data_MED
#
_chem_comp.id MED
_chem_comp.name D-METHIONINE
_chem_comp.type "D-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 2002-01-18
_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 ?
_chem_comp.formula_weight 149.211
_chem_comp.one_letter_code M
_chem_comp.three_letter_code MED
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details Corina
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 1KQ0
_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
MED N N N 0 1 N N N Y Y N 20.779 27.715 16.515 -1.228 1.830 0.137 N MED 1
MED CA CA C 0 1 N N R Y N N 19.604 28.469 15.985 -1.222 0.404 0.489 CA MED 2
MED C C C 0 1 N N N Y N Y 18.517 28.702 17.029 -2.505 -0.234 0.023 C MED 3
MED O O O 0 1 N N N Y N Y 18.753 29.040 18.193 -3.167 0.298 -0.836 O MED 4
MED CB CB C 0 1 N N N N N N 20.029 29.809 15.405 -0.035 -0.283 -0.189 CB MED 5
MED CG CG C 0 1 N N N N N N 20.938 30.640 16.249 1.271 0.280 0.377 CG MED 6
MED SD SD S 0 1 N N N N N N 21.032 32.191 15.335 2.679 -0.535 -0.427 SD MED 7
MED CE CE C 0 1 N N N N N N 19.498 32.908 15.736 4.110 0.251 0.363 CE MED 8
MED OXT OXT O 0 1 N Y N Y N Y 17.347 28.561 16.692 -2.912 -1.394 0.562 OXT MED 9
MED H H H 0 1 N N N Y Y N 21.429 27.546 15.774 -0.408 2.295 0.495 H MED 10
MED H2 HN2 H 0 1 N Y N Y Y N 21.223 28.252 17.233 -1.308 1.956 -0.861 H2 MED 11
MED HA HA H 0 1 N N N Y N N 19.179 27.833 15.194 -1.135 0.297 1.570 HA MED 12
MED HB2 HB1 H 0 1 N N N N N N 20.558 29.603 14.463 -0.080 -1.356 -0.001 HB2 MED 13
MED HB3 HB2 H 0 1 N N N N N N 19.103 30.394 15.302 -0.074 -0.101 -1.263 HB3 MED 14
MED HG2 HG1 H 0 1 N N N N N N 20.532 30.788 17.261 1.316 1.352 0.189 HG2 MED 15
MED HG3 HG2 H 0 1 N N N N N N 21.921 30.175 16.411 1.310 0.097 1.451 HG3 MED 16
MED HE1 HE1 H 0 1 N N N N N N 19.437 33.059 16.824 4.084 1.325 0.175 HE1 MED 17
MED HE2 HE2 H 0 1 N N N N N N 19.402 33.877 15.225 4.078 0.070 1.437 HE2 MED 18
MED HE3 HE3 H 0 1 N N N N N N 18.686 32.240 15.412 5.028 -0.168 -0.050 HE3 MED 19
MED HXT HXT H 0 1 N Y N Y N Y 16.780 28.747 17.431 -3.741 -1.765 0.230 HXT MED 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
MED N CA SING N N 1
MED N H SING N N 2
MED N H2 SING N N 3
MED CA C SING N N 4
MED CA CB SING N N 5
MED CA HA SING N N 6
MED C O DOUB N N 7
MED C OXT SING N N 8
MED CB CG SING N N 9
MED CB HB2 SING N N 10
MED CB HB3 SING N N 11
MED CG SD SING N N 12
MED CG HG2 SING N N 13
MED CG HG3 SING N N 14
MED SD CE SING N N 15
MED CE HE1 SING N N 16
MED CE HE2 SING N N 17
MED CE HE3 SING N N 18
MED 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
MED SMILES ACDLabs 10.04 O=C(O)C(N)CCSC
MED SMILES_CANONICAL CACTVS 3.341 CSCC[C@@H](N)C(O)=O
MED SMILES CACTVS 3.341 CSCC[CH](N)C(O)=O
MED SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 CSCC[C@H](C(=O)O)N
MED SMILES "OpenEye OEToolkits" 1.5.0 CSCCC(C(=O)O)N
MED 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-/m1/s1
MED InChIKey InChI 1.03 FFEARJCKVFRZRR-SCSAIBSYSA-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
MED "SYSTEMATIC NAME" ACDLabs 10.04 D-methionine
MED "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2R)-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
MED 'Create component' 2002-01-18 RCSB
MED 'Modify descriptor' 2011-06-04 RCSB
MED 'Modify backbone' 2023-11-03 PDBE
#
_pdbe_chem_comp_drugbank_details.comp_id MED
_pdbe_chem_comp_drugbank_details.drugbank_id DB02893
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name D-Methionine
_pdbe_chem_comp_drugbank_details.description ?
