data_HCS
#
_chem_comp.id HCS
_chem_comp.name '2-AMINO-4-MERCAPTO-BUTYRIC ACID'
_chem_comp.type 'L-PEPTIDE LINKING'
_chem_comp.pdbx_type ATOMP
_chem_comp.formula 'C4 H9 N O2 S'
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms L-Homocysteine
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2001-08-14
_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 135.185
_chem_comp.one_letter_code X
_chem_comp.three_letter_code HCS
_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 1JVI
_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
HCS N N N 0 1 N N N Y Y N -32.947 20.755 -1.085 1.814 0.239 0.817 N HCS 1
HCS CA CA C 0 1 N N S Y N N -33.008 21.975 -0.288 0.374 0.527 0.821 CA HCS 2
HCS CB CB C 0 1 N N N N N N -31.609 22.561 -0.103 -0.275 -0.101 -0.412 CB HCS 3
HCS CG CG C 0 1 N N N N N N -30.697 21.854 0.886 0.357 0.485 -1.676 CG HCS 4
HCS SD SD S 0 1 N N N N N N -29.170 22.857 0.998 -0.412 -0.259 -3.140 SD HCS 5
HCS C C C 0 1 N N N Y N Y -33.907 23.045 -0.921 -0.249 -0.050 2.066 C HCS 6
HCS OXT OXT O 0 1 N Y N Y N Y -34.122 23.004 -2.158 -1.326 0.536 2.611 OXT HCS 7
HCS O O O 0 1 N N N Y N Y -34.375 23.924 -0.164 0.219 -1.041 2.573 O HCS 8
HCS H H H 0 1 N N N Y Y N -33.880 20.363 -1.208 1.909 -0.765 0.833 H HCS 9
HCS H2 H2 H 0 1 N Y N Y Y N -32.299 20.074 -0.688 2.169 0.549 -0.074 H2 HCS 10
HCS HA HCA H 0 1 N N N Y N N -33.444 21.687 0.696 0.219 1.605 0.804 HCA HCS 11
HCS HB2 HB2 H 0 1 N N N N N N -31.101 22.634 -1.092 -0.120 -1.179 -0.395 HB2 HCS 12
HCS HB3 HB3 H 0 1 N N N N N N -31.688 23.639 0.167 -1.344 0.112 -0.409 HB3 HCS 13
HCS HG2 HG2 H 0 1 N N N N N N -31.177 21.670 1.875 0.202 1.564 -1.693 HG2 HCS 14
HCS HG3 HG3 H 0 1 N N N N N N -30.505 20.787 0.624 1.426 0.271 -1.679 HG3 HCS 15
HCS HD HD H 0 1 N N N N N N -28.599 22.415 1.616 0.268 0.375 -4.110 HD HCS 16
HCS HXT HXT H 0 1 N Y N Y N Y -34.678 23.666 -2.550 -1.726 0.165 3.410 HXT HCS 17
#
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
HCS N CA SING N N 1
HCS N H SING N N 2
HCS N H2 SING N N 3
HCS CA CB SING N N 4
HCS CA C SING N N 5
HCS CA HA SING N N 6
HCS CB CG SING N N 7
HCS CB HB2 SING N N 8
HCS CB HB3 SING N N 9
HCS CG SD SING N N 10
HCS CG HG2 SING N N 11
HCS CG HG3 SING N N 12
HCS SD HD SING N N 13
HCS C OXT SING N N 14
HCS C O DOUB N N 15
HCS OXT HXT SING N N 16
#
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
HCS SMILES ACDLabs 10.04 'O=C(O)C(N)CCS'
HCS SMILES_CANONICAL CACTVS 3.341 'N[C@@H](CCS)C(O)=O'
HCS SMILES CACTVS 3.341 'N[CH](CCS)C(O)=O'
HCS SMILES_CANONICAL 'OpenEye OEToolkits' 1.5.0 'C(CS)[C@@H](C(=O)O)N'
HCS SMILES 'OpenEye OEToolkits' 1.5.0 'C(CS)C(C(=O)O)N'
HCS InChI InChI 1.03 'InChI=1S/C4H9NO2S/c5-3(1-2-8)4(6)7/h3,8H,1-2,5H2,(H,6,7)/t3-/m0/s1'
HCS InChIKey InChI 1.03 FFFHZYDWPBMWHY-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
HCS 'SYSTEMATIC NAME' ACDLabs 10.04 L-homocysteine
HCS 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 1.5.0 '(2S)-2-amino-4-sulfanyl-butanoic 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
