data_CSS
#
_chem_comp.id CSS
_chem_comp.name S-MERCAPTOCYSTEINE
_chem_comp.type 'L-PEPTIDE LINKING'
_chem_comp.pdbx_type ATOMP
_chem_comp.formula 'C3 H7 N O2 S2'
_chem_comp.mon_nstd_parent_comp_id CYS
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 1999-07-08
_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 153.223
_chem_comp.one_letter_code C
_chem_comp.three_letter_code CSS
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details ?
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code ?
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
_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
CSS N N N 0 1 N N N Y Y N 12.713 30.986 7.305 -1.818 -0.475 1.901 N CSS 1
CSS CA CA C 0 1 N N R Y N N 12.265 29.648 7.704 -0.739 -0.390 0.908 CA CSS 2
CSS CB CB C 0 1 N N N N N N 10.783 29.652 8.102 -0.998 0.794 -0.025 CB CSS 3
CSS SG SG S 0 1 N N N N N N 10.441 30.435 9.708 0.350 0.920 -1.231 SG CSS 4
CSS SD SD S 0 1 N N N N N N 10.674 28.919 11.032 -0.130 -0.642 -2.468 SD CSS 5
CSS C C C 0 1 N N N Y N Y 12.450 28.660 6.583 0.578 -0.196 1.612 C CSS 6
CSS O O O 0 1 N N N Y N Y 12.518 27.459 6.806 0.617 0.386 2.670 O CSS 7
CSS OXT OXT O 0 1 N Y N Y N Y 12.468 29.172 5.362 1.708 -0.669 1.064 OXT CSS 8
CSS H H H 0 1 N N N Y Y N 12.587 31.655 8.064 -1.871 0.427 2.350 H CSS 9
CSS H2 HN2 H 0 1 N Y N Y Y N 12.252 31.297 6.449 -2.678 -0.594 1.387 HN2 CSS 10
CSS HA HA H 0 1 N N N Y N N 12.886 29.348 8.579 -0.708 -1.311 0.325 HA CSS 11
CSS HB2 HB2 H 0 1 N N N N N N 10.165 30.121 7.300 -1.942 0.643 -0.550 HB2 CSS 12
CSS HB3 HB3 H 0 1 N N N N N N 10.370 28.616 8.078 -1.050 1.712 0.559 HB3 CSS 13
CSS HD HD H 0 1 N N N N N N 10.495 29.327 11.870 0.869 -0.548 -3.362 HD CSS 14
CSS HXT HXT H 0 1 N Y N Y N Y 12.584 28.548 4.654 2.554 -0.545 1.516 HXT CSS 15
#
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
CSS N CA SING N N 1
CSS N H SING N N 2
CSS N H2 SING N N 3
CSS CA CB SING N N 4
CSS CA C SING N N 5
CSS CA HA SING N N 6
CSS CB SG SING N N 7
CSS CB HB2 SING N N 8
CSS CB HB3 SING N N 9
CSS SG SD SING N N 10
CSS SD HD SING N N 11
CSS C O DOUB N N 12
CSS C OXT SING N N 13
CSS OXT HXT SING N N 14
#
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
CSS SMILES ACDLabs 10.04 'O=C(O)C(N)CSS'
CSS SMILES_CANONICAL CACTVS 3.341 'N[C@@H](CSS)C(O)=O'
CSS SMILES CACTVS 3.341 'N[CH](CSS)C(O)=O'
CSS SMILES_CANONICAL 'OpenEye OEToolkits' 1.5.0 'C([C@@H](C(=O)O)N)SS'
CSS SMILES 'OpenEye OEToolkits' 1.5.0 'C(C(C(=O)O)N)SS'
CSS InChI InChI 1.03 'InChI=1S/C3H7NO2S2/c4-2(1-8-7)3(5)6/h2,7H,1,4H2,(H,5,6)/t2-/m0/s1'
CSS InChIKey InChI 1.03 XBKONSCREBSMCS-REOHCLBHSA-N
#
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
CSS 'SYSTEMATIC NAME' ACDLabs 10.04 3-disulfanyl-L-alanine
CSS 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 1.5.0 '(2R)-2-amino-3-disulfanyl-propanoic 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
CSS 'Create component' 1999-07-08 RCSB
CSS 'Modify descriptor' 2011-06-04 RCSB
CSS 'Modify leaving atom flag' 2021-08-28 PDBE
CSS 'Modify backbone' 2023-11-03 PDBE
CSS 'Modify PCM' 2024-09-27 PDBE
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id CSS
_pdbx_chem_comp_pcm.modified_residue_id CYS
_pdbx_chem_comp_pcm.type Sulfhydration
_pdbx_chem_comp_pcm.category 'Named protein modification'
_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 PTM-0106
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ?
