data_CY3
#
_chem_comp.id CY3
_chem_comp.name 2-AMINO-3-MERCAPTO-PROPIONAMIDE
_chem_comp.type 'L-PEPTIDE LINKING'
_chem_comp.pdbx_type ATOMP
_chem_comp.formula 'C3 H8 N2 O S'
_chem_comp.mon_nstd_parent_comp_id CYS
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 1999-10-22
_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 120.173
_chem_comp.one_letter_code C
_chem_comp.three_letter_code CY3
_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 1D7T
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
_chem_comp.pdbx_pcm N
#
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
CY3 N N N 0 1 N N N N N N 26.306 19.187 17.770 1.573 0.510 -0.051 N CY3 1
CY3 CA CA C 0 1 N N R N N N 25.303 18.321 17.058 0.128 0.451 0.208 CA CY3 2
CY3 C C C 0 1 N N N N N N 25.480 18.521 15.550 -0.109 0.003 1.627 C CY3 3
CY3 O O O 0 1 N N N N N N 26.048 19.490 15.082 0.685 -0.734 2.171 O CY3 4
CY3 CB CB C 0 1 N N N N N N 23.862 18.721 17.466 -0.523 -0.541 -0.755 CB CY3 5
CY3 SG SG S 0 1 N N N N N N 23.197 18.022 18.994 -0.237 -0.002 -2.464 SG CY3 6
CY3 N1 N1 N 0 1 N N N N N N 25.014 17.616 14.753 -1.204 0.422 2.292 N1 CY3 7
CY3 H H H 0 1 N N N N N N 26.063 20.093 18.083 1.683 0.711 -1.033 H CY3 8
CY3 H2 HN2 H 0 1 N Y N N N N 26.244 20.167 17.493 1.932 -0.420 0.095 H2 CY3 9
CY3 HA HA H 0 1 N N N N N N 25.496 17.284 17.300 -0.307 1.439 0.061 HA CY3 10
CY3 HB2 1HB H 0 1 N N N N N N 23.199 18.422 16.665 -0.087 -1.529 -0.609 HB2 CY3 11
CY3 HB3 2HB H 0 1 N N N N N N 23.812 19.801 17.532 -1.595 -0.585 -0.563 HB3 CY3 12
CY3 HG HG H 0 1 N N N N N N 22.313 18.267 19.244 -0.872 -0.984 -3.128 HG CY3 13
CY3 HN11 1HN1 H 0 0 N N N N N N 24.559 16.831 15.116 -1.357 0.134 3.205 HN11 CY3 14
CY3 HN12 2HN1 H 0 0 N N N N N N 25.111 17.698 13.778 -1.839 1.012 1.857 HN12 CY3 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
CY3 N CA SING N N 1
CY3 N H SING N N 2
CY3 N H2 SING N N 3
CY3 CA C SING N N 4
CY3 CA CB SING N N 5
CY3 CA HA SING N N 6
CY3 C O DOUB N N 7
CY3 C N1 SING N N 8
CY3 CB SG SING N N 9
CY3 CB HB2 SING N N 10
CY3 CB HB3 SING N N 11
CY3 SG HG SING N N 12
CY3 N1 HN11 SING N N 13
CY3 N1 HN12 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
CY3 SMILES ACDLabs 10.04 'O=C(N)C(N)CS'
CY3 SMILES_CANONICAL CACTVS 3.341 'N[C@@H](CS)C(N)=O'
CY3 SMILES CACTVS 3.341 'N[CH](CS)C(N)=O'
CY3 SMILES_CANONICAL 'OpenEye OEToolkits' 1.5.0 'C([C@@H](C(=O)N)N)S'
CY3 SMILES 'OpenEye OEToolkits' 1.5.0 'C(C(C(=O)N)N)S'
CY3 InChI InChI 1.03 'InChI=1S/C3H8N2OS/c4-2(1-7)3(5)6/h2,7H,1,4H2,(H2,5,6)/t2-/m0/s1'
CY3 InChIKey InChI 1.03 YEDNBEGNKOANMB-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
CY3 'SYSTEMATIC NAME' ACDLabs 10.04 L-cysteinamide
CY3 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 1.5.0 '(2R)-2-amino-3-sulfanyl-propanamide'
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
CY3 'Create component' 1999-10-22 RCSB
CY3 'Modify descriptor' 2011-06-04 RCSB
CY3 'Modify PCM' 2024-09-27 PDBE
#
_pdbe_chem_comp_drugbank_details.comp_id CY3
_pdbe_chem_comp_drugbank_details.drugbank_id DB03275
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name Cysteinamide
_pdbe_chem_comp_drugbank_details.description ?
