S1 S 0 1 Y N N N N N 16.018 66.559 9.491 6.390 0.329 1.353 S04 GDY 21
GDY S22 S2 S 0 1 N N N N N N 20.284 63.778 17.304 -4.230 1.018 0.253 S22 GDY 22
GDY H1 H1 H 0 1 N N N N N N 19.430 61.417 12.348 -0.335 2.153 -1.196 H1 GDY 23
GDY H2 H2 H 0 1 N N N N N N 15.888 62.090 15.701 -0.505 -2.503 0.449 H2 GDY 24
GDY H3 H3 H 0 1 N N N N N N 17.952 60.756 17.443 -3.001 -2.555 -0.040 H3 GDY 25
GDY H5 H5 H 0 1 N N N N N N 19.094 67.468 8.078 8.057 -1.691 -1.098 H5 GDY 26
GDY H6 H6 H 0 1 N N N N N N 19.018 64.920 8.612 6.038 -0.518 -2.114 H6 GDY 27
GDY H7 H7 H 0 1 N N N N N N 16.880 68.768 8.690 8.433 -1.179 1.359 H7 GDY 28
GDY H8 H8 H 0 1 N N N N N N 15.786 63.853 10.600 4.360 2.067 0.034 H8 GDY 29
GDY H9 H9 H 0 1 N N N N N N 16.184 63.223 8.965 4.451 1.465 -1.638 H9 GDY 30
GDY H10 H10 H 0 1 N N N N N N 18.217 62.326 9.661 3.207 -0.574 -0.973 H10 GDY 31
GDY H11 H11 H 0 1 N N N N N N 18.345 63.425 11.077 3.115 0.028 0.700 H11 GDY 32
GDY H12 H12 H 0 1 N N N N N N 19.983 61.306 14.753 -2.509 1.044 -0.915 H12 GDY 33
GDY H13 H13 H 0 1 N N N N N N 15.344 62.188 13.300 1.660 -1.374 0.177 H13 GDY 34
GDY H14 H14 H 0 1 N N N N N N 19.581 64.292 20.605 -7.327 -0.501 0.238 H14 GDY 35
#
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
GDY C01 C02 SING Y N 1
GDY C01 C05 DOUB Y N 2
GDY C02 C03 DOUB Y N 3
GDY C05 S04 SING Y N 4
GDY C03 S04 SING Y N 5
GDY C03 C06 SING N N 6
GDY C06 C07 SING N N 7
GDY C07 O08 SING N N 8
GDY O08 C09 SING N N 9
GDY C09 C10 DOUB Y N 10
GDY C09 C14 SING Y N 11
GDY C10 C11 SING Y N 12
GDY C14 C13 DOUB Y N 13
GDY C11 C12 DOUB Y N 14
GDY C13 C12 SING Y N 15
GDY C12 C15 SING N N 16
GDY C15 C16 DOUB N Z 17
GDY S22 C16 SING N N 18
GDY S22 C20 SING N N 19
GDY C16 C17 SING N N 20
GDY C20 O21 DOUB N N 21
GDY C20 N19 SING N N 22
GDY C17 N19 SING N N 23
GDY C17 O18 DOUB N N 24
GDY C10 H1 SING N N 25
GDY C13 H2 SING N N 26
GDY C15 H3 SING N N 27
GDY C01 H5 SING N N 28
GDY C02 H6 SING N N 29
GDY C05 H7 SING N N 30
GDY C06 H8 SING N N 31
GDY C06 H9 SING N N 32
GDY C07 H10 SING N N 33
GDY C07 H11 SING N N 34
GDY C11 H12 SING N N 35
GDY C14 H13 SING N N 36
GDY N19 H14 SING N N 37
#
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
GDY SMILES ACDLabs 12.01 c1cc(ccc1OCCc2cccs2)[C@H]=C3C(NC(=O)S3)=O
GDY InChI InChI 1.03 InChI=1S/C16H13NO3S2/c18-15-14(22-16(19)17-15)10-11-3-5-12(6-4-11)20-8-7-13-2-1-9-21-13/h1-6,9-10H,7-8H2,(H,17,18,19)
GDY InChIKey InChI 1.03 NTKWOUHXDKSPIX-UHFFFAOYSA-N
GDY SMILES_CANONICAL CACTVS 3.385 O=C1NC(=O)/C(S1)=C/c2ccc(OCCc3sccc3)cc2
GDY SMILES CACTVS 3.385 O=C1NC(=O)C(S1)=Cc2ccc(OCCc3sccc3)cc2
GDY SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 c1cc(sc1)CCOc2ccc(cc2)C=C3C(=O)NC(=O)S3
GDY SMILES "OpenEye OEToolkits" 2.0.6 c1cc(sc1)CCOc2ccc(cc2)C=C3C(=O)NC(=O)S3
#
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
GDY "SYSTEMATIC NAME" ACDLabs 12.01 (5Z)-5-({4-[2-(thiophen-2-yl)ethoxy]phenyl}methylidene)-1,3-thiazolidine-2,4-dione