HCS 'Create component' 2001-08-14 RCSB
HCS 'Modify descriptor' 2011-06-04 RCSB
HCS 'Modify backbone' 2023-11-03 PDBE
HCS 'Modify synonyms' 2024-02-28 PDBE
HCS 'Modify PCM' 2024-09-27 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id HCS
_pdbx_chem_comp_synonyms.name L-Homocysteine
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
#
loop_
_pdbx_chem_comp_pcm.pcm_id
_pdbx_chem_comp_pcm.comp_id
_pdbx_chem_comp_pcm.modified_residue_id
_pdbx_chem_comp_pcm.type
_pdbx_chem_comp_pcm.category
_pdbx_chem_comp_pcm.position
_pdbx_chem_comp_pcm.polypeptide_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
1 HCS ? None 'Non-standard residue' 'Amino-acid side chain' 'Any position' ? ? ? ?
2 HCS CYS None 'Covalent chemical modification' 'Amino-acid side chain' 'Any position' SD SG ? ?
3 HCS TYR None 'Covalent chemical modification' 'Amino-acid side chain' 'Any position' CB OH ? ?
#
_pdbe_chem_comp_drugbank_details.comp_id HCS
_pdbe_chem_comp_drugbank_details.drugbank_id DB04422
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name Homocysteine
_pdbe_chem_comp_drugbank_details.description
'Homocysteine is a thiol-containing amino acid formed by a demethylation of methionine.'
_pdbe_chem_comp_drugbank_details.cas_number 6027-13-0
_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
HCS L-Homocysteine wwPDB ?
HCS Homocysteine DrugBank ?
HCS 'L-2-amino-4-mercaptobutyric acid' DrugBank ?
HCS L-Homocysteine DrugBank ?
#
_pdbe_chem_comp_drugbank_classification.comp_id HCS
_pdbe_chem_comp_drugbank_classification.drugbank_id DB04422
_pdbe_chem_comp_drugbank_classification.parent 'L-alpha-amino acids'
_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-alpha-amino acids. These are alpha amino acids which have the L-configuration of the alpha-carbon atom.'
#
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
HCS DB04422 'S-ribosylhomocysteine lyase' 'Bacillus subtilis (strain 168)' O34667 unknown 1
HCS DB04422 '5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase' 'Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)' Q9X112 unknown 2
HCS DB04422 'Methionine synthase' 'Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)' Q9WYA5 unknown 3
#
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
HCS N N 3.805 1.732 1
HCS CA C 5.104 0.983 2
HCS CB C 5.104 -0.517 3
HCS CG C 3.805 -1.268 4
HCS SD S 3.805 -2.768 5
HCS C C 6.404 1.732 6
HCS OXT O 7.702 0.983 7
HCS O 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
HCS CA N SINGLE BEGINDASH 1
HCS CA CB SINGLE NONE 2
HCS CA C SINGLE NONE 3
HCS CB CG SINGLE NONE 4
HCS CG SD SINGLE NONE 5
HCS C OXT SINGLE NONE 6
HCS C O DOUBLE NONE 7
#
_pdbe_chem_comp_substructure.comp_id HCS
_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
HCS O F1 1
HCS C F1 1
HCS CA F1 1
HCS N F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id HCS
_pdbe_chem_comp_rdkit_properties.exactmw 135.035
