data_WD8
#
_chem_comp.id WD8
_chem_comp.name "methyl N-(propan-2-yl)-N-(thiophene-3-carbonyl)glycinate"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C11 H15 N O3 S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2022-09-02
_chem_comp.pdbx_modified_date 2022-10-28
_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 241.307
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code WD8
_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 7FP1
_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
WD8 C7 C1 C 0 1 Y N N N N N 28.774 16.745 39.052 1.451 0.790 0.171 C7 WD8 1
WD8 C8 C2 C 0 1 Y N N N N N 27.394 17.028 38.971 2.683 1.494 -0.095 C8 WD8 2
WD8 C9 C3 C 0 1 Y N N N N N 26.799 16.352 37.991 3.717 0.682 -0.283 C9 WD8 3
WD8 O1 O1 O 0 1 N N N N N N 29.133 13.964 43.041 -1.270 -2.640 -0.616 O1 WD8 4
WD8 C1 C4 C 0 1 N N N N N N 30.603 17.143 42.318 -2.221 1.729 -0.002 C1 WD8 5
WD8 C5 C5 C 0 1 N N N N N N 30.401 13.391 42.788 -1.593 -3.731 0.286 C5 WD8 6
WD8 C6 C6 C 0 1 N N N N N N 29.588 17.372 40.094 0.166 1.466 0.413 C6 WD8 7
WD8 C4 C7 C 0 1 N N N N N N 28.620 14.932 42.252 -1.247 -1.404 -0.094 C4 WD8 8
WD8 C3 C8 C 0 1 N N N N N N 29.514 15.260 41.158 -0.919 -0.222 -0.969 C3 WD8 9
WD8 C2 C9 C 0 1 N N N N N N 31.946 16.423 42.530 -3.285 0.780 0.551 C2 WD8 10
WD8 O2 O2 O 0 1 N N N N N N 30.063 18.469 39.957 0.119 2.441 1.139 O2 WD8 11
WD8 C10 C10 C 0 1 Y N N N N N 29.177 15.865 38.127 1.598 -0.562 0.169 C10 WD8 12
WD8 S S1 S 0 1 Y N N N N N 27.853 15.411 37.190 3.217 -0.995 -0.141 S WD8 13
WD8 N N1 N 0 1 N N N N N N 29.865 16.647 41.191 -0.959 1.004 -0.169 N WD8 14
WD8 C C11 C 0 1 N N N N N N 29.720 17.221 43.553 -2.678 2.276 -1.355 C WD8 15
WD8 O O3 O 0 1 N N N N N N 27.567 15.435 42.483 -1.488 -1.239 1.079 O WD8 16
WD8 H1 H1 H 0 1 N N N N N N 26.880 17.714 39.628 2.757 2.571 -0.137 H1 WD8 17
WD8 H2 H2 H 0 1 N N N N N N 25.747 16.421 37.758 4.724 1.008 -0.495 H2 WD8 18
WD8 H3 H3 H 0 1 N N N N N N 30.867 18.184 42.081 -2.075 2.556 0.694 H3 WD8 19
WD8 H4 H4 H 0 1 N N N N N N 30.618 12.628 43.550 -0.859 -3.767 1.091 H4 WD8 20
WD8 H5 H5 H 0 1 N N N N N N 30.400 12.924 41.792 -2.586 -3.572 0.707 H5 WD8 21
WD8 H6 H6 H 0 1 N N N N N N 31.172 14.175 42.825 -1.577 -4.673 -0.262 H6 WD8 22
WD8 H7 H7 H 0 1 N N N N N N 29.014 15.036 40.204 0.078 -0.348 -1.392 H7 WD8 23
WD8 H8 H8 H 0 1 N N N N N N 30.428 14.654 41.244 -1.649 -0.154 -1.776 H8 WD8 24
WD8 H9 H9 H 0 1 N N N N N N 32.457 16.850 43.405 -3.431 -0.047 -0.144 H9 WD8 25
WD8 H10 H10 H 0 1 N N N N N N 31.765 15.351 42.698 -2.959 0.390 1.516 H10 WD8 26
WD8 H11 H11 H 0 1 N N N N N N 32.576 16.553 41.638 -4.224 1.319 0.676 H11 WD8 27
WD8 H12 H12 H 0 1 N N N N N N 30.187 15.505 38.002 0.798 -1.266 0.343 H12 WD8 28
WD8 H13 H13 H 0 1 N N N N N N 30.307 17.603 44.401 -3.617 2.815 -1.231 H13 WD8 29
WD8 H14 H14 H 0 1 N N N N N N 28.875 17.898 43.358 -1.920 2.953 -1.749 H14 WD8 30
WD8 H15 H15 H 0 1 N N N N N N 29.338 16.218 43.794 -2.824 1.449 -2.051 H15 WD8 31
#
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
WD8 S C9 SING Y N 1
