(Translated by https://www.hiragana.jp/)
data_SER # _chem_comp.id SER _chem_comp.name SERINE _chem_comp.type "L-PEPTIDE LINKING" _chem_comp.pdbx_type ATOMP _chem_comp.formula "C3 H7 N O3" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 1999-07-08 _chem_comp.pdbx_modified_date 2023-11-03 _chem_comp.pdbx_ambiguous_flag N _chem_comp.pdbx_release_status REL _chem_comp.pdbx_replaced_by ? _chem_comp.pdbx_replaces SEG _chem_comp.formula_weight 105.093 _chem_comp.one_letter_code S _chem_comp.three_letter_code SER _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 ? _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 SER N N N 0 1 N N N Y Y N 88.198 -7.658 -9.979 1.525 0.493 -0.608 N SER 1 SER CA CA C 0 1 N N S Y N N 87.782 -7.276 -11.358 0.100 0.469 -0.252 CA SER 2 SER C C C 0 1 N N N Y N Y 88.571 -6.062 -11.818 -0.053 0.004 1.173 C SER 3 SER O O O 0 1 N N N Y N Y 89.008 -5.296 -10.944 0.751 -0.760 1.649 O SER 4 SER CB CB C 0 1 N N N N N N 86.286 -6.966 -11.391 -0.642 -0.489 -1.184 CB SER 5 SER OG OG O 0 1 N N N N N N 85.543 -8.096 -10.989 -0.496 -0.049 -2.535 OG SER 6 SER OXT OXT O 0 1 N Y N Y N Y 88.737 -5.884 -13.035 -1.084 0.440 1.913 OXT SER 7 SER H H H 0 1 N N N Y Y N 87.668 -8.473 -9.670 1.867 -0.449 -0.499 H SER 8 SER H2 HN2 H 0 1 N Y N Y Y N 88.118 -6.879 -9.325 1.574 0.707 -1.593 H2 SER 9 SER HA HA H 0 1 N N N Y N N 87.988 -8.129 -12.045 -0.316 1.471 -0.354 HA SER 10 SER HB2 1HB H 0 1 N N N N N N 86.034 -6.065 -10.783 -0.225 -1.491 -1.081 HB2 SER 11 SER HB3 2HB H 0 1 N N N N N N 85.961 -6.588 -12.388 -1.699 -0.507 -0.920 HB3 SER 12 SER HG HG H 0 1 N N N N N N 84.613 -7.903 -11.009 -0.978 -0.679 -3.088 HG SER 13 SER HXT HXT H 0 1 N Y N Y N Y 89.230 -5.124 -13.322 -1.183 0.142 2.828 HXT SER 14 # 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 SER N CA SING N N 1 SER N H SING N N 2 SER N H2 SING N N 3 SER CA C SING N N 4 SER CA CB SING N N 5 SER CA HA SING N N 6 SER C O DOUB N N 7 SER C OXT SING N N 8 SER CB OG SING N N 9 SER CB HB2 SING N N 10 SER CB HB3 SING N N 11 SER OG HG SING N N 12 SER OXT HXT SING N N 13 # 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 SER SMILES ACDLabs 10.04 O=C(O)C(N)CO SER SMILES_CANONICAL CACTVS 3.341 N[C@@H](CO)C(O)=O SER SMILES CACTVS 3.341 N[CH](CO)C(O)=O SER SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C([C@@H](C(=O)O)N)O SER SMILES "OpenEye OEToolkits" 1.5.0 C(C(C(=O)O)N)O SER InChI InChI 1.03 InChI=1S/C3H7NO3/c4-2(1-5)3(6)7/h2,5H,1,4H2,(H,6,7)/t2-/m0/s1 SER InChIKey InChI 1.03 MTCFGRXMJLQNBG-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 SER "SYSTEMATIC NAME" ACDLabs 10.04 L-serine SER "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2S)-2-amino-3-hydroxy-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 SER 'Create component' 1999-07-08 RCSB SER 'Modify descriptor' 2011-06-04 RCSB SER 'Modify backbone' 2023-11-03 PDBE # _pdbe_chem_comp_drugbank_details.comp_id SER _pdbe_chem_comp_drugbank_details.drugbank_id DB00133 _pdbe_chem_comp_drugbank_details.type 'small molecule' _pdbe_chem_comp_drugbank_details.name Serine _pdbe_chem_comp_drugbank_details.description 