_pdbe_chem_comp_rdkit_properties.amw 135.188
_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 4
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 8
_pdbe_chem_comp_rdkit_properties.NumAtoms 17
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 4
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.750
_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 65.813
_pdbe_chem_comp_rdkit_properties.tpsa 63.320
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.282
_pdbe_chem_comp_rdkit_properties.CrippenMR 34.081
_pdbe_chem_comp_rdkit_properties.chi0v 4.488
_pdbe_chem_comp_rdkit_properties.chi1v 1.994
_pdbe_chem_comp_rdkit_properties.chi2v 0.465
_pdbe_chem_comp_rdkit_properties.chi3v 0.465
_pdbe_chem_comp_rdkit_properties.chi4v 0.196
_pdbe_chem_comp_rdkit_properties.chi0n 12.672
_pdbe_chem_comp_rdkit_properties.chi1n 5.797
_pdbe_chem_comp_rdkit_properties.chi2n 0.363
_pdbe_chem_comp_rdkit_properties.chi3n 0.363
_pdbe_chem_comp_rdkit_properties.chi4n 0.099
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.220
_pdbe_chem_comp_rdkit_properties.kappa1 1.436
_pdbe_chem_comp_rdkit_properties.kappa2 3.742
_pdbe_chem_comp_rdkit_properties.kappa3 2.873
_pdbe_chem_comp_rdkit_properties.Phi 0.672
#
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
HCS UniChem DrugBank DB04422
HCS UniChem 'Guide to Pharmacology' 5198
HCS UniChem 'KEGG LIGAND' C00155
HCS UniChem ChEBI 17588
HCS UniChem ChEBI 58199
HCS UniChem ZINC ZINC000000895077
HCS UniChem fdasrs 0LVT1QZ0BA
HCS UniChem SureChEMBL SCHEMBL35837
HCS UniChem HMDB HMDB0000742
HCS UniChem 'PubChem TPHARMA' 14747714
HCS UniChem NMRShiftDB 60020612
HCS UniChem ACTor 6027-13-0
HCS UniChem Recon 'hcys_L'
HCS UniChem BindingDb 50242405
HCS UniChem 'EPA CompTox Dashboard' DTXSID3041039
HCS UniChem MetaboLights MTBLC17588
HCS UniChem MetaboLights MTBLC58199
HCS UniChem BRENDA 234082
HCS UniChem BRENDA 305
HCS UniChem BRENDA 747
HCS UniChem Rhea 58199
HCS UniChem ChemicalBook CB1112199
HCS UniChem MedChemExpress HY-W010347
HCS UniChem 'Probes And Drugs' PD006228
HCS UniChem CCDC EMANIR
HCS UniChem Nikkaji J228C
HCS UniChem eMolecules 1938844
HCS UniChem PubChem 6971015
HCS UniChem PubChem 91552
HCS UniChem Mcule MCULE-4021115723
#
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
HCS N -1.381 1.067 -1.443 ETKDGv3 1
HCS CA -0.530 -0.001 -0.917 ETKDGv3 2
HCS CB 0.506 0.560 0.081 ETKDGv3 3
HCS CG 1.538 -0.494 0.497 ETKDGv3 4
HCS SD 2.756 0.229 1.639 ETKDGv3 5
HCS C -1.393 -1.052 -0.276 ETKDGv3 6
HCS OXT -2.220 -0.719 0.794 ETKDGv3 7
HCS O -1.368 -2.237 -0.704 ETKDGv3 8
HCS H -0.787 1.726 -1.998 ETKDGv3 9
HCS H2 -1.789 1.612 -0.648 ETKDGv3 10
HCS HA 0.016 -0.459 -1.774 ETKDGv3 11
HCS HB2 -0.011 0.951 0.986 ETKDGv3 12
HCS HB3 1.041 1.409 -0.398 ETKDGv3 13
HCS HG2 1.036 -1.338 1.015 ETKDGv3 14
HCS HG3 2.069 -0.886 -0.396 ETKDGv3 15
HCS HD 3.321 1.051 0.645 ETKDGv3 16
HCS HXT -2.803 -1.419 1.236 ETKDGv3 17
#