data_YCM
#
_chem_comp.id YCM
_chem_comp.name 'S-(2-AMINO-2-OXOETHYL)-L-CYSTEINE'
_chem_comp.type 'L-PEPTIDE LINKING'
_chem_comp.pdbx_type ATOMP
_chem_comp.formula 'C5 H10 N2 O3 S'
_chem_comp.mon_nstd_parent_comp_id CYS
_chem_comp.pdbx_synonyms CYSTEINE-S-ACETAMIDE
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2002-02-18
_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 178.209
_chem_comp.one_letter_code C
_chem_comp.three_letter_code YCM
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag Y
_chem_comp.pdbx_ideal_coordinates_details ?
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 1L0Q
_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
YCM N N N 0 1 N N N Y Y N -6.736 0.559 23.412 3.035 -1.472 -0.440 N YCM 1
YCM CA CA C 0 1 N N R Y N N -6.236 0.928 22.087 1.665 -1.164 -0.766 CA YCM 2
YCM CB CB C 0 1 N N N N N N -7.105 2.039 21.482 1.076 -0.107 0.172 CB YCM 3
YCM SG SG S 0 1 N N N N N N -8.858 1.643 21.390 1.832 1.542 -0.014 SG YCM 4
YCM CD CD C 0 1 N N N N N N -8.914 0.063 20.530 0.824 2.422 1.200 CD YCM 5
YCM CE CE C 0 1 N N N N N N -8.191 -0.044 19.214 1.261 3.865 1.246 CE YCM 6
YCM OZ1 OZ1 O 0 1 N N N N N N -7.020 -0.405 19.168 1.227 4.600 0.261 OZ1 YCM 7
YCM NZ2 NZ2 N 0 1 N N N N N N -8.882 0.287 18.133 1.707 4.267 2.484 NZ2 YCM 8
YCM C C C 0 1 N N N Y N Y -4.786 1.389 22.025 1.500 -0.794 -2.231 C YCM 9
YCM O O O 0 1 N N N Y N Y -4.251 1.566 20.932 2.436 -0.664 -3.010 O YCM 10
YCM OXT OXT O 0 1 N Y N Y N Y ? ? ? 0.208 -0.605 -2.593 OXT YCM 11
YCM H H H 0 1 N N N Y Y N -6.158 -0.179 23.814 3.758 -1.236 -1.098 H YCM 12
YCM H2 HN2 H 0 1 N Y N Y Y N -7.722 0.300 23.388 3.225 -2.090 0.331 H2 YCM 13
YCM HA HA H 0 1 N N N Y N N -6.290 -0.023 21.508 1.117 -2.104 -0.627 HA YCM 14
YCM HB2 1HB H 0 1 N N N N N N -6.950 2.996 22.031 1.217 -0.414 1.214 HB2 YCM 15
YCM HB3 2HB H 0 1 N N N N N N -6.719 2.331 20.477 0.000 0.000 0.000 HB3 YCM 16
YCM HD2 1HD H 0 1 N N N N N N -8.552 -0.740 21.213 -0.230 2.382 0.908 HD2 YCM 17
YCM HD3 2HD H 0 1 N N N N N N -9.977 -0.241 20.390 0.926 1.938 2.175 HD3 YCM 18
YCM HZ21 1HZ H 0 0 N N N N N N -9.856 0.587 18.171 2.021 5.225 2.601 HZ21 YCM 19
YCM HZ22 2HZ H 0 0 N N N N N N -8.392 0.214 17.241 1.735 3.644 3.285 HZ22 YCM 20
YCM HXT HXT H 0 1 N Y N Y N Y 0.904 0.287 -0.038 0.125 -0.356 -3.538 HXT YCM 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
YCM N CA SING N N 1
