data_W8A
#
_chem_comp.id W8A
_chem_comp.name "{[(2S)-1-oxo-1-(2-oxoimidazolidin-1-yl)propan-2-yl]sulfanyl}acetic acid"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C8 H12 N2 O4 S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2020-09-29
_chem_comp.pdbx_modified_date 2020-12-11
_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 232.257
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code W8A
_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 5RVE
_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
W8A C01 C1 C 0 1 N N N N N N -44.097 -28.223 1.294 -0.040 -0.867 -1.648 C01 W8A 1
W8A C02 C2 C 0 1 N N S N N N -44.928 -29.432 1.763 -0.032 -0.213 -0.265 C02 W8A 2
W8A C04 C3 C 0 1 N N N N N N -44.647 -32.470 1.502 -2.809 -0.724 0.033 C04 W8A 3
W8A C05 C4 C 0 1 N N N N N N -43.513 -32.569 2.504 -4.193 -0.171 0.257 C05 W8A 4
W8A C08 C5 C 0 1 N N N N N N -46.396 -29.193 2.073 1.096 0.783 -0.187 C08 W8A 5
W8A C11 C6 C 0 1 N N N N N N -48.184 -29.042 3.816 3.540 1.224 0.142 C11 W8A 6
W8A C12 C7 C 0 1 N N N N N N -48.136 -29.051 5.307 4.695 0.239 0.409 C12 W8A 7
W8A C14 C8 C 0 1 N N N N N N -45.979 -29.250 4.514 2.725 -0.916 0.218 C14 W8A 8
W8A N10 N1 N 0 1 N N N N N N -46.837 -29.191 3.387 2.355 0.359 0.043 N10 W8A 9
W8A N13 N2 N 0 1 N N N N N N -46.764 -29.170 5.682 4.037 -1.076 0.432 N13 W8A 10
W8A O06 O1 O 0 1 N N N N N N -43.277 -33.756 2.585 -4.354 1.019 0.388 O06 W8A 11
W8A O07 O2 O 0 1 N N N N N N -42.941 -31.691 3.250 -5.246 -1.001 0.310 O07 W8A 12
W8A O09 O3 O 0 1 N N N N N N -47.267 -29.104 1.317 0.871 1.966 -0.331 O09 W8A 13
W8A O15 O4 O 0 1 N N N N N N -44.828 -29.318 4.469 1.940 -1.844 0.185 O15 W8A 14
W8A S03 S1 S 0 1 N N N N N N -44.725 -30.903 0.648 -1.610 0.637 0.011 S03 W8A 15
W8A H013 H1 H 0 0 N N N N N N -44.251 -27.381 1.985 0.909 -1.378 -1.814 H013 W8A 16
W8A H012 H2 H 0 0 N N N N N N -43.031 -28.494 1.279 -0.855 -1.588 -1.705 H012 W8A 17
W8A H011 H3 H 0 0 N N N N N N -44.415 -27.930 0.283 -0.178 -0.101 -2.411 H011 W8A 18
W8A H021 H4 H 0 0 N N N N N N -44.468 -29.767 2.704 0.106 -0.979 0.498 H021 W8A 19
W8A H041 H5 H 0 0 N N N N N N -45.596 -32.620 2.037 -2.559 -1.415 0.838 H041 W8A 20
W8A H042 H6 H 0 0 N N N N N N -44.518 -33.266 0.754 -2.778 -1.251 -0.921 H042 W8A 21
W8A H111 H7 H 0 0 N N N N N N -48.600 -28.091 3.451 3.435 1.924 0.972 H111 W8A 22
W8A H112 H8 H 0 0 N N N N N N -48.799 -29.876 3.447 3.704 1.761 -0.792 H112 W8A 23
W8A H122 H9 H 0 0 N N N N N N -48.556 -28.115 5.704 5.430 0.285 -0.394 H122 W8A 24
W8A H121 H10 H 0 0 N N N N N N -48.709 -29.905 5.698 5.163 0.449 1.371 H121 W8A 25
W8A H131 H11 H 0 0 N N N N N N -46.417 -29.193 6.619 4.483 -1.925 0.579 H131 W8A 26
W8A H1 H12 H 0 1 N N N N N N -42.335 -32.123 3.841 -6.114 -0.600 0.455 H1 W8A 27
#
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
W8A S03 C04 SING N N 1
W8A S03 C02 SING N N 2
W8A C01 C02 SING N N 3
