data_HSE
#
_chem_comp.id HSE
_chem_comp.name L-HOMOSERINE
_chem_comp.type 'L-PEPTIDE LINKING'
_chem_comp.pdbx_type ATOMP
_chem_comp.formula 'C4 H9 N O3'
_chem_comp.mon_nstd_parent_comp_id SER
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2000-02-02
_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 119.119
_chem_comp.one_letter_code S
_chem_comp.three_letter_code HSE
_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 1EBU
_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
HSE N NA N 0 1 N N N Y Y N 38.590 23.620 61.202 1.734 0.369 0.174 NA HSE 1
HSE CA C1 C 0 1 N N S Y N N 39.987 23.730 61.744 0.278 0.519 0.296 C1 HSE 2
HSE C C2 C 0 1 N N N Y N Y 39.848 23.878 63.264 -0.174 -0.032 1.623 C2 HSE 3
HSE C3 C3 C 0 1 N N N N N N 40.654 24.925 61.000 -0.410 -0.246 -0.835 C3 HSE 4
HSE O O1 O 0 1 N N N Y N Y 40.876 23.981 63.977 0.434 -0.939 2.139 O1 HSE 5
HSE OXT O2 O 0 1 N Y N Y N Y 38.651 23.875 63.662 -1.252 0.484 2.233 O2 HSE 6
HSE C4 C4 C 0 1 N N N N N N 42.098 25.192 61.412 0.048 0.314 -2.183 C4 HSE 7
HSE O3 O3 O 0 1 N N N N N N 42.680 26.296 60.710 -0.594 -0.400 -3.240 O3 HSE 8
HSE H HN1 H 0 1 N N N Y Y N 38.682 23.521 60.191 1.977 0.653 -0.763 HN1 HSE 9
HSE H2 HN2 H 0 1 N Y N Y Y N 37.985 24.393 61.480 1.930 -0.618 0.237 HN2 HSE 10
HSE HA H1 H 0 1 N N N Y N N 40.647 22.848 61.573 0.015 1.575 0.233 H1 HSE 11
HSE H31 H31 H 0 1 N N N N N N 40.583 24.785 59.896 -0.147 -1.302 -0.772 H31 HSE 12
HSE H32 H32 H 0 1 N N N N N N 40.038 25.847 61.114 -1.490 -0.134 -0.744 H32 HSE 13
HSE HXT HO2 H 0 1 N Y N Y N Y 38.564 23.966 64.603 -1.542 0.130 3.084 HO2 HSE 14
HSE H41 H41 H 0 1 N N N N N N 42.179 25.332 62.515 -0.214 1.370 -2.246 H41 HSE 15
HSE H42 H42 H 0 1 N N N N N N 42.721 24.274 61.300 1.129 0.202 -2.273 H42 HSE 16
HSE HO3 HO3 H 0 1 N N N N N N 43.579 26.462 60.966 -0.278 -0.017 -4.069 HO3 HSE 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
HSE N CA SING N N 1
HSE N H SING N N 2
HSE N H2 SING N N 3
HSE CA C SING N N 4
HSE CA C3 SING N N 5
HSE CA HA SING N N 6
HSE C O DOUB N N 7
HSE C OXT SING N N 8
HSE C3 C4 SING N N 9
HSE C3 H31 SING N N 10
HSE C3 H32 SING N N 11
HSE OXT HXT SING N N 12
HSE C4 O3 SING N N 13
HSE C4 H41 SING N N 14
HSE C4 H42 SING N N 15
HSE O3 HO3 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
HSE SMILES ACDLabs 10.04 'O=C(O)C(N)CCO'
HSE SMILES_CANONICAL CACTVS 3.341 'N[C@@H](CCO)C(O)=O'
HSE SMILES CACTVS 3.341 'N[CH](CCO)C(O)=O'
HSE SMILES_CANONICAL 'OpenEye OEToolkits' 1.5.0 'C(CO)[C@@H](C(=O)O)N'
HSE SMILES 'OpenEye OEToolkits' 1.5.0 'C(CO)C(C(=O)O)N'
HSE InChI InChI 1.03 'InChI=1S/C4H9NO3/c5-3(1-2-6)4(7)8/h3,6H,1-2,5H2,(H,7,8)/t3-/m0/s1'
HSE InChIKey InChI 1.03 UKAUYVFTDYCKQA-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
HSE 'SYSTEMATIC NAME' ACDLabs 10.04 L-homoserine
HSE 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 1.5.0 '(2S)-2-amino-4-hydroxy-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
HSE 'Create component' 2000-02-02 RCSB
HSE 'Modify descriptor' 2011-06-04 RCSB
HSE 'Modify backbone' 2023-11-03 PDBE
HSE 'Modify PCM' 2024-09-27 PDBE
#
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
_pdbx_chem_comp_pcm.first_instance_model_db_code
1 HSE ? None 'Non-standard residue' 'Amino-acid side chain' 'Any position' ? ? ? ? 1CIR
2 HSE CYS None 'Covalent chemical modification' 'Amino-acid side chain' 'Any position' C4 SG ? ? 1NWH
3 HSE LLP None 'Covalent chemical modification' 'Amino-acid side chain' 'Any position' N "C4'" ? ? 8ZIF
#
_pdbe_chem_comp_drugbank_details.comp_id HSE
_pdbe_chem_comp_drugbank_details.drugbank_id DB04193
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name L-Homoserine
_pdbe_chem_comp_drugbank_details.description ?
