data_SME
#
_chem_comp.id SME
_chem_comp.name 'METHIONINE SULFOXIDE'
_chem_comp.type 'L-PEPTIDE LINKING'
_chem_comp.pdbx_type ATOMP
_chem_comp.formula 'C5 H11 N O3 S'
_chem_comp.mon_nstd_parent_comp_id MET
_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 165.211
_chem_comp.one_letter_code M
_chem_comp.three_letter_code SME
_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 1BA6
_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
SME N N N 0 1 N N N Y Y N 7.763 -0.195 -10.134 -1.797 -0.400 -1.472 N SME 1
SME CA CA C 0 1 N N S Y N N 6.958 0.781 -10.922 -0.566 0.400 -1.524 CA SME 2
SME CB CB C 0 1 N N N N N N 5.987 -0.007 -11.847 0.285 0.107 -0.288 CB SME 3
SME CG CG C 0 1 N N N N N N 5.729 0.796 -13.133 -0.504 0.467 0.972 CG SME 4
SME S S S 0 1 N N R N N N 4.691 -0.181 -14.233 0.506 0.120 2.438 S SME 5
SME OE OE O 0 1 N N N N N N 5.421 -1.423 -14.572 0.742 -1.277 2.530 OE SME 6
SME CE CE C 0 1 N N N N N N 4.760 0.909 -15.665 -0.648 0.626 3.743 CE SME 7
SME C C C 0 1 N N N Y N Y 6.186 1.682 -9.946 0.210 0.046 -2.765 C SME 8
SME O O O 0 1 N N N Y N Y 5.088 2.131 -10.217 0.137 -1.067 -3.227 O SME 9
SME OXT OXT O 0 1 N Y N Y N Y 6.817 1.912 -8.824 0.985 0.968 -3.358 OXT SME 10
SME H 1HN H 0 1 N N N Y Y N 7.570 -0.314 -9.184 -2.230 -0.208 -0.581 H SME 11
SME H2 2HN H 0 1 N Y N Y Y N 8.248 -0.869 -10.726 -1.512 -1.368 -1.453 H2 SME 12
SME HA HA H 0 1 N N N Y N N 7.644 1.398 -11.474 -0.823 1.459 -1.546 HA SME 13
SME HB2 1HB H 0 1 N N N N N N 5.051 -0.194 -11.341 1.198 0.702 -0.326 HB2 SME 14
SME HB3 2HB H 0 1 N N N N N N 6.421 -0.960 -12.111 0.542 -0.951 -0.266 HB3 SME 15
SME HG2 1HG H 0 1 N N N N N N 6.662 1.016 -13.632 -1.417 -0.127 1.011 HG2 SME 16
SME HG3 2HG H 0 1 N N N N N N 5.223 1.722 -12.902 -0.761 1.526 0.950 HG3 SME 17
SME HE1 1HE H 0 1 N N N N N N 4.397 1.889 -15.391 -0.182 0.477 4.717 HE1 SME 18
SME HE2 2HE H 0 1 N N N N N N 4.143 0.505 -16.454 -0.899 1.679 3.617 HE2 SME 19
SME HE3 3HE H 0 1 N N N N N N 5.780 0.986 -16.011 -1.555 0.025 3.678 HE3 SME 20
SME HXT HXT H 0 1 N Y N Y N Y 6.339 2.469 -8.220 1.484 0.741 -4.154 HXT SME 21
#
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
SME N CA SING N N 1
SME N H SING N N 2
SME N H2 SING N N 3
SME CA CB SING N N 4
SME CA C SING N N 5
SME CA HA SING N N 6
SME CB CG SING N N 7
SME CB HB2 SING N N 8
SME CB HB3 SING N N 9
SME CG S SING N N 10
SME CG HG2 SING N N 11
SME CG HG3 SING N N 12
SME S OE DOUB N N 13
SME S CE SING N N 14
SME CE HE1 SING N N 15
SME CE HE2 SING N N 16
SME CE HE3 SING N N 17
SME C O DOUB N N 18
SME C OXT SING N N 19
SME OXT HXT SING N N 20
#
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
SME SMILES ACDLabs 10.04 'O=C(O)C(N)CCS(=O)C'
SME SMILES_CANONICAL CACTVS 3.341 'C[S@@](=O)CC[C@H](N)C(O)=O'
SME SMILES CACTVS 3.341 'C[S](=O)CC[CH](N)C(O)=O'
SME SMILES_CANONICAL 'OpenEye OEToolkits' 1.5.0 'C[S@@](=O)CC[C@@H](C(=O)O)N'