W8A O09 C08 DOUB N N 4
W8A C04 C05 SING N N 5
W8A C02 C08 SING N N 6
W8A C08 N10 SING N N 7
W8A C05 O06 DOUB N N 8
W8A C05 O07 SING N N 9
W8A N10 C11 SING N N 10
W8A N10 C14 SING N N 11
W8A C11 C12 SING N N 12
W8A O15 C14 DOUB N N 13
W8A C14 N13 SING N N 14
W8A C12 N13 SING N N 15
W8A C01 H013 SING N N 16
W8A C01 H012 SING N N 17
W8A C01 H011 SING N N 18
W8A C02 H021 SING N N 19
W8A C04 H041 SING N N 20
W8A C04 H042 SING N N 21
W8A C11 H111 SING N N 22
W8A C11 H112 SING N N 23
W8A C12 H122 SING N N 24
W8A C12 H121 SING N N 25
W8A N13 H131 SING N N 26
W8A O07 H1 SING N N 27
#
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
W8A SMILES ACDLabs 12.01 CC(C(N1CCNC1=O)=O)SCC(=O)O
W8A InChI InChI 1.03 InChI=1S/C8H12N2O4S/c1-5(15-4-6(11)12)7(13)10-3-2-9-8(10)14/h5H,2-4H2,1H3,(H,9,14)(H,11,12)/t5-/m0/s1
W8A InChIKey InChI 1.03 VUVWCZPJVQECKW-YFKPBYRVSA-N
W8A SMILES_CANONICAL CACTVS 3.385 C[C@H](SCC(O)=O)C(=O)N1CCNC1=O
W8A SMILES CACTVS 3.385 C[CH](SCC(O)=O)C(=O)N1CCNC1=O
W8A SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 C[C@@H](C(=O)N1CCNC1=O)SCC(=O)O
W8A SMILES "OpenEye OEToolkits" 2.0.7 CC(C(=O)N1CCNC1=O)SCC(=O)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
W8A "SYSTEMATIC NAME" ACDLabs 12.01 "{[(2S)-1-oxo-1-(2-oxoimidazolidin-1-yl)propan-2-yl]sulfanyl}acetic acid"
W8A "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "2-[(2~{S})-1-oxidanylidene-1-(2-oxidanylideneimidazolidin-1-yl)propan-2-yl]sulfanylethanoic acid"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
W8A 'Create component' 2020-09-29 RCSB
W8A 'Initial release' 2020-12-16 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
W8A C01 C 4.299 0.810 1
W8A C02 C 5.598 0.060 2
W8A C04 C 4.299 -2.190 3
W8A C05 C 4.299 -3.690 4
W8A C08 C 6.897 0.810 5
W8A C11 C 5.684 3.191 6
W8A C12 C 6.147 4.618 7
W8A C14 C 8.111 3.191 8
W8A N10 N 6.897 2.310 9
W8A N13 N 7.647 4.618 10
W8A O06 O 3.000 -4.440 11
W8A O07 O 5.598 -4.440 12
W8A O09 O 8.196 0.060 13
W8A O15 O 9.537 2.728 14
W8A S03 S 5.598 -1.440 15
#
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
W8A S03 C04 SINGLE NONE 1
W8A S03 C02 SINGLE NONE 2
W8A C02 C01 SINGLE BEGINWEDGE 3
W8A O09 C08 DOUBLE NONE 4
W8A C04 C05 SINGLE NONE 5
W8A C02 C08 SINGLE NONE 6
W8A C08 N10 SINGLE NONE 7
W8A C05 O06 DOUBLE NONE 8
W8A C05 O07 SINGLE NONE 9
W8A N10 C11 SINGLE NONE 10
W8A N10 C14 SINGLE NONE 11
W8A C11 C12 SINGLE NONE 12
W8A O15 C14 DOUBLE NONE 13
W8A C14 N13 SINGLE NONE 14
W8A C12 N13 SINGLE 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
W8A MurckoScaffold S1 scaffold O=C1NCCN1 InChI=1S/C3H6N2O/c6-3-4-1-2-5-3/h1-2H2,(H2,4,5,6) YAMHXTCMCPHKLN-UHFFFAOYSA-N
W8A amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-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
W8A C11 S1 1
W8A C12 S1 1
W8A C14 S1 1
W8A N10 S1 1
W8A N13 S1 1
W8A O15 S1 1
W8A N10 F1 1
W8A C08 F1 1
W8A O09 F1 1
