data_SWW
#
_chem_comp.id SWW
_chem_comp.name '(2~{S})-2-azanyl-3-(2-hydroxyethylsulfanyl)propanoic acid'
_chem_comp.type 'L-peptide linking'
_chem_comp.pdbx_type HETAIN
_chem_comp.formula 'C5 H11 N O3 S'
_chem_comp.mon_nstd_parent_comp_id SER
_chem_comp.pdbx_synonyms 'S-(2-hydroxyethyl)-D-cysteine'
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2020-12-02
_chem_comp.pdbx_modified_date 2024-09-27
_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 165.211
_chem_comp.one_letter_code S
_chem_comp.three_letter_code SWW
_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 7B3U
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBE
_chem_comp.pdbx_pcm Y
#
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
SWW N N N 0 1 N N N Y Y N -17.268 14.156 -1.863 -1.728 1.766 -0.064 N SWW 1
SWW CA CA C 0 1 N N S Y N N -16.985 13.701 -0.516 -1.670 0.373 0.401 CA SWW 2
SWW C C C 0 1 N N N Y N Y -15.864 12.634 -0.470 -2.905 -0.360 -0.055 C SWW 3
SWW O O O 0 1 N N N Y N Y -15.326 12.398 0.586 -3.559 0.071 -0.975 O SWW 4
SWW C05 C05 C 0 1 N N N N N N -16.598 14.876 0.406 -0.429 -0.307 -0.181 C05 SWW 5
SWW C07 C07 C 0 1 N N N N N N -19.115 16.393 0.440 2.404 -0.444 -0.307 C07 SWW 6
SWW C08 C08 C 0 1 N N N N N N -20.047 15.974 -0.702 3.752 0.111 0.159 C08 SWW 7
SWW O09 O09 O 0 1 N N N N N N -19.914 14.622 -1.056 4.809 -0.621 -0.465 O09 SWW 8
SWW S06 S06 S 0 1 N N N N N N -17.373 16.480 -0.035 1.062 0.484 0.485 S06 SWW 9
SWW OXT O1 O 0 1 N Y N Y N Y -15.554 12.006 -1.601 -3.278 -1.493 0.561 O1 SWW 10
SWW H H1 H 0 1 N N N Y Y N -17.996 14.841 -1.838 -0.943 2.296 0.283 H1 SWW 11
SWW H2 H041 H 0 0 N Y N Y Y N -16.443 14.560 -2.258 -1.777 1.809 -1.071 H041 SWW 12
SWW HA H031 H 0 0 N N N Y N N -17.894 13.241 -0.102 -1.618 0.355 1.489 H031 SWW 13
SWW H052 H052 H 0 0 N N N N N N -16.899 14.620 1.433 -0.433 -1.362 0.091 H052 SWW 14
SWW H051 H051 H 0 0 N N N N N N -15.506 15.000 0.364 -0.437 -0.211 -1.267 H051 SWW 15
SWW H072 H072 H 0 0 N N N N N N -19.427 17.386 0.796 2.325 -0.345 -1.390 H072 SWW 16
SWW H071 H071 H 0 0 N N N N N N -19.216 15.662 1.256 2.330 -1.496 -0.033 H071 SWW 17
SWW H081 H081 H 0 0 N N N N N N -19.819 16.591 -1.584 3.826 1.163 -0.116 H081 SWW 18
SWW H082 H082 H 0 0 N N N N N N -21.086 16.153 -0.389 3.831 0.011 1.241 H082 SWW 19
SWW H091 H091 H 0 0 N N N N N N -20.513 14.420 -1.765 5.694 -0.322 -0.215 H091 SWW 20