GDY "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 5-[[4-(2-thiophen-2-ylethoxy)phenyl]methylidene]-1,3-thiazolidine-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
GDY 'Create component' 2018-05-18 RCSB
GDY 'Initial release' 2019-05-22 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
GDY C10 C 9.271 -0.050 1
GDY C13 C 6.673 1.450 2
GDY C15 C 7.972 3.700 3
GDY C17 C 9.428 5.942 4
GDY C20 C 11.645 4.955 5
GDY C01 C 3.000 -5.804 6
GDY C02 C 4.004 -4.690 7
GDY C03 C 5.374 -5.300 8
GDY C05 C 3.750 -7.103 9
GDY C06 C 6.673 -4.550 10
GDY C07 C 6.673 -3.050 11
GDY C09 C 7.972 -0.800 12
GDY C11 C 9.271 1.450 13
GDY C12 C 7.972 2.200 14
GDY C14 C 6.673 -0.050 15
GDY C16 C 9.271 4.450 16
GDY N19 N 10.895 6.254 17
GDY O08 O 7.972 -2.300 18
GDY O18 O 8.313 6.946 19
GDY O21 O 13.137 4.798 20
GDY S04 S 5.217 -6.792 21
GDY S22 S 10.641 3.840 22
#
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
GDY C01 C02 SINGLE NONE 1
GDY C01 C05 DOUBLE NONE 2
GDY C02 C03 DOUBLE NONE 3
GDY C05 S04 SINGLE NONE 4
GDY C03 S04 SINGLE NONE 5
GDY C03 C06 SINGLE NONE 6
GDY C06 C07 SINGLE NONE 7
GDY C07 O08 SINGLE NONE 8
GDY O08 C09 SINGLE NONE 9
GDY C09 C10 DOUBLE NONE 10
GDY C09 C14 SINGLE NONE 11
GDY C10 C11 SINGLE NONE 12
GDY C14 C13 DOUBLE NONE 13
GDY C11 C12 DOUBLE NONE 14
GDY C13 C12 SINGLE NONE 15
GDY C12 C15 SINGLE ENDUPRIGHT 16
GDY C15 C16 DOUBLE NONE 17
GDY S22 C16 SINGLE ENDUPRIGHT 18
GDY S22 C20 SINGLE NONE 19
GDY C16 C17 SINGLE ENDUPRIGHT 20
GDY C20 O21 DOUBLE NONE 21
GDY C20 N19 SINGLE NONE 22
GDY C17 N19 SINGLE NONE 23
GDY C17 O18 DOUBLE NONE 24
#
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
GDY MurckoScaffold S1 scaffold O=C1NC(=O)/C(=C/c2ccc(OCCc3cccs3)cc2)S1 InChI=1S/C16H13NO3S2/c18-15-14(22-16(19)17-15)10-11-3-5-12(6-4-11)20-8-7-13-2-1-9-21-13/h1-6,9-10H,7-8H2,(H,17,18,19)/b14-10- NTKWOUHXDKSPIX-UVTDQMKNSA-N
GDY amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
GDY phenyl F2 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
GDY thiophen F3 fragment c1ccsc1 InChI=1S/C4H4S/c1-2-4-5-3-1/h1-4H YTPLMLYBLZKORZ-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
GDY C10 S1 1
GDY C13 S1 1
GDY C15 S1 1
GDY C17 S1 1
GDY C20 S1 1
GDY C01 S1 1
GDY C02 S1 1
GDY C03 S1 1
GDY C05 S1 1
GDY C06 S1 1
GDY C07 S1 1
GDY C09 S1 1
GDY C11 S1 1
GDY C12 S1 1
GDY C14 S1 1
GDY C16 S1 1
GDY N19 S1 1
GDY O08 S1 1
GDY O18 S1 1
GDY O21 S1 1
GDY S04 S1 1
GDY S22 S1 1
GDY N19 F1 1
GDY C17 F1 1
GDY O18 F1 1
GDY C16 F1 1
GDY C10 F2 1
GDY C09 F2 1
GDY C14 F2 1
GDY C13 F2 1
GDY C12 F2 1
GDY C11 F2 1
GDY C03 F3 1
GDY C02 F3 1
GDY C01 F3 1
GDY C05 F3 1
GDY S04 F3 1
#
_pdbe_chem_comp_rdkit_properties.comp_id GDY
_pdbe_chem_comp_rdkit_properties.exactmw 331.034
_pdbe_chem_comp_rdkit_properties.amw 331.418
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 4
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 1
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 5
_pdbe_chem_comp_rdkit_properties.NumHBD 1
_pdbe_chem_comp_rdkit_properties.NumHBA 5
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 22