W8A C02 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id W8A
_pdbe_chem_comp_rdkit_properties.exactmw 232.052
_pdbe_chem_comp_rdkit_properties.amw 232.261
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 6
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 2
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 5
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 5
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 15
_pdbe_chem_comp_rdkit_properties.NumAtoms 27
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 7
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 3
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.625
_pdbe_chem_comp_rdkit_properties.NumRings 1
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_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 108.004
_pdbe_chem_comp_rdkit_properties.tpsa 86.710
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.256
_pdbe_chem_comp_rdkit_properties.CrippenMR 54.668
_pdbe_chem_comp_rdkit_properties.chi0v 7.752
_pdbe_chem_comp_rdkit_properties.chi1v 4.159
_pdbe_chem_comp_rdkit_properties.chi2v 1.786
_pdbe_chem_comp_rdkit_properties.chi3v 1.786
_pdbe_chem_comp_rdkit_properties.chi4v 0.960
_pdbe_chem_comp_rdkit_properties.chi0n 18.936
_pdbe_chem_comp_rdkit_properties.chi1n 9.198
_pdbe_chem_comp_rdkit_properties.chi2n 1.138
_pdbe_chem_comp_rdkit_properties.chi3n 1.138
_pdbe_chem_comp_rdkit_properties.chi4n 0.596
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.240
_pdbe_chem_comp_rdkit_properties.kappa1 3.376
_pdbe_chem_comp_rdkit_properties.kappa2 5.014
_pdbe_chem_comp_rdkit_properties.kappa3 3.120
_pdbe_chem_comp_rdkit_properties.Phi 1.129
#
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
W8A UniChem PDBe W8A
W8A UniChem PubChem 155289181
#
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
W8A C01 1.289 -1.513 1.537 ETKDGv3 1
W8A C02 1.021 -0.707 0.264 ETKDGv3 2
W8A C04 2.922 1.286 0.313 ETKDGv3 3
W8A C05 3.224 1.375 -1.147 ETKDGv3 4
W8A C08 -0.298 -1.098 -0.362 ETKDGv3 5
W8A C11 -2.630 -0.342 -1.087 ETKDGv3 6
W8A C12 -3.776 0.434 -0.393 ETKDGv3 7
W8A C14 -2.004 0.194 1.080 ETKDGv3 8
W8A N10 -1.535 -0.397 -0.120 ETKDGv3 9
W8A N13 -3.310 0.704 0.958 ETKDGv3 10
W8A O06 2.911 2.410 -1.794 ETKDGv3 11
W8A O07 3.834 0.307 -1.798 ETKDGv3 12
W8A O09 -0.302 -2.069 -1.167 ETKDGv3 13
W8A O15 -1.358 0.227 2.159 ETKDGv3 14
W8A S03 1.123 1.101 0.577 ETKDGv3 15
W8A H013 1.278 -2.600 1.307 ETKDGv3 16
W8A H012 0.530 -1.312 2.318 ETKDGv3 17
W8A H011 2.288 -1.260 1.949 ETKDGv3 18
W8A H021 1.813 -0.977 -0.466 ETKDGv3 19
W8A H041 3.480 0.444 0.772 ETKDGv3 20
W8A H042 3.255 2.222 0.808 ETKDGv3 21
W8A H111 -2.298 0.186 -2.007 ETKDGv3 22
W8A H112 -2.963 -1.371 -1.342 ETKDGv3 23
W8A H122 -4.703 -0.178 -0.357 ETKDGv3 24
W8A H121 -3.977 1.393 -0.918 ETKDGv3 25
W8A H131 -3.851 1.189 1.707 ETKDGv3 26
W8A H1 4.036 0.350 -2.789 ETKDGv3 27
#