SWW HXT H2 H 0 1 N Y N Y N Y -14.867 11.371 -1.433 -4.077 -1.928 0.233 H2 SWW 21
#
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
SWW N CA SING N N 1
SWW O09 C08 SING N N 2
SWW C08 C07 SING N N 3
SWW CA C SING N N 4
SWW CA C05 SING N N 5
SWW C O DOUB N N 6
SWW S06 C05 SING N N 7
SWW S06 C07 SING N N 8
SWW C OXT SING N N 9
SWW N H SING N N 10
SWW N H2 SING N N 11
SWW CA HA SING N N 12
SWW C05 H052 SING N N 13
SWW C05 H051 SING N N 14
SWW C07 H072 SING N N 15
SWW C07 H071 SING N N 16
SWW C08 H081 SING N N 17
SWW C08 H082 SING N N 18
SWW O09 H091 SING N N 19
SWW OXT HXT SING N N 20
#
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
SWW InChI InChI 1.03 'InChI=1S/C5H11NO3S/c6-4(5(8)9)3-10-2-1-7/h4,7H,1-3,6H2,(H,8,9)/t4-/m1/s1'
SWW InChIKey InChI 1.03 MWFRVMDVLYIXJF-SCSAIBSYSA-N
SWW SMILES_CANONICAL CACTVS 3.385 'N[C@H](CSCCO)C(O)=O'
SWW SMILES CACTVS 3.385 'N[CH](CSCCO)C(O)=O'
SWW SMILES_CANONICAL 'OpenEye OEToolkits' 2.0.7 'C(CSC[C@H](C(=O)O)N)O'
SWW SMILES 'OpenEye OEToolkits' 2.0.7 'C(CSCC(C(=O)O)N)O'
#
_pdbx_chem_comp_identifier.comp_id SWW
_pdbx_chem_comp_identifier.type 'SYSTEMATIC NAME'
_pdbx_chem_comp_identifier.program 'OpenEye OEToolkits'
_pdbx_chem_comp_identifier.program_version 2.0.7
_pdbx_chem_comp_identifier.identifier '(2~{S})-2-azanyl-3-(2-hydroxyethylsulfanyl)propanoic acid'
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id SWW
_pdbx_chem_comp_synonyms.name 'S-(2-hydroxyethyl)-D-cysteine'
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
SWW 'Create component' 2020-12-02 PDBE
SWW 'Modify linking type' 2020-12-02 PDBE
SWW 'Initial release' 2022-01-12 RCSB
SWW 'Modify backbone' 2023-11-03 PDBE
SWW 'Modify PCM' 2024-09-27 PDBE
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id SWW
_pdbx_chem_comp_pcm.modified_residue_id ?
_pdbx_chem_comp_pcm.type None
_pdbx_chem_comp_pcm.category 'Non-standard residue'
_pdbx_chem_comp_pcm.position 'Amino-acid side chain'
_pdbx_chem_comp_pcm.polypeptide_position 'Any position'
_pdbx_chem_comp_pcm.comp_id_linking_atom ?
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom ?
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ?
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ?
#
_pdbe_chem_comp_synonyms.comp_id SWW
_pdbe_chem_comp_synonyms.name S-(2-hydroxyethyl)-D-cysteine
_pdbe_chem_comp_synonyms.provenance wwPDB
_pdbe_chem_comp_synonyms.type ?