YCM N H SING N N 2
YCM N H2 SING N N 3
YCM CA CB SING N N 4
YCM CA C SING N N 5
YCM CA HA SING N N 6
YCM CB SG SING N N 7
YCM CB HB2 SING N N 8
YCM CB HB3 SING N N 9
YCM SG CD SING N N 10
YCM CD CE SING N N 11
YCM CD HD2 SING N N 12
YCM CD HD3 SING N N 13
YCM CE OZ1 DOUB N N 14
YCM CE NZ2 SING N N 15
YCM NZ2 HZ21 SING N N 16
YCM NZ2 HZ22 SING N N 17
YCM C O DOUB N N 18
YCM C OXT SING N N 19
YCM 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
YCM SMILES ACDLabs 10.04 'O=C(O)C(N)CSCC(=O)N'
YCM SMILES_CANONICAL CACTVS 3.341 'N[C@@H](CSCC(N)=O)C(O)=O'
YCM SMILES CACTVS 3.341 'N[CH](CSCC(N)=O)C(O)=O'
YCM SMILES_CANONICAL 'OpenEye OEToolkits' 1.5.0 'C([C@@H](C(=O)O)N)SCC(=O)N'
YCM SMILES 'OpenEye OEToolkits' 1.5.0 'C(C(C(=O)O)N)SCC(=O)N'
YCM InChI InChI 1.03 'InChI=1S/C5H10N2O3S/c6-3(5(9)10)1-11-2-4(7)8/h3H,1-2,6H2,(H2,7,8)(H,9,10)/t3-/m0/s1'
YCM InChIKey InChI 1.03 VFKYKPOTSJWPIU-VKHMYHEASA-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
YCM 'SYSTEMATIC NAME' ACDLabs 10.04 'S-(2-amino-2-oxoethyl)-L-cysteine'
YCM 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 1.5.0 '(2R)-2-amino-3-(2-amino-2-oxo-ethyl)sulfanyl-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
YCM 'Create component' 2002-02-18 RCSB
YCM 'Modify descriptor' 2011-06-04 RCSB
YCM 'Modify synonyms' 2021-03-01 PDBE
YCM 'Modify backbone' 2023-11-03 PDBE
YCM 'Modify PCM' 2024-09-27 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id YCM
_pdbx_chem_comp_synonyms.name CYSTEINE-S-ACETAMIDE
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id YCM
_pdbx_chem_comp_pcm.modified_residue_id CYS
_pdbx_chem_comp_pcm.type Acetamidation
_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 ?
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ?
#
_pdbe_chem_comp_drugbank_details.comp_id YCM
_pdbe_chem_comp_drugbank_details.drugbank_id DB02987
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name Cysteine-S-acetamide
_pdbe_chem_comp_drugbank_details.description ?
_pdbe_chem_comp_drugbank_details.cas_number 17528-66-4
_pdbe_chem_comp_drugbank_details.mechanism_of_action ?
#
loop_
_pdbe_chem_comp_synonyms.comp_id
_pdbe_chem_comp_synonyms.name
_pdbe_chem_comp_synonyms.provenance
_pdbe_chem_comp_synonyms.type
YCM CYSTEINE-S-ACETAMIDE wwPDB ?
YCM Cysteine-S-acetamide DrugBank ?
YCM S-(Carbamoylmethyl)cysteine DrugBank ?
YCM S-Carbamidomethylcysteine DrugBank ?
