data_C3Y
#
_chem_comp.id C3Y
_chem_comp.name S-[(1S)-1-HYDROXY-1-(HYDROXYAMINO)ETHYL]-L-CYSTEINE
_chem_comp.type "L-PEPTIDE LINKING"
_chem_comp.pdbx_type ATOMP
_chem_comp.formula "C5 H12 N2 O4 S"
_chem_comp.mon_nstd_parent_comp_id CYS
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2007-04-02
_chem_comp.pdbx_modified_date 2011-06-04
_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 196.225
_chem_comp.one_letter_code C
_chem_comp.three_letter_code C3Y
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details "OpenEye OEToolkits"
_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
#
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
C3Y N N N 0 1 N N N N N N 32.300 39.601 22.841 -4.379 1.679 0.722 N C3Y 1
C3Y CA CA C 0 1 N N N N N N 33.549 40.322 23.100 -4.528 2.403 -0.516 CA C3Y 2
C3Y C C C 0 1 N N N N N N 33.398 41.365 24.194 -5.829 2.058 -1.222 C C3Y 3
C3Y O O O 0 1 N N N N N N 33.266 40.975 25.360 -6.601 1.187 -0.839 O C3Y 4
C3Y CB CB C 0 1 N N N N N N 34.154 40.796 21.812 -3.309 2.236 -1.427 CB C3Y 5
C3Y SG SG S 0 1 N N N N N N 35.927 41.158 21.899 -3.097 0.552 -2.062 SG C3Y 6
C3Y C1 C1 C 0 1 N N N N N N 36.821 43.623 22.581 -0.412 1.221 -2.194 C1 C3Y 7
C3Y O2 O2 O 0 1 N N N N N N 34.871 43.694 21.435 -1.776 1.741 -4.096 O2 C3Y 8
C3Y N1 N1 N 0 1 N N N N N N 36.560 43.290 20.307 -1.248 -0.558 -3.671 N1 C3Y 9
C3Y O3 O3 O 0 1 N N N N N N 35.709 43.027 19.163 -0.213 -0.336 -4.664 O3 C3Y 10
C3Y C2 C2 C 0 1 N N N N N N 36.049 42.929 21.537 -1.566 0.753 -3.087 C2 C3Y 11
C3Y OXT OXT O 0 1 N Y N N N N 33.476 42.643 23.879 -6.048 2.801 -2.333 OXT C3Y 12
C3Y HN1 1HN H 0 1 N N N N N N 31.824 39.437 23.705 -5.191 1.518 1.294 HN1 C3Y 13
C3Y HN2 2HN H 0 1 N N N N N N 31.718 40.148 22.239 -3.455 1.529 1.091 HN2 C3Y 14
C3Y HA HA H 0 1 N N N N N N 34.291 39.631 23.527 -4.610 3.457 -0.225 HA C3Y 15
C3Y HBC1 1HBC H 0 0 N N N N N N 34.009 40.005 21.061 -2.397 2.494 -0.878 HBC1 C3Y 16
C3Y HBC2 2HBC H 0 0 N N N N N N 33.652 41.741 21.558 -3.380 2.909 -2.288 HBC2 C3Y 17
C3Y HOT HOT H 0 1 N N N N N N 33.415 43.168 24.668 -6.887 2.555 -2.778 HOT C3Y 18
C3Y H1C1 1H1C H 0 0 N N N N N N 37.847 43.796 22.225 -0.602 2.214 -1.773 H1C1 C3Y 19
C3Y H1C2 2H1C H 0 0 N N N N N N 36.344 44.588 22.809 0.513 1.333 -2.773 H1C2 C3Y 20
C3Y H1C3 3H1C H 0 0 N N N N N N 36.848 43.003 23.490 -0.212 0.523 -1.374 H1C3 C3Y 21
C3Y H1 H1 H 0 1 N N N N N N 37.407 42.775 20.173 -2.022 -0.858 -4.262 H1 C3Y 22
C3Y H3 H3 H 0 1 N N N N N N 34.804 42.969 19.447 0.422 -1.019 -4.388 H3 C3Y 23
C3Y H5 H5 H 0 1 N N N N N N 34.528 43.866 22.304 -2.532 1.438 -4.626 H5 C3Y 24
#
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
C3Y O2 H5 SING N N 1
C3Y N CA SING N N 2
C3Y CA C SING N N 3
C3Y C O DOUB N N 4
C3Y CA CB SING N N 5
C3Y CB SG SING N N 6
C3Y N1 O3 SING N N 7
C3Y SG C2 SING N N 8
C3Y C1 C2 SING N N 9
C3Y O2 C2 SING N N 10
C3Y N1 C2 SING N N 11
C3Y C OXT SING N N 12
C3Y N HN1 SING N N 13
C3Y N HN2 SING N N 14
C3Y CA HA SING N N 15
C3Y CB HBC1 SING N N 16
C3Y CB HBC2 SING N N 17
C3Y OXT HOT SING N N 18
C3Y C1 H1C1 SING N N 19
C3Y C1 H1C2 SING N N 20
C3Y C1 H1C3 SING N N 21
C3Y N1 H1 SING N N 22
C3Y O3 H3 SING N N 23
#
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
C3Y SMILES ACDLabs 10.04 O=C(O)C(N)CSC(O)(NO)C
C3Y SMILES_CANONICAL CACTVS 3.341 C[C@@](O)(NO)SC[C@H](N)C(O)=O
C3Y SMILES CACTVS 3.341 C[C](O)(NO)SC[CH](N)C(O)=O
C3Y SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C[C@](NO)(O)SC[C@@H](C(=O)O)N
C3Y SMILES "OpenEye OEToolkits" 1.5.0 CC(NO)(O)SCC(C(=O)O)N
C3Y InChI InChI 1.03 InChI=1S/C5H12N2O4S/c1-5(10,7-11)12-2-3(6)4(8)9/h3,7,10-11H,2,6H2,1H3,(H,8,9)/t3-,5-/m0/s1
C3Y InChIKey InChI 1.03 XIYHYGCLIYYYPL-UCORVYFPSA-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