_pdbe_chem_comp_drugbank_details.cas_number 672-15-1
_pdbe_chem_comp_drugbank_details.mechanism_of_action ?
#
_pdbe_chem_comp_drugbank_classification.comp_id HSE
_pdbe_chem_comp_drugbank_classification.drugbank_id DB04193
_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_
_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
HSE N N 3.805 1.732 1
HSE CA C 5.104 0.983 2
HSE C C 6.404 1.732 3
HSE C3 C 5.104 -0.517 4
HSE O O 7.702 0.983 5
HSE OXT O 6.404 3.232 6
HSE C4 C 3.805 -1.268 7
HSE O3 O 3.805 -2.768 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
HSE CA N SINGLE BEGINDASH 1
HSE CA C SINGLE NONE 2
HSE CA C3 SINGLE NONE 3
HSE C O DOUBLE NONE 4
HSE C OXT SINGLE NONE 5
HSE C3 C4 SINGLE NONE 6
HSE C4 O3 SINGLE NONE 7
#
_pdbe_chem_comp_substructure.comp_id HSE
_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
HSE O F1 1
HSE C F1 1
HSE CA F1 1
HSE N F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id HSE
_pdbe_chem_comp_rdkit_properties.exactmw 119.058
_pdbe_chem_comp_rdkit_properties.amw 119.120
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 4
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 4
_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 59.858
_pdbe_chem_comp_rdkit_properties.tpsa 83.550
_pdbe_chem_comp_rdkit_properties.CrippenClogP -1.219
_pdbe_chem_comp_rdkit_properties.CrippenMR 27.314
_pdbe_chem_comp_rdkit_properties.chi0v 3.672
_pdbe_chem_comp_rdkit_properties.chi1v 1.586
_pdbe_chem_comp_rdkit_properties.chi2v 0.363
_pdbe_chem_comp_rdkit_properties.chi3v 0.363
_pdbe_chem_comp_rdkit_properties.chi4v 0.099
_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 -0.610
_pdbe_chem_comp_rdkit_properties.kappa1 1.274
_pdbe_chem_comp_rdkit_properties.kappa2 3.399
_pdbe_chem_comp_rdkit_properties.kappa3 2.544
_pdbe_chem_comp_rdkit_properties.Phi 0.541
#
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
HSE UniChem ChEMBL CHEMBL11722
HSE UniChem DrugBank DB04193
HSE UniChem PDBe HSE
HSE UniChem 'KEGG LIGAND' C00263
HSE UniChem ChEBI 15699
HSE UniChem ChEBI 57476
HSE UniChem ZINC ZINC000000895146
HSE UniChem eMolecules 518497
HSE UniChem fdasrs 6KA95X0IVO
HSE UniChem HMDB HMDB0000719
HSE UniChem 'PubChem TPHARMA' 15146514
HSE UniChem NMRShiftDB 60018693
HSE UniChem ACTor 1927-25-9
HSE UniChem Recon 'hom_L'
HSE UniChem MetaboLights MTBLC15699
HSE UniChem MetaboLights MTBLC57476
HSE UniChem BRENDA 203564
HSE UniChem BRENDA 345
HSE UniChem BRENDA 9897
HSE UniChem Rhea 57476
HSE UniChem ChemicalBook CB2854094
HSE UniChem ChemicalBook CB72130885
HSE UniChem MedChemExpress HY-W002292
HSE UniChem 'Probes And Drugs' PD006892
HSE UniChem 'EPA CompTox Dashboard' DTXSID5075159
HSE UniChem SureChEMBL SCHEMBL29649
HSE UniChem 'PubChem TPHARMA' 14747553
HSE UniChem PubChem 12647
HSE UniChem PubChem 6971022
HSE UniChem Nikkaji J9.199E
#
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
HSE N -0.917 -1.505 -0.436 ETKDGv3 1
HSE CA -0.584 -0.208 0.160 ETKDGv3 2
HSE C -1.773 0.709 0.084 ETKDGv3 3
HSE C3 0.609 0.443 -0.571 ETKDGv3 4
HSE O -2.386 0.867 -1.007 ETKDGv3 5
HSE OXT -2.181 1.409 1.215 ETKDGv3 6
HSE C4 1.934 -0.308 -0.373 ETKDGv3 7
HSE O3 2.256 -0.414 0.987 ETKDGv3 8
HSE H -1.788 -1.865 0.019 ETKDGv3 9
HSE H2 -0.171 -2.190 -0.179 ETKDGv3 10
HSE HA -0.327 -0.352 1.234 ETKDGv3 11
HSE H31 0.391 0.501 -1.661 ETKDGv3 12
HSE H32 0.744 1.484 -0.202 ETKDGv3 13
HSE HXT -2.973 2.039 1.179 ETKDGv3 14
HSE H41 2.745 0.228 -0.916 ETKDGv3 15
HSE H42 1.870 -1.325 -0.812 ETKDGv3 16
HSE HO3 2.552 0.487 1.280 ETKDGv3 17
#