_pdbe_chem_comp_drugbank_details.cas_number 348-67-4
_pdbe_chem_comp_drugbank_details.mechanism_of_action ?
#
_pdbe_chem_comp_drugbank_classification.comp_id MED
_pdbe_chem_comp_drugbank_classification.drugbank_id DB02893
_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
MED DB02893 'Methionine aminopeptidase 2' Humans P50579 yes 1
MED DB02893 'Transcriptional regulator, HTH_3 family' 'Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)' Q9KQN0 unknown 2
#
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
MED N N 4.299 1.875 1
MED CA C 5.598 1.125 2
MED C C 6.897 1.875 3
MED O O 8.196 1.125 4
MED CB C 5.598 -0.375 5
MED CG C 4.299 -1.125 6
MED SD S 4.299 -2.625 7
MED CE C 3.000 -3.375 8
MED 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
MED CA N SINGLE BEGINWEDGE 1
MED CA C SINGLE NONE 2
MED CA CB SINGLE NONE 3
MED C O DOUBLE NONE 4
MED C OXT SINGLE NONE 5
MED CB CG SINGLE NONE 6
MED CG SD SINGLE NONE 7
MED SD CE SINGLE NONE 8
#
_pdbe_chem_comp_substructure.comp_id MED
_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
MED O F1 1
MED C F1 1
MED CA F1 1
MED N F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id MED
_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
MED UniChem DrugBank DB02893
MED UniChem 'PubChem DOTF' 125299323
MED UniChem 'KEGG LIGAND' C00855
MED UniChem ChEBI 16867
MED UniChem ChEBI 57932
MED UniChem ZINC ZINC000001532766
MED UniChem eMolecules 526391
MED UniChem fdasrs 868496F25R
MED UniChem NMRShiftDB 60018872
MED UniChem BindingDb 50463194
MED UniChem 'EPA CompTox Dashboard' DTXSID90883369
MED UniChem MetaboLights MTBLC16867
MED UniChem MetaboLights MTBLC57932
MED UniChem BRENDA 1500
MED UniChem BRENDA 230479
MED UniChem BRENDA 957
MED UniChem Rhea 57932
MED UniChem ChemicalBook CB5748697
MED UniChem MedChemExpress HY-13694
MED UniChem 'Probes And Drugs' PD007976
MED UniChem CCDC ANUPOQ
MED UniChem Nikkaji J9.192H
MED UniChem SureChEMBL SCHEMBL126688
MED UniChem 'PubChem TPHARMA' 14772272
MED UniChem 'PubChem TPHARMA' 15194696
MED UniChem PubChem 6992109
MED UniChem PubChem 84815
MED UniChem Mcule MCULE-9944164883
#
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
MED N -1.863 -1.645 0.279 ETKDGv3 1
MED CA -1.557 -0.510 -0.599 ETKDGv3 2
MED C -1.711 0.814 0.106 ETKDGv3 3
MED O -1.497 0.916 1.345 ETKDGv3 4
MED CB -0.171 -0.676 -1.262 ETKDGv3 5
MED CG 1.036 -0.550 -0.316 ETKDGv3 6
MED SD 1.521 1.198 -0.083 ETKDGv3 7
MED CE 2.881 0.824 1.068 ETKDGv3 8
MED OXT -2.049 1.945 -0.630 ETKDGv3 9
MED H -2.867 -1.580 0.566 ETKDGv3 10
MED H2 -1.293 -1.597 1.153 ETKDGv3 11
MED HA -2.302 -0.523 -1.426 ETKDGv3 12
MED HB2 -0.068 0.059 -2.091 ETKDGv3 13
MED HB3 -0.139 -1.683 -1.733 ETKDGv3 14
MED HG2 1.897 -1.083 -0.775 ETKDGv3 15
MED HG3 0.832 -1.025 0.664 ETKDGv3 16
MED HE1 3.631 0.171 0.575 ETKDGv3 17
MED HE2 3.373 1.773 1.367 ETKDGv3 18
MED HE3 2.486 0.324 1.976 ETKDGv3 19
MED HXT -2.140 2.849 -0.181 ETKDGv3 20
#