#
_pdbe_chem_comp_drugbank_details.comp_id CSS
_pdbe_chem_comp_drugbank_details.drugbank_id DB02761
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name S-Mercaptocysteine
_pdbe_chem_comp_drugbank_details.description ?
_pdbe_chem_comp_drugbank_details.cas_number 5652-32-4
_pdbe_chem_comp_drugbank_details.mechanism_of_action ?
#
_pdbe_chem_comp_drugbank_classification.comp_id CSS
_pdbe_chem_comp_drugbank_classification.drugbank_id DB02761
_pdbe_chem_comp_drugbank_classification.parent L-cysteine-S-conjugates
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class 'Carboxylic acids and derivatives'
_pdbe_chem_comp_drugbank_classification.superclass 'Organic acids and derivatives'
_pdbe_chem_comp_drugbank_classification.description
'This compound belongs to the class of organic compounds known as l-cysteine-s-conjugates. These are compounds containing L-cysteine where the thio-group is conjugated.'
#
loop_
_pdbe_chem_comp_drugbank_targets.comp_id
_pdbe_chem_comp_drugbank_targets.drugbank_id
_pdbe_chem_comp_drugbank_targets.name
_pdbe_chem_comp_drugbank_targets.organism
_pdbe_chem_comp_drugbank_targets.uniprot_id
_pdbe_chem_comp_drugbank_targets.pharmacologically_active
_pdbe_chem_comp_drugbank_targets.ordinal
CSS DB02761 'Cysteine desulfurase' 'Escherichia coli (strain K12)' P77444 unknown 1
CSS DB02761 'Thiosulfate sulfurtransferase GlpE' 'Shigella flexneri' P0A6V7 unknown 2
CSS DB02761 'Hydroxylamine reductase' 'Desulfovibrio desulfuricans (strain ATCC 27774 / DSM 6949)' Q01770 unknown 3
CSS DB02761 '3-mercaptopyruvate sulfurtransferase' 'Leishmania major' Q7K9G0 unknown 4
CSS DB02761 'L-cysteine/cystine lyase C-DES' 'Synechocystis sp. (strain PCC 6714)' Q9ZHG9 unknown 5
CSS DB02761 '3-mercaptopyruvate sulfurtransferase' 'Escherichia coli (strain K12)' P31142 unknown 6
CSS DB02761 'Hydroxylamine reductase' 'Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / NCIMB 8303)' P31101 unknown 7
CSS DB02761 'Thiosulfate sulfurtransferase' Humans Q16762 unknown 8
CSS DB02761 Sulfurtransferase 'Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)' Q5SJI0 unknown 9
#
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
CSS N N 3.805 1.732 1
CSS CA C 5.104 0.983 2
CSS CB C 5.104 -0.517 3
CSS SG S 6.404 -1.268 4
CSS SD S 6.404 -2.768 5
CSS C C 6.404 1.732 6
CSS O O 7.702 0.983 7
CSS OXT O 6.404 3.232 8
#
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
CSS CA N SINGLE BEGINDASH 1
CSS CA CB SINGLE NONE 2
CSS CA C SINGLE NONE 3
CSS CB SG SINGLE NONE 4
CSS SG SD SINGLE NONE 5
CSS C O DOUBLE NONE 6
CSS C OXT SINGLE NONE 7
#
_pdbe_chem_comp_substructure.comp_id CSS
_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
CSS O F1 1
CSS C F1 1
CSS CA F1 1
