data_MET
#
_chem_comp.id MET
_chem_comp.name METHIONINE
_chem_comp.type 'L-PEPTIDE LINKING'
_chem_comp.pdbx_type ATOMP
_chem_comp.formula 'C5 H11 N O2 S'
_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 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 149.211
_chem_comp.one_letter_code M
_chem_comp.three_letter_code MET
_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 EBI
_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
MET N N N 0 1 N N N Y Y N 16.161 15.756 51.903 -1.816 0.142 -1.166 N MET 1
MET CA CA C 0 1 N N S Y N N 15.084 16.739 51.596 -0.392 0.499 -1.214 CA MET 2
MET C C C 0 1 N N N Y N Y 13.846 15.930 51.367 0.206 0.002 -2.504 C MET 3
MET O O O 0 1 N N N Y N Y 12.795 16.510 51.424 -0.236 -0.989 -3.033 O MET 4
MET CB CB C 0 1 N N N N N N 15.401 17.530 50.317 0.334 -0.145 -0.032 CB MET 5
MET CG CG C 0 1 N N N N N N 16.183 18.846 50.502 -0.273 0.359 1.277 CG MET 6
MET SD SD S 0 1 N N N N N N 17.852 18.653 51.063 0.589 -0.405 2.678 SD MET 7
MET CE CE C 0 1 N N N N N N 18.614 17.814 49.556 -0.314 0.353 4.056 CE MET 8
MET OXT OXT O 0 1 N Y N Y N Y 13.865 14.721 51.154 1.232 0.661 -3.066 OXT MET 9
MET H H H 0 1 N N N Y Y N 17.004 16.307 52.059 -1.865 -0.864 -1.220 H MET 10
MET H2 HN2 H 0 1 N Y N Y Y N 16.270 15.035 51.189 -2.149 0.399 -0.248 H2 MET 11
MET HA HA H 0 1 N N N Y N N 14.975 17.472 52.429 -0.287 1.582 -1.158 HA MET 12
MET HB2 1HB H 0 1 N N N N N N 15.935 16.873 49.591 1.391 0.119 -0.068 HB2 MET 13
MET HB3 2HB H 0 1 N N N N N N 14.459 17.728 49.754 0.229 -1.229 -0.088 HB3 MET 14
MET HG2 1HG H 0 1 N N N N N N 16.160 19.442 49.560 -1.330 0.094 1.313 HG2 MET 15
MET HG3 2HG H 0 1 N N N N N N 15.625 19.532 51.181 -0.168 1.442 1.333 HG3 MET 16
MET HE1 1HE H 0 1 N N N N N N 19.664 17.692 49.909 0.090 -0.010 5.000 HE1 MET 17
MET HE2 2HE H 0 1 N N N N N N 18.107 16.882 49.211 -0.207 1.436 4.008 HE2 MET 18
MET HE3 3HE H 0 1 N N N N N N 18.487 18.349 48.586 -1.369 0.088 3.988 HE3 MET 19
MET HXT HXT H 0 1 N Y N Y N Y 13.079 14.207 51.008 1.616 0.342 -3.894 HXT MET 20
#
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
MET N CA SING N N 1
MET N H SING N N 2
MET N H2 SING N N 3
MET CA C SING N N 4
MET CA CB SING N N 5
MET CA HA SING N N 6
MET C O DOUB N N 7
MET C OXT SING N N 8
MET CB CG SING N N 9
MET CB HB2 SING N N 10
MET CB HB3 SING N N 11
MET CG SD SING N N 12
MET CG HG2 SING N N 13
MET CG HG3 SING N N 14
MET SD CE SING N N 15
MET CE HE1 SING N N 16
MET CE HE2 SING N N 17
MET CE HE3 SING N N 18
MET OXT HXT SING N N 19
#
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
MET SMILES ACDLabs 10.04 'O=C(O)C(N)CCSC'
MET SMILES_CANONICAL CACTVS 3.341 'CSCC[C@H](N)C(O)=O'
MET SMILES CACTVS 3.341 'CSCC[CH](N)C(O)=O'
MET SMILES_CANONICAL 'OpenEye OEToolkits' 1.5.0 'CSCC[C@@H](C(=O)O)N'
MET SMILES 'OpenEye OEToolkits' 1.5.0 'CSCCC(C(=O)O)N'
MET InChI InChI 1.03 'InChI=1S/C5H11NO2S/c1-9-3-2-4(6)5(7)8/h4H,2-3,6H2,1H3,(H,7,8)/t4-/m0/s1'
MET InChIKey InChI 1.03 FFEARJCKVFRZRR-BYPYZUCNSA-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
MET 'SYSTEMATIC NAME' ACDLabs 10.04 L-methionine
MET 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 1.5.0 '(2S)-2-amino-4-methylsulfanyl-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
MET 'Create component' 1999-07-08 EBI
MET 'Modify descriptor' 2011-06-04 RCSB
MET 'Modify backbone' 2023-11-03 PDBE
MET 'Modify PCM' 2024-09-27 PDBE
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id MET
_pdbx_chem_comp_pcm.modified_residue_id ORN
_pdbx_chem_comp_pcm.type Methionylation
_pdbx_chem_comp_pcm.category 'Amino acid'
_pdbx_chem_comp_pcm.position 'Amino-acid side chain'
_pdbx_chem_comp_pcm.polypeptide_position 'Any position'
_pdbx_chem_comp_pcm.comp_id_linking_atom C
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom NE
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ?