WD8 S C10 SING Y N 2
WD8 C9 C8 DOUB Y N 3
WD8 C10 C7 DOUB Y N 4
WD8 C8 C7 SING Y N 5
WD8 C7 C6 SING N N 6
WD8 O2 C6 DOUB N N 7
WD8 C6 N SING N N 8
WD8 C3 N SING N N 9
WD8 C3 C4 SING N N 10
WD8 N C1 SING N N 11
WD8 C4 O DOUB N N 12
WD8 C4 O1 SING N N 13
WD8 C1 C2 SING N N 14
WD8 C1 C SING N N 15
WD8 C5 O1 SING N N 16
WD8 C8 H1 SING N N 17
WD8 C9 H2 SING N N 18
WD8 C1 H3 SING N N 19
WD8 C5 H4 SING N N 20
WD8 C5 H5 SING N N 21
WD8 C5 H6 SING N N 22
WD8 C3 H7 SING N N 23
WD8 C3 H8 SING N N 24
WD8 C2 H9 SING N N 25
WD8 C2 H10 SING N N 26
WD8 C2 H11 SING N N 27
WD8 C10 H12 SING N N 28
WD8 C H13 SING N N 29
WD8 C H14 SING N N 30
WD8 C H15 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
WD8 SMILES ACDLabs 12.01 O=C(N(CC(=O)OC)C(C)C)c1ccsc1
WD8 InChI InChI 1.06 InChI=1S/C11H15NO3S/c1-8(2)12(6-10(13)15-3)11(14)9-4-5-16-7-9/h4-5,7-8H,6H2,1-3H3
WD8 InChIKey InChI 1.06 AEHZWZVCFANNEB-UHFFFAOYSA-N
WD8 SMILES_CANONICAL CACTVS 3.385 COC(=O)CN(C(C)C)C(=O)c1cscc1
WD8 SMILES CACTVS 3.385 COC(=O)CN(C(C)C)C(=O)c1cscc1
WD8 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 CC(C)N(CC(=O)OC)C(=O)c1ccsc1
WD8 SMILES "OpenEye OEToolkits" 2.0.7 CC(C)N(CC(=O)OC)C(=O)c1ccsc1
#
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
WD8 "SYSTEMATIC NAME" ACDLabs 12.01 "methyl N-(propan-2-yl)-N-(thiophene-3-carbonyl)glycinate"
WD8 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "methyl 2-[propan-2-yl(thiophen-3-ylcarbonyl)amino]ethanoate"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
WD8 'Create component' 2022-09-02 RCSB
WD8 'Initial release' 2022-11-02 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
WD8 C7 C 4.299 -2.221 1
WD8 C8 C 5.513 -3.103 2
WD8 C9 C 5.049 -4.529 3
WD8 O1 O 6.897 3.779 4
WD8 C1 C 6.897 -0.721 5
WD8 C5 C 8.196 4.529 6
WD8 C6 C 4.299 -0.721 7
WD8 C4 C 6.897 2.279 8
WD8 C3 C 5.598 1.529 9
WD8 C2 C 8.196 0.029 10
WD8 O2 O 3.000 0.029 11
WD8 C10 C 3.086 -3.103 12
WD8 S S 3.549 -4.529 13
WD8 N N 5.598 0.029 14
WD8 C C 6.897 -2.221 15
WD8 O O 8.196 1.529 16
#
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
WD8 S C9 SINGLE NONE 1
WD8 S C10 SINGLE NONE 2
WD8 C9 C8 DOUBLE NONE 3
WD8 C10 C7 DOUBLE NONE 4
WD8 C8 C7 SINGLE NONE 5
WD8 C7 C6 SINGLE NONE 6
WD8 O2 C6 DOUBLE NONE 7
WD8 C6 N SINGLE NONE 8
WD8 C3 N SINGLE NONE 9
WD8 C3 C4 SINGLE NONE 10
WD8 N C1 SINGLE NONE 11
WD8 C4 O DOUBLE NONE 12
WD8 C4 O1 SINGLE NONE 13
WD8 C1 C2 SINGLE NONE 14
WD8 C1 C SINGLE NONE 15
WD8 C5 O1 SINGLE NONE 16
#
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
WD8 MurckoScaffold S1 scaffold c1ccsc1 InChI=1S/C4H4S/c1-2-4-5-3-1/h1-4H YTPLMLYBLZKORZ-UHFFFAOYSA-N
WD8 amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
WD8 peptide F2 fragment NCC=O InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2 LYIIBVSRGJSHAV-UHFFFAOYSA-N
WD8 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
WD8 C7 S1 1
WD8 C8 S1 1
WD8 C9 S1 1
WD8 C10 S1 1
WD8 S S1 1
WD8 N F1 1
WD8 C6 F1 1
WD8 O2 F1 1
WD8 C7 F1 1
WD8 O F2 1
WD8 C4 F2 1
WD8 C3 F2 1
WD8 N F2 1
WD8 C9 F3 1
WD8 C8 F3 1
WD8 C7 F3 1
WD8 C10 F3 1
WD8 S F3 1