CSS N F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id CSS
_pdbe_chem_comp_rdkit_properties.exactmw 152.992
_pdbe_chem_comp_rdkit_properties.amw 153.228
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 5
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 5
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 8
_pdbe_chem_comp_rdkit_properties.NumAtoms 15
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 5
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.667
_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 66.161
_pdbe_chem_comp_rdkit_properties.tpsa 63.320
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.024
_pdbe_chem_comp_rdkit_properties.CrippenMR 37.055
_pdbe_chem_comp_rdkit_properties.chi0v 5.213
_pdbe_chem_comp_rdkit_properties.chi1v 3.244
_pdbe_chem_comp_rdkit_properties.chi2v 0.858
_pdbe_chem_comp_rdkit_properties.chi3v 0.858
_pdbe_chem_comp_rdkit_properties.chi4v 0.480
_pdbe_chem_comp_rdkit_properties.chi0n 10.580
_pdbe_chem_comp_rdkit_properties.chi1n 4.714
_pdbe_chem_comp_rdkit_properties.chi2n 0.332
_pdbe_chem_comp_rdkit_properties.chi3n 0.332
_pdbe_chem_comp_rdkit_properties.chi4n 0.081
_pdbe_chem_comp_rdkit_properties.hallKierAlpha 0.130
_pdbe_chem_comp_rdkit_properties.kappa1 2.070
_pdbe_chem_comp_rdkit_properties.kappa2 4.053
_pdbe_chem_comp_rdkit_properties.kappa3 3.173
_pdbe_chem_comp_rdkit_properties.Phi 1.049
#
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
CSS UniChem DrugBank DB02761
CSS UniChem 'KEGG LIGAND' C01962
CSS UniChem ChEBI 28839
CSS UniChem ChEBI 58591
CSS UniChem fdasrs 3RZ74WA9J2
CSS UniChem SureChEMBL SCHEMBL187770
CSS UniChem PubChem 165331
CSS UniChem NMRShiftDB 60020490
CSS UniChem ACTor 5652-32-4
CSS UniChem Recon thcys
CSS UniChem Nikkaji J2.365.199H
CSS UniChem MetaboLights MTBLC28839
CSS UniChem MetaboLights MTBLC58591
CSS UniChem BRENDA 220990
CSS UniChem BRENDA 30456
CSS UniChem BRENDA 63260
CSS UniChem BRENDA 72410
CSS UniChem Rhea 58591
CSS UniChem 'Probes And Drugs' PD007659
CSS UniChem 'EPA CompTox Dashboard' DTXSID00205073
CSS UniChem PubChem 45266695
#
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
CSS N 0.214 -1.420 0.518 ETKDGv3 1
CSS CA -0.474 -0.126 0.507 ETKDGv3 2
CSS CB 0.530 1.038 0.547 ETKDGv3 3
CSS SG 1.627 1.091 -0.921 ETKDGv3 4
CSS SD 3.342 0.316 0.087 ETKDGv3 5
CSS C -1.425 -0.003 -0.658 ETKDGv3 6
CSS O -1.108 -0.437 -1.798 ETKDGv3 7
CSS OXT -2.647 0.639 -0.480 ETKDGv3 8
CSS H 0.677 -1.588 -0.404 ETKDGv3 9
CSS H2 -0.500 -2.174 0.642 ETKDGv3 10
CSS HA -1.080 -0.059 1.438 ETKDGv3 11
CSS HB2 1.121 0.985 1.486 ETKDGv3 12
CSS HB3 -0.033 1.996 0.582 ETKDGv3 13
CSS HD 3.051 -1.006 -0.294 ETKDGv3 14
CSS HXT -3.294 0.747 -1.252 ETKDGv3 15
#