_pdbe_chem_comp_drugbank_details.cas_number 74401-72-2
_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
CY3 2-amino-3-mercapto-propionamide DrugBank ?
CY3 Cysteinamide DrugBank ?
CY3 L-Cysteinamide DrugBank ?
#
_pdbe_chem_comp_drugbank_classification.comp_id CY3
_pdbe_chem_comp_drugbank_classification.drugbank_id DB03275
_pdbe_chem_comp_drugbank_classification.parent 'Alpha amino acid amides'
_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 alpha amino acid amides. These are amide derivatives of alpha amino acids.'
#
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
CY3 N N 3.805 1.215 1
CY3 CA C 5.104 0.465 2
CY3 C C 6.404 1.215 3
CY3 O O 6.404 2.715 4
CY3 CB C 5.104 -1.035 5
CY3 SG S 3.805 -1.785 6
CY3 N1 N 7.702 0.465 7
#
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
CY3 CA N SINGLE BEGINDASH 1
CY3 CA C SINGLE NONE 2
CY3 CA CB SINGLE NONE 3
CY3 C O DOUBLE NONE 4
CY3 C N1 SINGLE NONE 5
CY3 CB SG SINGLE NONE 6
#
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
CY3 amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
CY3 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
CY3 N1 F1 1
CY3 C F1 1
CY3 O F1 1
CY3 CA F1 1
CY3 O F2 1
CY3 C F2 1
CY3 CA F2 1
CY3 N F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id CY3
_pdbe_chem_comp_rdkit_properties.exactmw 120.036
_pdbe_chem_comp_rdkit_properties.amw 120.177
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 4
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 4
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 7
_pdbe_chem_comp_rdkit_properties.NumAtoms 15
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 4
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 1
_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 58.618
_pdbe_chem_comp_rdkit_properties.tpsa 69.110
_pdbe_chem_comp_rdkit_properties.CrippenClogP -1.271
_pdbe_chem_comp_rdkit_properties.CrippenMR 31.023
_pdbe_chem_comp_rdkit_properties.chi0v 4.027
_pdbe_chem_comp_rdkit_properties.chi1v 1.764
_pdbe_chem_comp_rdkit_properties.chi2v 0.493
_pdbe_chem_comp_rdkit_properties.chi3v 0.493
_pdbe_chem_comp_rdkit_properties.chi4v 0.131
_pdbe_chem_comp_rdkit_properties.chi0n 11.211
_pdbe_chem_comp_rdkit_properties.chi1n 5.053
_pdbe_chem_comp_rdkit_properties.chi2n 0.299
_pdbe_chem_comp_rdkit_properties.chi3n 0.299
_pdbe_chem_comp_rdkit_properties.chi4n 0.044
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.220
_pdbe_chem_comp_rdkit_properties.kappa1 1.193
_pdbe_chem_comp_rdkit_properties.kappa2 2.873
_pdbe_chem_comp_rdkit_properties.kappa3 2.472
_pdbe_chem_comp_rdkit_properties.Phi 0.490
#
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
CY3 UniChem DrugBank DB03275
CY3 UniChem fdasrs 055X467671
CY3 UniChem SureChEMBL SCHEMBL358881
CY3 UniChem 'PubChem TPHARMA' 16644820
CY3 UniChem 'EPA CompTox Dashboard' DTXSID40225396
CY3 UniChem 'Probes And Drugs' PD059821
CY3 UniChem PubChem 6540253
#
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
CY3 N -1.027 -0.707 -1.312 ETKDGv3 1
CY3 CA -0.231 -0.024 -0.289 ETKDGv3 2
CY3 C 1.181 -0.548 -0.306 ETKDGv3 3
CY3 O 1.393 -1.787 -0.403 ETKDGv3 4
CY3 CB -0.839 -0.244 1.106 ETKDGv3 5
CY3 SG -2.428 0.629 1.292 ETKDGv3 6
CY3 N1 2.286 0.345 -0.162 ETKDGv3 7
CY3 H -0.576 -0.544 -2.242 ETKDGv3 8
CY3 H2 -1.964 -0.248 -1.370 ETKDGv3 9
CY3 HA -0.212 1.068 -0.510 ETKDGv3 10
CY3 HB2 -0.146 0.137 1.888 ETKDGv3 11
CY3 HB3 -1.002 -1.329 1.284 ETKDGv3 12
CY3 HG -1.828 1.901 1.233 ETKDGv3 13
CY3 HN11 2.133 1.372 -0.049 ETKDGv3 14
CY3 HN12 3.263 -0.022 -0.161 ETKDGv3 15
#