SME SMILES 'OpenEye OEToolkits' 1.5.0 'CS(=O)CCC(C(=O)O)N'
SME InChI InChI 1.03 'InChI=1S/C5H11NO3S/c1-10(9)3-2-4(6)5(7)8/h4H,2-3,6H2,1H3,(H,7,8)/t4-,10+/m0/s1'
SME InChIKey InChI 1.03 QEFRNWWLZKMPFJ-ZXPFJRLXSA-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
SME 'SYSTEMATIC NAME' ACDLabs 10.04 '(2S)-2-amino-4-[(R)-methylsulfinyl]butanoic acid'
SME 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 1.5.0 '(2S)-2-amino-4-[(R)-methylsulfinyl]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
SME 'Create component' 1999-07-08 RCSB
SME 'Modify descriptor' 2011-06-04 RCSB
SME 'Modify backbone' 2023-11-03 PDBE
SME 'Modify PCM' 2024-09-27 PDBE
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id SME
_pdbx_chem_comp_pcm.modified_residue_id MET
_pdbx_chem_comp_pcm.type Oxidation
_pdbx_chem_comp_pcm.category 'Named protein modification'
_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 ?
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom ?
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession PTM-0480
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession PTM-0469
#
_pdbe_chem_comp_drugbank_details.comp_id SME
_pdbe_chem_comp_drugbank_details.drugbank_id DB02235
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name 'L-methionine (R)-S-oxide'
_pdbe_chem_comp_drugbank_details.description ?
_pdbe_chem_comp_drugbank_details.cas_number 62697-73-8
_pdbe_chem_comp_drugbank_details.mechanism_of_action ?
#
loop_
_pdbe_chem_comp_synonyms.comp_id
_pdbe_chem_comp_synonyms.name
_pdbe_chem_comp_synonyms.provenance
_pdbe_chem_comp_synonyms.type
SME 'L-methionine (R)-S-oxide' DrugBank ?
SME 'Methionine Sulfoxide' DrugBank ?
#
_pdbe_chem_comp_drugbank_classification.comp_id SME
_pdbe_chem_comp_drugbank_classification.drugbank_id DB02235
_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_
_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
SME DB02235 'Amyloid-beta precursor protein' Humans P05067 yes 1
SME DB02235 'Thymidylate synthase' Yeast P12461 unknown 2
SME DB02235 Catalase 'Micrococcus luteus' P29422 unknown 3
SME DB02235 Protease 'Bacillus sp. KSM-KP43' Q93UV9 unknown 4
#
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
SME N N 3.805 1.875 1
SME CA C 5.104 1.125 2
SME CB C 5.104 -0.375 3
SME CG C 6.404 -1.125 4
SME S S 6.404 -2.625 5
SME OE O 5.104 -3.375 6
SME CE C 7.702 -3.375 7
SME C C 6.404 1.875 8
SME O O 7.702 1.125 9
SME OXT O 6.404 3.375 10
#
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
SME CA N SINGLE BEGINDASH 1
SME CA CB SINGLE NONE 2
SME CA C SINGLE NONE 3
SME CB CG SINGLE NONE 4
SME CG S SINGLE NONE 5
SME S OE DOUBLE NONE 6
SME S CE SINGLE BEGINWEDGE 7
SME C O DOUBLE NONE 8
SME C OXT SINGLE NONE 9
#
_pdbe_chem_comp_substructure.comp_id SME
_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
SME O F1 1
SME C F1 1
SME CA F1 1