#
_pdbe_chem_comp_drugbank_classification.comp_id YCM
_pdbe_chem_comp_drugbank_classification.drugbank_id DB02987
_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
YCM DB02987 'Ribonuclease pancreatic' Humans P07998 unknown 1
YCM DB02987 "2'-5'-oligoadenylate synthase 1" Humans P00973 unknown 2
#
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
YCM N N 3.805 2.857 1
YCM CA C 5.104 2.107 2
YCM CB C 5.104 0.608 3
YCM SG S 6.404 -0.142 4
YCM CD C 6.404 -1.643 5
YCM CE C 7.702 -2.393 6
YCM OZ1 O 9.002 -1.643 7
YCM NZ2 N 7.702 -3.893 8
YCM C C 6.404 2.857 9
YCM O O 7.702 2.107 10
YCM OXT O 6.404 4.357 11
#
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
YCM CA N SINGLE BEGINDASH 1
YCM CA CB SINGLE NONE 2
YCM CA C SINGLE NONE 3
YCM CB SG SINGLE NONE 4
YCM SG CD SINGLE NONE 5
YCM CD CE SINGLE NONE 6
YCM CE OZ1 DOUBLE NONE 7
YCM CE NZ2 SINGLE NONE 8
YCM C O DOUBLE NONE 9
YCM C OXT SINGLE NONE 10
#
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
YCM amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
YCM peptide F2 fragment NCC=O InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2 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
YCM NZ2 F1 1
YCM CE F1 1
YCM OZ1 F1 1
YCM CD F1 1
YCM O F2 1
YCM C F2 1
YCM CA F2 1
YCM N F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id YCM
_pdbe_chem_comp_rdkit_properties.exactmw 178.041
_pdbe_chem_comp_rdkit_properties.amw 178.213
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 5
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 5
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 6
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 5
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 11
_pdbe_chem_comp_rdkit_properties.NumAtoms 21
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 6
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 1
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.600
_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 82.488
_pdbe_chem_comp_rdkit_properties.tpsa 106.410
_pdbe_chem_comp_rdkit_properties.CrippenClogP -1.383
_pdbe_chem_comp_rdkit_properties.CrippenMR 42.131
_pdbe_chem_comp_rdkit_properties.chi0v 5.844
_pdbe_chem_comp_rdkit_properties.chi1v 3.034
_pdbe_chem_comp_rdkit_properties.chi2v 1.051
_pdbe_chem_comp_rdkit_properties.chi3v 1.051
_pdbe_chem_comp_rdkit_properties.chi4v 0.478
_pdbe_chem_comp_rdkit_properties.chi0n 15.027
_pdbe_chem_comp_rdkit_properties.chi1n 6.915
_pdbe_chem_comp_rdkit_properties.chi2n 0.479
_pdbe_chem_comp_rdkit_properties.chi3n 0.479
_pdbe_chem_comp_rdkit_properties.chi4n 0.159
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.750
_pdbe_chem_comp_rdkit_properties.kappa1 2.367
_pdbe_chem_comp_rdkit_properties.kappa2 4.974
_pdbe_chem_comp_rdkit_properties.kappa3 5.682
_pdbe_chem_comp_rdkit_properties.Phi 1.070
#
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
YCM UniChem SureChEMBL 1848592
YCM UniChem fdasrs LAH55Q7GIH
YCM UniChem PubChem 17754220
YCM UniChem PubChem 36688842
YCM UniChem 'Probes And Drugs' PD007476
YCM UniChem DrugBank DB02987
#
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
YCM N -0.930 -0.696 1.293 ETKDGv3 1
YCM CA -1.555 0.384 0.528 ETKDGv3 2
YCM CB -0.770 0.661 -0.762 ETKDGv3 3
YCM SG 0.903 1.302 -0.382 ETKDGv3 4
YCM CD 1.797 -0.249 -0.736 ETKDGv3 5
YCM CE 3.245 -0.069 -0.414 ETKDGv3 6
YCM OZ1 4.056 0.243 -1.326 ETKDGv3 7
YCM NZ2 3.707 -0.206 0.929 ETKDGv3 8
YCM C -2.991 0.054 0.214 ETKDGv3 9
YCM O -3.275 -0.956 -0.485 ETKDGv3 10
YCM OXT -4.009 0.869 0.698 ETKDGv3 11
YCM H -1.007 -1.594 0.760 ETKDGv3 12
YCM H2 -1.455 -0.819 2.190 ETKDGv3 13
YCM HA -1.538 1.309 1.147 ETKDGv3 14
YCM HB2 -0.726 -0.250 -1.397 ETKDGv3 15
YCM HB3 -1.297 1.446 -1.346 ETKDGv3 16
YCM HD2 1.385 -1.077 -0.124 ETKDGv3 17
YCM HD3 1.680 -0.508 -1.810 ETKDGv3 18
YCM HZ21 3.042 -0.441 1.699 ETKDGv3 19
YCM HZ22 4.717 -0.068 1.156 ETKDGv3 20
YCM HXT -4.980 0.663 0.497 ETKDGv3 21
#