_pdbe_chem_comp_rdkit_properties.NumAtoms 35
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 6
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 2
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.125
_pdbe_chem_comp_rdkit_properties.NumRings 3
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 2
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 1
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 1
_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 0
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 154.055
_pdbe_chem_comp_rdkit_properties.tpsa 55.400
_pdbe_chem_comp_rdkit_properties.CrippenClogP 3.122
_pdbe_chem_comp_rdkit_properties.CrippenMR 87.925
_pdbe_chem_comp_rdkit_properties.chi0v 12.121
_pdbe_chem_comp_rdkit_properties.chi1v 7.213
_pdbe_chem_comp_rdkit_properties.chi2v 3.474
_pdbe_chem_comp_rdkit_properties.chi3v 3.474
_pdbe_chem_comp_rdkit_properties.chi4v 2.247
_pdbe_chem_comp_rdkit_properties.chi0n 23.488
_pdbe_chem_comp_rdkit_properties.chi1n 12.027
_pdbe_chem_comp_rdkit_properties.chi2n 2.115
_pdbe_chem_comp_rdkit_properties.chi3n 2.115
_pdbe_chem_comp_rdkit_properties.chi4n 1.259
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.050
_pdbe_chem_comp_rdkit_properties.kappa1 5.865
_pdbe_chem_comp_rdkit_properties.kappa2 6.807
_pdbe_chem_comp_rdkit_properties.kappa3 3.777
_pdbe_chem_comp_rdkit_properties.Phi 1.815
#
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
GDY UniChem PDBe GDY
GDY UniChem eMolecules 32457215
GDY UniChem BindingDb 50378619
GDY UniChem 'Probes And Drugs' PD051110
GDY UniChem PubChem 53394148
#
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
GDY C10 -0.876 1.451 -0.706 ETKDGv3 1
GDY C13 -1.385 -1.273 -0.214 ETKDGv3 2
GDY C15 -3.870 -0.933 -0.655 ETKDGv3 3
GDY C17 -6.301 -0.981 -0.233 ETKDGv3 4
GDY C20 -6.737 0.807 1.191 ETKDGv3 5
GDY C01 6.930 -0.849 0.093 ETKDGv3 6
GDY C02 5.813 -0.109 -0.533 ETKDGv3 7
GDY C03 5.053 0.556 0.337 ETKDGv3 8
GDY C05 6.984 -0.745 1.419 ETKDGv3 9
GDY C06 3.816 1.326 -0.009 ETKDGv3 10
GDY C07 2.594 0.413 0.001 ETKDGv3 11
GDY C09 0.141 0.637 -0.394 ETKDGv3 12
GDY C11 -2.256 0.930 -0.795 ETKDGv3 13
GDY C12 -2.511 -0.365 -0.534 ETKDGv3 14
GDY C14 -0.134 -0.803 -0.141 ETKDGv3 15
GDY C16 -4.971 -0.380 -0.123 ETKDGv3 16
GDY N19 -7.298 -0.304 0.507 ETKDGv3 17
GDY O08 1.434 1.174 -0.320 ETKDGv3 18
GDY O18 -6.555 -2.009 -0.916 ETKDGv3 19
GDY O21 -7.434 1.551 1.929 ETKDGv3 20
GDY S04 5.649 0.283 1.991 ETKDGv3 21
GDY S22 -4.981 1.082 0.939 ETKDGv3 22
GDY H1 -0.693 2.500 -0.901 ETKDGv3 23
GDY H2 -1.573 -2.324 -0.030 ETKDGv3 24
GDY H3 -3.957 -1.890 -1.156 ETKDGv3 25
GDY H5 7.642 -1.432 -0.476 ETKDGv3 26
GDY H6 5.622 -0.119 -1.598 ETKDGv3 27
GDY H7 7.728 -1.221 2.044 ETKDGv3 28
GDY H8 3.676 2.140 0.734 ETKDGv3 29
GDY H9 3.929 1.790 -1.013 ETKDGv3 30
GDY H10 2.474 -0.037 1.011 ETKDGv3 31
GDY H11 2.728 -0.395 -0.752 ETKDGv3 32
GDY H12 -3.047 1.603 -1.098 ETKDGv3 33
GDY H13 0.669 -1.486 0.101 ETKDGv3 34
GDY H14 -8.301 -0.589 0.555 ETKDGv3 35
#