(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
#