'A non-essential amino acid occurring in natural form as the L-isomer. It is synthesized from glycine or threonine. It is involved in the biosynthesis of purines; pyrimidines; and other amino acids.' _pdbe_chem_comp_drugbank_details.cas_number 56-45-1 _pdbe_chem_comp_drugbank_details.mechanism_of_action 'L-Serine plays a role in cell growth and development (cellular proliferation). The conversion of L-serine to glycine by serine hydroxymethyltransferase results in the formation of the one-carbon units necessary for the synthesis of the purine bases, adenine and guanine. These bases when linked to the phosphate ester of pentose sugars are essential components of DNA and RNA and the end products of energy producing metabolic pathways, ATP and GTP. In addition, L-serine conversion to glycine via this same enzyme provides the one-carbon units necessary for production of the pyrimidine nucleotide, deoxythymidine monophosphate, also an essential component of DNA.' # loop_ _pdbe_chem_comp_synonyms.comp_id _pdbe_chem_comp_synonyms.name _pdbe_chem_comp_synonyms.provenance _pdbe_chem_comp_synonyms.type SER '(S)-2-Amino-3-hydroxypropanoic acid' DrugBank ? SER (S)-Serine DrugBank ? SER 'alpha-Amino-beta-hydroxypropionic acid' DrugBank ? SER beta-Hydroxyalanine DrugBank ? SER L-Serine DrugBank ? SER Ser DrugBank ? SER Serine DrugBank ? SER Serinum DrugBank ? # _pdbe_chem_comp_drugbank_classification.comp_id SER _pdbe_chem_comp_drugbank_classification.drugbank_id DB00133 _pdbe_chem_comp_drugbank_classification.parent 'Serine and derivatives' _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 serine and derivatives. These are compounds containing serine or a derivative thereof resulting from reaction of serine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom.' # 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 SER DB00133 'Cystathionine beta-synthase' Humans P35520 unknown 1 SER DB00133 'L-serine dehydratase/L-threonine deaminase' Humans P20132 unknown 2 SER DB00133 'Serine racemase' Humans Q9GZT4 unknown 3 SER DB00133 'Serine palmitoyltransferase 2' Humans O15270 unknown 4 SER DB00133 'Serine palmitoyltransferase 1' Humans O15269 unknown 5 SER DB00133 'Serine--tRNA ligase, cytoplasmic' Humans P49591 unknown 6 SER DB00133 'Serine--pyruvate aminotransferase' Humans P21549 unknown 7 # 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 SER N N 3.805 1.215 1 SER CA C 5.104 0.465 2 SER C C 6.404 1.215 3 SER O O 7.702 0.465 4 SER CB C 5.104 -1.035 5 SER OG O 3.805 -1.785 6 SER OXT O 6.404 2.715 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 SER CA N SINGLE BEGINDASH 1 SER CA C SINGLE NONE 2 SER CA CB SINGLE NONE 3 SER C O DOUBLE NONE 4 SER C OXT SINGLE NONE 5 SER CB OG SINGLE NONE 6 # _pdbe_chem_comp_substructure.comp_id SER _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 SER O F1 1 SER C F1 1 SER CA F1 1 SER N F1 1 # _pdbe_chem_comp_rdkit_properties.comp_id SER _pdbe_chem_comp_rdkit_properties.exactmw 105.043 _pdbe_chem_comp_rdkit_properties.amw 105.093 _pdbe_chem_comp_rdkit_properties.lipinskiHBA 4 _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 4 _pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 7 _pdbe_chem_comp_rdkit_properties.NumAtoms 14 _pdbe_chem_comp_rdkit_properties.NumHeteroatoms 4 _pdbe_chem_comp_rdkit_properties.NumAmideBonds 0 _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 50.683 _pdbe_chem_comp_rdkit_properties.tpsa 83.550 _pdbe_chem_comp_rdkit_properties.CrippenClogP -1.609 _pdbe_chem_comp_rdkit_properties.CrippenMR 22.697 _pdbe_chem_comp_rdkit_properties.chi0v 3.172 _pdbe_chem_comp_rdkit_properties.chi1v 1.336 _pdbe_chem_comp_rdkit_properties.chi2v 0.290 _pdbe_chem_comp_rdkit_properties.chi3v 0.290 _pdbe_chem_comp_rdkit_properties.chi4v 0.042 _pdbe_chem_comp_rdkit_properties.chi0n 10.172 _pdbe_chem_comp_rdkit_properties.chi1n 4.547 _pdbe_chem_comp_rdkit_properties.chi2n 0.290 _pdbe_chem_comp_rdkit_properties.chi3n 0.290 _pdbe_chem_comp_rdkit_properties.chi4n 0.042 _pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.610 _pdbe_chem_comp_rdkit_properties.kappa1 1.209 _pdbe_chem_comp_rdkit_properties.kappa2 2.544 _pdbe_chem_comp_rdkit_properties.kappa3 2.132 _pdbe_chem_comp_rdkit_properties.Phi 0.439 # 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 SER UniChem ChEMBL CHEMBL11298 SER UniChem DrugBank DB00133 SER UniChem PDBe SER SER UniChem 'Guide to Pharmacology' 726 SER UniChem 'KEGG LIGAND' C00065 SER UniChem ChEBI 17115 SER UniChem ChEBI 33384 SER UniChem ZINC ZINC000000895034 SER UniChem fdasrs 452VLY9402 SER UniChem PharmGKB PA451330 SER UniChem HMDB HMDB0000187 SER UniChem Recon 'ser_L' SER UniChem BindingDb 50357212 SER UniChem 'EPA CompTox Dashboard' DTXSID60883230 SER UniChem DrugCentral 4127 SER UniChem MetaboLights MTBLC33384 SER UniChem BRENDA 145040 SER UniChem BRENDA 145952 SER UniChem BRENDA 262 SER UniChem BRENDA 35658 SER UniChem BRENDA 870 SER UniChem BRENDA 930 SER UniChem BRENDA 95 SER UniChem Rhea 33384 SER UniChem ChemicalBook CB5673304 SER UniChem DailyMed SERINE SER UniChem ClinicalTrials L-SERINE SER UniChem ClinicalTrials SERINE SER UniChem rxnorm SERINE SER UniChem MedChemExpress HY-N0650 SER UniChem 'Probes And Drugs' PD010212 SER UniChem MetaboLights MTBLC17115 SER UniChem eMolecules 514205 SER UniChem SureChEMBL SCHEMBL1775 SER UniChem 'PubChem TPHARMA' 15119722 SER UniChem 'PubChem TPHARMA' 16532479 SER UniChem PubChem 5951 SER UniChem PubChem 6857581 SER UniChem Mcule MCULE-5604658333 SER UniChem Mcule MCULE-6118038121 SER UniChem NMRShiftDB 60006048 SER UniChem ACTor 25821-52-7 SER UniChem Nikkaji J1.195I # 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 SER N -0.210 -1.527 0.638 ETKDGv3 1 SER CA 0.151 -0.465 -0.305 ETKDGv3 2 SER C 1.353 0.291 0.190 ETKDGv3 3 SER O 1.414 0.686 1.386 ETKDGv3 4 SER CB -1.029 0.486 -0.581 ETKDGv3 5 SER OG -1.415 1.175 0.580 ETKDGv3 6 SER OXT 2.389 0.591 -0.690 ETKDGv3 7 SER H -1.006 -2.075 0.236 ETKDGv3 8 SER H2 -0.542 -1.109 1.537 ETKDGv3 9 SER HA 0.428 -0.945 -1.270 ETKDGv3 10 SER HB2 -1.885 -0.086 -1.009 ETKDGv3 11 SER HB3 -0.724 1.231 -1.347 ETKDGv3 12 SER HG -2.126 0.635 1.014 ETKDGv3 13 SER HXT 3.201 1.112 -0.379 ETKDGv3 14 #