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ?
#
_pdbe_chem_comp_drugbank_details.comp_id MET
_pdbe_chem_comp_drugbank_details.drugbank_id DB00134
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name Methionine
_pdbe_chem_comp_drugbank_details.description
'A sulfur containing essential amino acid that is important in many body functions. It is a chelating agent for heavy metals.'
_pdbe_chem_comp_drugbank_details.cas_number 63-68-3
_pdbe_chem_comp_drugbank_details.mechanism_of_action
'The mechanism of the possible anti-hepatotoxic activity of L-methionine is not entirely clear. It is thought that metabolism of high doses of acetaminophen in the liver lead to decreased levels of hepatic glutathione and increased oxidative stress. L-methionine is a precursor to L-cysteine. L-cysteine itself may have antioxidant activity. L-cysteine is also a precursor to the antioxidant glutathione. Antioxidant activity of L-methionine and metabolites of L-methionine appear to account for its possible anti-hepatotoxic activity. Recent research suggests that methionine itself has free-radical scavenging activity by virtue of its sulfur, as well as its chelating ability.'
#
loop_
_pdbe_chem_comp_synonyms.comp_id
_pdbe_chem_comp_synonyms.name
_pdbe_chem_comp_synonyms.provenance
_pdbe_chem_comp_synonyms.type
MET '(2S)-2-amino-4-(methylsulfanyl)butanoic acid' DrugBank ?
MET '(S)-2-amino-4-(methylthio)butanoic acid' DrugBank ?
MET '(S)-2-amino-4-(methylthio)butyric acid' DrugBank ?
MET (S)-methionine DrugBank ?
MET 'L-(−)-methionine' DrugBank ?
MET 'L-a-Amino-g-methylthiobutyric acid' DrugBank ?
MET L-Methionine DrugBank ?
MET 'L-α-amino-γ-methylmercaptobutyric acid' DrugBank ?
MET M DrugBank ?
MET Met DrugBank ?
MET Methionine DrugBank ?
MET Acimethin DrugBank 'International brand'
#
_pdbe_chem_comp_drugbank_classification.comp_id MET
_pdbe_chem_comp_drugbank_classification.drugbank_id DB00134
_pdbe_chem_comp_drugbank_classification.parent 'Methionine 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 methionine and derivatives. These are compounds containing methionine or a derivative thereof resulting from reaction of methionine 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
MET DB00134 'Methionine synthase reductase' Humans Q9UBK8 unknown 1
MET DB00134 'Methionine synthase' Humans Q99707 unknown 2
MET DB00134 'Methionine aminopeptidase 2' Humans P50579 unknown 3
MET DB00134 'Betaine--homocysteine S-methyltransferase 1' Humans Q93088 unknown 4
MET DB00134 'S-methylmethionine--homocysteine S-methyltransferase BHMT2' Humans Q9H2M3 unknown 5
#
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
MET N N 4.299 1.875 1
MET CA C 5.598 1.125 2
MET C C 6.897 1.875 3
MET O O 8.196 1.125 4
MET CB C 5.598 -0.375 5
MET CG C 4.299 -1.125 6
MET SD S 4.299 -2.625 7
MET CE C 3.000 -3.375 8
MET OXT O 6.897 3.375 9
#
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
MET CA N SINGLE BEGINDASH 1
MET CA C SINGLE NONE 2
MET CA CB SINGLE NONE 3
MET C O DOUBLE NONE 4
MET C OXT SINGLE NONE 5
MET CB CG SINGLE NONE 6
MET CG SD SINGLE NONE 7
MET SD CE SINGLE NONE 8
#
_pdbe_chem_comp_substructure.comp_id MET
_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
MET O F1 1
MET C F1 1
MET CA F1 1
MET N F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id MET
_pdbe_chem_comp_rdkit_properties.exactmw 149.051
_pdbe_chem_comp_rdkit_properties.amw 149.215
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 6