C3Y "SYSTEMATIC NAME" ACDLabs 10.04 S-[(1S)-1-hydroxy-1-(hydroxyamino)ethyl]-L-cysteine
C3Y "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2R)-2-amino-3-[(1S)-1-hydroxy-1-(hydroxyamino)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
C3Y 'Create component' 2007-04-02 RCSB
C3Y 'Modify descriptor' 2011-06-04 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
C3Y N N 10.301 1.732 1
C3Y CA C 10.301 0.233 2
C3Y C C 11.600 -0.517 3
C3Y O O 12.899 0.233 4
C3Y CB C 9.002 -0.517 5
C3Y SG S 7.702 0.233 6
C3Y C1 C 5.654 0.781 7
C3Y O2 O 7.154 -1.817 8
C3Y N1 N 5.104 -1.268 9
C3Y O3 O 3.805 -0.517 10
C3Y C2 C 6.404 -0.517 11
C3Y OXT O 11.600 -2.018 12
#
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
C3Y CA N SINGLE BEGINDASH 1
C3Y CA C SINGLE NONE 2
C3Y C O DOUBLE NONE 3
C3Y CA CB SINGLE NONE 4
C3Y CB SG SINGLE NONE 5
C3Y N1 O3 SINGLE NONE 6
C3Y SG C2 SINGLE NONE 7
C3Y C2 C1 SINGLE BEGINWEDGE 8
C3Y O2 C2 SINGLE NONE 9
C3Y N1 C2 SINGLE NONE 10
C3Y C OXT SINGLE NONE 11
#
_pdbe_chem_comp_substructure.comp_id C3Y
_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
C3Y O F1 1
C3Y C F1 1
C3Y CA F1 1
C3Y N F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id C3Y
_pdbe_chem_comp_rdkit_properties.exactmw 196.052
_pdbe_chem_comp_rdkit_properties.amw 196.228
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 6
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 6
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 9
_pdbe_chem_comp_rdkit_properties.NumHBD 5
_pdbe_chem_comp_rdkit_properties.NumHBA 7
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 12
_pdbe_chem_comp_rdkit_properties.NumAtoms 24
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 7
_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 2
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 91.004
_pdbe_chem_comp_rdkit_properties.tpsa 115.810
_pdbe_chem_comp_rdkit_properties.CrippenClogP -1.224
_pdbe_chem_comp_rdkit_properties.CrippenMR 43.615
_pdbe_chem_comp_rdkit_properties.chi0v 6.252
_pdbe_chem_comp_rdkit_properties.chi1v 3.217
_pdbe_chem_comp_rdkit_properties.chi2v 1.246
_pdbe_chem_comp_rdkit_properties.chi3v 1.246
_pdbe_chem_comp_rdkit_properties.chi4v 0.533
_pdbe_chem_comp_rdkit_properties.chi0n 17.436
_pdbe_chem_comp_rdkit_properties.chi1n 7.967
_pdbe_chem_comp_rdkit_properties.chi2n 0.600
_pdbe_chem_comp_rdkit_properties.chi3n 0.600
_pdbe_chem_comp_rdkit_properties.chi4n 0.178
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.340
_pdbe_chem_comp_rdkit_properties.kappa1 2.580
_pdbe_chem_comp_rdkit_properties.kappa2 4.629
_pdbe_chem_comp_rdkit_properties.kappa3 4.520
_pdbe_chem_comp_rdkit_properties.Phi 0.995
#
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
C3Y UniChem PDBe C3Y
C3Y UniChem ZINC ZINC000064426402
C3Y UniChem PubChem 52946603
#
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
C3Y N 2.578 0.153 -1.002 ETKDGv3 1
C3Y CA 2.224 0.090 0.419 ETKDGv3 2
C3Y C 2.988 -1.025 1.071 ETKDGv3 3
C3Y O 3.719 -0.790 2.070 ETKDGv3 4
C3Y CB 0.712 -0.116 0.622 ETKDGv3 5
C3Y SG -0.224 1.357 0.069 ETKDGv3 6
C3Y C1 -2.918 1.711 -0.296 ETKDGv3 7
C3Y O2 -2.222 0.200 1.401 ETKDGv3 8
C3Y N1 -1.994 -0.523 -0.838 ETKDGv3 9
C3Y O3 -1.691 -0.103 -2.093 ETKDGv3 10
C3Y C2 -1.911 0.618 0.093 ETKDGv3 11
C3Y OXT 2.879 -2.324 0.582 ETKDGv3 12
C3Y HN1 2.141 -0.650 -1.512 ETKDGv3 13
C3Y HN2 2.193 1.033 -1.413 ETKDGv3 14
C3Y HA 2.519 1.049 0.902 ETKDGv3 15
C3Y HBC1 0.380 -1.021 0.071 ETKDGv3 16
C3Y HBC2 0.510 -0.267 1.704 ETKDGv3 17
C3Y HOT 3.385 -3.087 1.017 ETKDGv3 18
C3Y H1C1 -2.689 2.123 -1.302 ETKDGv3 19
C3Y H1C2 -3.950 1.300 -0.303 ETKDGv3 20
C3Y H1C3 -2.879 2.543 0.439 ETKDGv3 21
C3Y H1 -2.979 -0.877 -0.860 ETKDGv3 22
C3Y H3 -0.953 -0.696 -2.384 ETKDGv3 23
C3Y H5 -1.818 -0.695 1.543 ETKDGv3 24
#