#
_pdbe_chem_comp_rdkit_properties.comp_id WD8
_pdbe_chem_comp_rdkit_properties.exactmw 241.077
_pdbe_chem_comp_rdkit_properties.amw 241.312
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 4
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 0
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 7
_pdbe_chem_comp_rdkit_properties.NumHBD 0
_pdbe_chem_comp_rdkit_properties.NumHBA 4
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 16
_pdbe_chem_comp_rdkit_properties.NumAtoms 31
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 5
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 1
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.455
_pdbe_chem_comp_rdkit_properties.NumRings 1
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 1
_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 119.897
_pdbe_chem_comp_rdkit_properties.tpsa 46.610
_pdbe_chem_comp_rdkit_properties.CrippenClogP 1.717
_pdbe_chem_comp_rdkit_properties.CrippenMR 62.242
_pdbe_chem_comp_rdkit_properties.chi0v 8.397
_pdbe_chem_comp_rdkit_properties.chi1v 4.462
_pdbe_chem_comp_rdkit_properties.chi2v 1.827
_pdbe_chem_comp_rdkit_properties.chi3v 1.827
_pdbe_chem_comp_rdkit_properties.chi4v 1.154
_pdbe_chem_comp_rdkit_properties.chi0n 22.580
_pdbe_chem_comp_rdkit_properties.chi1n 11.146
_pdbe_chem_comp_rdkit_properties.chi2n 1.317
_pdbe_chem_comp_rdkit_properties.chi3n 1.317
_pdbe_chem_comp_rdkit_properties.chi4n 0.710
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.360
_pdbe_chem_comp_rdkit_properties.kappa1 3.100
_pdbe_chem_comp_rdkit_properties.kappa2 5.650
_pdbe_chem_comp_rdkit_properties.kappa3 3.064
_pdbe_chem_comp_rdkit_properties.Phi 1.095
#
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
WD8 UniChem ZINC ZINC000047951765
WD8 UniChem PubChem 55028598
WD8 UniChem Mcule MCULE-3812665217
#
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
WD8 C7 -2.121 -0.803 0.842 ETKDGv3 1
WD8 C8 -2.820 -1.080 -0.439 ETKDGv3 2
WD8 C9 -3.837 -1.931 -0.338 ETKDGv3 3
WD8 O1 2.769 -0.739 0.118 ETKDGv3 4
WD8 C1 0.016 1.886 -0.528 ETKDGv3 5
WD8 C5 3.750 -1.312 0.973 ETKDGv3 6
WD8 C6 -0.981 0.128 0.956 ETKDGv3 7
WD8 C4 1.499 -1.297 -0.050 ETKDGv3 8
WD8 C3 0.503 -0.611 -0.931 ETKDGv3 9
WD8 C2 1.484 2.294 -0.368 ETKDGv3 10
WD8 O2 -0.706 0.646 2.073 ETKDGv3 11
WD8 C10 -2.643 -1.442 1.893 ETKDGv3 12
WD8 S -4.010 -2.442 1.355 ETKDGv3 13
WD8 N -0.181 0.463 -0.192 ETKDGv3 14
WD8 C -0.503 2.192 -1.937 ETKDGv3 15
WD8 O 1.171 -2.348 0.566 ETKDGv3 16
WD8 H1 -2.547 -0.618 -1.379 ETKDGv3 17
WD8 H2 -4.463 -2.244 -1.162 ETKDGv3 18
WD8 H3 -0.577 2.518 0.173 ETKDGv3 19
WD8 H4 4.670 -0.693 0.939 ETKDGv3 20
WD8 H5 3.996 -2.341 0.635 ETKDGv3 21
WD8 H6 3.374 -1.340 2.018 ETKDGv3 22
WD8 H7 -0.233 -1.348 -1.311 ETKDGv3 23
WD8 H8 1.039 -0.210 -1.815 ETKDGv3 24
WD8 H9 1.838 2.034 0.652 ETKDGv3 25
WD8 H10 2.128 1.783 -1.114 ETKDGv3 26
WD8 H11 1.589 3.392 -0.505 ETKDGv3 27
WD8 H12 -2.286 -1.367 2.912 ETKDGv3 28
WD8 H13 0.112 1.693 -2.715 ETKDGv3 29
WD8 H14 -1.554 1.848 -2.034 ETKDGv3 30
WD8 H15 -0.475 3.287 -2.121 ETKDGv3 31
#