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 4
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 9
_pdbe_chem_comp_rdkit_properties.NumAtoms 20
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 4
_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 1
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 74.275
_pdbe_chem_comp_rdkit_properties.tpsa 63.320
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.151
_pdbe_chem_comp_rdkit_properties.CrippenMR 38.610
_pdbe_chem_comp_rdkit_properties.chi0v 4.988
_pdbe_chem_comp_rdkit_properties.chi1v 2.607
_pdbe_chem_comp_rdkit_properties.chi2v 0.618
_pdbe_chem_comp_rdkit_properties.chi3v 0.618
_pdbe_chem_comp_rdkit_properties.chi4v 0.273
_pdbe_chem_comp_rdkit_properties.chi0n 15.172
_pdbe_chem_comp_rdkit_properties.chi1n 7.093
_pdbe_chem_comp_rdkit_properties.chi2n 0.414
_pdbe_chem_comp_rdkit_properties.chi3n 0.414
_pdbe_chem_comp_rdkit_properties.chi4n 0.125
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.220
_pdbe_chem_comp_rdkit_properties.kappa1 1.507
_pdbe_chem_comp_rdkit_properties.kappa2 4.639
_pdbe_chem_comp_rdkit_properties.kappa3 4.294
_pdbe_chem_comp_rdkit_properties.Phi 0.777
#
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
MET UniChem DrugBank DB00134
MET UniChem 'Guide to Pharmacology' 4814
MET UniChem 'KEGG LIGAND' C00073
MET UniChem ChEBI 16643
MET UniChem ChEBI 57844
MET UniChem ZINC ZINC000001532529
MET UniChem eMolecules 514491
MET UniChem atlas methionine
MET UniChem fdasrs AE28F7PNPL
MET UniChem SureChEMBL SCHEMBL4226
MET UniChem PharmGKB PA450423
MET UniChem HMDB HMDB0000696
MET UniChem 'PubChem TPHARMA' 14772273
MET UniChem NMRShiftDB 60018689
MET UniChem ACTor 24425-78-3
MET UniChem ACTor 3654-96-4
MET UniChem ACTor 58576-49-1
MET UniChem Recon 'met_L'
MET UniChem BindingDb 50142500
MET UniChem 'EPA CompTox Dashboard' DTXSID5040548
MET UniChem DrugCentral 3347
MET UniChem MetaboLights MTBLC16643
MET UniChem MetaboLights MTBLC57844
MET UniChem BRENDA 136827
MET UniChem BRENDA 138053
MET UniChem BRENDA 230480
MET UniChem BRENDA 242044
MET UniChem BRENDA 256541
MET UniChem BRENDA 266992
MET UniChem BRENDA 468
MET UniChem BRENDA 678
MET UniChem BRENDA 692
MET UniChem BRENDA 88
MET UniChem Rhea 57844
MET UniChem DailyMed METHIONINE
MET UniChem ClinicalTrials L-METHIONINE
MET UniChem ClinicalTrials METHIONINE
MET UniChem rxnorm METHIONINE
MET UniChem MedChemExpress HY-N0326
MET UniChem 'Probes And Drugs' PD010211
MET UniChem CCDC LMETON
MET UniChem Nikkaji J9.174J
MET UniChem PubChem 6137
MET UniChem PubChem 6992087
MET UniChem Mcule MCULE-3383932641
MET UniChem Mcule MCULE-7228063662
MET UniChem ACTor 26062-47-5
MET UniChem ACTor 33807-07-7
#
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
MET N -2.828 -0.323 -0.901 ETKDGv3 1
MET CA -1.516 -0.350 -0.252 ETKDGv3 2
MET C -1.587 0.411 1.041 ETKDGv3 3
MET O -1.959 1.616 1.051 ETKDGv3 4
MET CB -0.423 0.210 -1.193 ETKDGv3 5
MET CG 1.007 -0.050 -0.695 ETKDGv3 6
MET SD 1.524 1.198 0.537 ETKDGv3 7
MET CE 3.165 0.461 0.816 ETKDGv3 8
MET OXT -1.226 -0.212 2.232 ETKDGv3 9
MET H -2.813 -0.979 -1.716 ETKDGv3 10
MET H2 -3.011 0.636 -1.278 ETKDGv3 11
MET HA -1.274 -1.411 -0.017 ETKDGv3 12
MET HB2 -0.576 1.298 -1.369 ETKDGv3 13
MET HB3 -0.527 -0.293 -2.180 ETKDGv3 14
MET HG2 1.700 0.014 -1.561 ETKDGv3 15
MET HG3 1.087 -1.071 -0.265 ETKDGv3 16
MET HE1 3.743 0.444 -0.132 ETKDGv3 17
MET HE2 3.715 1.073 1.560 ETKDGv3 18
MET HE3 3.058 -0.571 1.209 ETKDGv3 19
MET HXT -1.258 0.290 3.111 ETKDGv3 20
#