SME N F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id SME
_pdbe_chem_comp_rdkit_properties.exactmw 165.046
_pdbe_chem_comp_rdkit_properties.amw 165.214
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 4
_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 10
_pdbe_chem_comp_rdkit_properties.NumAtoms 21
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 5
_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 2
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 77.526
_pdbe_chem_comp_rdkit_properties.tpsa 80.390
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.833
_pdbe_chem_comp_rdkit_properties.CrippenMR 39.162
_pdbe_chem_comp_rdkit_properties.chi0v 5.397
_pdbe_chem_comp_rdkit_properties.chi1v 3.107
_pdbe_chem_comp_rdkit_properties.chi2v 0.743
_pdbe_chem_comp_rdkit_properties.chi3v 0.743
_pdbe_chem_comp_rdkit_properties.chi4v 0.335
_pdbe_chem_comp_rdkit_properties.chi0n 15.580
_pdbe_chem_comp_rdkit_properties.chi1n 7.259
_pdbe_chem_comp_rdkit_properties.chi2n 0.455
_pdbe_chem_comp_rdkit_properties.chi3n 0.455
_pdbe_chem_comp_rdkit_properties.chi4n 0.146
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.420
_pdbe_chem_comp_rdkit_properties.kappa1 1.840
_pdbe_chem_comp_rdkit_properties.kappa2 4.404
_pdbe_chem_comp_rdkit_properties.kappa3 4.458
_pdbe_chem_comp_rdkit_properties.Phi 0.810
#
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
SME UniChem DrugBank DB02235
SME UniChem 'KEGG LIGAND' C15998
SME UniChem ChEBI 49032
SME UniChem ChEBI 58773
SME UniChem ZINC ZINC000001529567
SME UniChem MetaboLights MTBLC49032
SME UniChem MetaboLights MTBLC58773
SME UniChem BRENDA 16102
SME UniChem BRENDA 17716
SME UniChem BRENDA 22025
SME UniChem BRENDA 25592
SME UniChem BRENDA 3924
SME UniChem BRENDA 4709
SME UniChem BRENDA 51132
SME UniChem BRENDA 52637
SME UniChem BRENDA 57252
SME UniChem BRENDA 8608
SME UniChem Rhea 58773
SME UniChem 'Probes And Drugs' PD016266
SME UniChem PubChem 11862103
SME UniChem SureChEMBL SCHEMBL689456
SME UniChem PubChem 10062737
#
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
SME N -1.736 -1.568 1.120 ETKDGv3 1
SME CA -1.340 -0.208 0.743 ETKDGv3 2
SME CB -0.293 -0.235 -0.389 ETKDGv3 3
SME CG 1.062 -0.780 0.076 ETKDGv3 4
SME S 2.279 -0.661 -1.256 ETKDGv3 5
SME OE 3.487 -1.403 -0.699 ETKDGv3 6
SME CE 2.812 1.062 -1.250 ETKDGv3 7
SME C -2.547 0.566 0.288 ETKDGv3 8
SME O -3.325 0.080 -0.578 ETKDGv3 9
SME OXT -2.790 1.835 0.803 ETKDGv3 10
SME H -2.513 -1.505 1.819 ETKDGv3 11
SME H2 -0.944 -2.015 1.634 ETKDGv3 12
SME HA -0.909 0.310 1.630 ETKDGv3 13
SME HB2 -0.669 -0.853 -1.234 ETKDGv3 14
SME HB3 -0.145 0.802 -0.762 ETKDGv3 15
SME HG2 0.966 -1.849 0.355 ETKDGv3 16
SME HG3 1.426 -0.210 0.957 ETKDGv3 17
SME HE1 3.681 1.181 -1.930 ETKDGv3 18
SME HE2 3.106 1.364 -0.224 ETKDGv3 19
SME HE3 1.985 1.711 -1.603 ETKDGv3 20
SME HXT -3.592 2.374 0.500 ETKDGv3 21
#