#
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
SWW N N 5.104 2.857 1
SWW CA C 6.404 2.107 2
SWW C C 7.702 2.857 3
SWW O O 9.002 2.107 4
SWW C05 C 6.404 0.608 5
SWW C07 C 5.104 -1.643 6
SWW C08 C 3.805 -2.393 7
SWW O09 O 3.805 -3.893 8
SWW S06 S 5.104 -0.142 9
SWW OXT O 7.702 4.357 10
#
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
SWW CA N SINGLE BEGINWEDGE 1
SWW O09 C08 SINGLE NONE 2
SWW C08 C07 SINGLE NONE 3
SWW CA C SINGLE NONE 4
SWW CA C05 SINGLE NONE 5
SWW C O DOUBLE NONE 6
SWW S06 C05 SINGLE NONE 7
SWW S06 C07 SINGLE NONE 8
SWW C OXT SINGLE NONE 9
#
_pdbe_chem_comp_substructure.comp_id SWW
_pdbe_chem_comp_substructure.substructure_name peptide
_pdbe_chem_comp_substructure.id F1
_pdbe_chem_comp_substructure.substructure_type fragment
_pdbe_chem_comp_substructure.substructure_smiles NCC=O
_pdbe_chem_comp_substructure.substructure_inchis InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2
_pdbe_chem_comp_substructure.substructure_inchikeys LYIIBVSRGJSHAV-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
SWW O F1 1
SWW C F1 1
SWW CA F1 1
SWW N F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id SWW
_pdbe_chem_comp_rdkit_properties.exactmw 165.046
_pdbe_chem_comp_rdkit_properties.amw 165.214
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 4
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 4
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 7
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 5
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 10
_pdbe_chem_comp_rdkit_properties.NumAtoms 21
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 5
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.800
_pdbe_chem_comp_rdkit_properties.NumRings 0
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_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 1
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 79.156
_pdbe_chem_comp_rdkit_properties.tpsa 83.550
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.876
_pdbe_chem_comp_rdkit_properties.CrippenMR 40.022
_pdbe_chem_comp_rdkit_properties.chi0v 5.397
_pdbe_chem_comp_rdkit_properties.chi1v 2.811
_pdbe_chem_comp_rdkit_properties.chi2v 0.915
_pdbe_chem_comp_rdkit_properties.chi3v 0.915
_pdbe_chem_comp_rdkit_properties.chi4v 0.409
_pdbe_chem_comp_rdkit_properties.chi0n 15.580
_pdbe_chem_comp_rdkit_properties.chi1n 7.205
_pdbe_chem_comp_rdkit_properties.chi2n 0.434
_pdbe_chem_comp_rdkit_properties.chi3n 0.434
_pdbe_chem_comp_rdkit_properties.chi4n 0.136
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.260
_pdbe_chem_comp_rdkit_properties.kappa1 1.909
_pdbe_chem_comp_rdkit_properties.kappa2 5.519
_pdbe_chem_comp_rdkit_properties.kappa3 4.603
_pdbe_chem_comp_rdkit_properties.Phi 1.054
#
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
SWW UniChem ZINC ZINC000006753336
SWW UniChem BRENDA 97088
SWW UniChem ChemicalBook CB61454349
SWW UniChem 'EPA CompTox Dashboard' DTXSID50469562
SWW UniChem 'PubChem TPHARMA' 16725291
SWW UniChem PubChem 11622387
SWW UniChem PubChem 40640040
SWW UniChem Nikkaji J2.240.369I
#
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
SWW N -2.762 1.067 -0.607 ETKDGv3 1
SWW CA -1.998 0.351 0.420 ETKDGv3 2
SWW C -2.168 -1.137 0.278 ETKDGv3 3
SWW O -2.307 -1.664 -0.859 ETKDGv3 4
SWW C05 -0.509 0.752 0.421 ETKDGv3 5
SWW C07 2.014 0.836 -0.605 ETKDGv3 6
SWW C08 2.761 -0.280 0.120 ETKDGv3 7
SWW O09 2.951 -1.368 -0.742 ETKDGv3 8
SWW S06 0.350 0.285 -1.130 ETKDGv3 9
SWW OXT -2.123 -1.943 1.411 ETKDGv3 10
SWW H -2.348 0.895 -1.551 ETKDGv3 11
SWW H2 -2.693 2.094 -0.421 ETKDGv3 12
SWW HA -2.417 0.635 1.410 ETKDGv3 13
SWW H052 -0.008 0.263 1.283 ETKDGv3 14
SWW H051 -0.430 1.852 0.562 ETKDGv3 15
SWW H072 1.946 1.732 0.048 ETKDGv3 16
SWW H071 2.587 1.125 -1.512 ETKDGv3 17
SWW H081 2.189 -0.601 1.017 ETKDGv3 18
SWW H082 3.749 0.108 0.453 ETKDGv3 19
SWW H091 3.435 -2.055 -0.215 ETKDGv3 20
SWW HXT -2.217 -2.949 1.337 ETKDGv3 21
#