data_OMT
#
_chem_comp.id OMT
_chem_comp.name S-DIOXYMETHIONINE
_chem_comp.type 'L-PEPTIDE LINKING'
_chem_comp.pdbx_type ATOMP
_chem_comp.formula 'C5 H11 N O4 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 181.210
_chem_comp.one_letter_code M
_chem_comp.three_letter_code OMT
_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
_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
OMT N N N 0 1 N N N Y Y N 56.236 15.538 10.375 1.865 -0.268 -1.813 N OMT 1
OMT CA CA C 0 1 N N S Y N N 56.345 16.774 11.129 0.427 -0.568 -1.765 CA OMT 2
OMT CB CB C 0 1 N N N N N N 56.266 16.522 12.612 -0.176 0.028 -0.493 CB OMT 3
OMT CG CG C 0 1 N N N N N N 55.866 17.677 13.474 0.512 -0.577 0.731 CG OMT 4
OMT SD SD S 0 1 N N N N N N 54.172 17.790 13.527 -0.203 0.130 2.240 SD OMT 5
OMT CE CE C 0 1 N N N N N N 53.526 16.340 13.611 0.783 -0.753 3.479 CE OMT 6
OMT C C C 0 1 N N N Y N Y 57.764 17.157 10.815 -0.250 0.028 -2.971 C OMT 7
OMT O O O 0 1 N N N Y N Y 58.609 16.262 10.740 0.190 1.034 -3.476 O OMT 8
OMT OXT OXT O 0 1 N Y N Y N Y 58.021 18.462 10.683 -1.343 -0.556 -3.485 OXT OMT 9
OMT OD1 OD1 O 0 1 N N N N N N 53.875 18.606 14.675 -1.558 -0.283 2.347 OD1 OMT 10
OMT OD2 OD2 O 0 1 N N N N N N 53.614 18.434 12.390 0.114 1.514 2.297 OD2 OMT 11
OMT H 1HN H 0 1 N N N Y Y N 56.289 15.708 9.370 2.258 -0.594 -0.942 H OMT 12
OMT H2 2HN H 0 1 N Y N Y Y N 55.391 15.022 10.622 1.951 0.736 -1.812 H2 OMT 13
OMT HA HA H 0 1 N N N Y N N 55.551 17.516 10.879 0.282 -1.648 -1.764 HA OMT 14
OMT HB2 1HB H 0 1 N N N N N N 55.588 15.658 12.807 -1.242 -0.194 -0.457 HB2 OMT 15
OMT HB3 2HB H 0 1 N N N N N N 57.236 16.107 12.971 -0.030 1.108 -0.494 HB3 OMT 16
OMT HG2 1HG H 0 1 N N N N N N 56.315 17.616 14.492 1.578 -0.355 0.696 HG2 OMT 17
OMT HG3 2HG H 0 1 N N N N N N 56.340 18.630 13.145 0.366 -1.658 0.732 HG3 OMT 18
OMT HE1 1HE H 0 1 N N N N N N 52.414 16.414 13.645 0.477 -0.440 4.477 HE1 OMT 19
OMT HE2 2HE H 0 1 N N N N N N 53.873 15.680 12.781 0.626 -1.826 3.370 HE2 OMT 20
OMT HE3 3HE H 0 1 N N N N N N 53.931 15.753 14.468 1.838 -0.523 3.334 HE3 OMT 21
OMT HXT HXT H 0 1 N Y N Y N Y 58.917 18.704 10.484 -1.779 -0.172 -4.259 HXT OMT 22
#
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
OMT N CA SING N N 1
OMT N H SING N N 2
OMT N H2 SING N N 3
OMT CA CB SING N N 4
OMT CA C SING N N 5
OMT CA HA SING N N 6
OMT CB CG SING N N 7
OMT CB HB2 SING N N 8
OMT CB HB3 SING N N 9
OMT CG SD SING N N 10
OMT CG HG2 SING N N 11
OMT CG HG3 SING N N 12
OMT SD CE SING N N 13
OMT SD OD1 DOUB N N 14
OMT SD OD2 DOUB N N 15
OMT CE HE1 SING N N 16
OMT CE HE2 SING N N 17
OMT CE HE3 SING N N 18
OMT C O DOUB N N 19
OMT C OXT SING N N 20
OMT OXT HXT SING N N 21
#
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
OMT SMILES ACDLabs 10.04 'O=S(=O)(C)CCC(C(=O)O)N'
OMT SMILES_CANONICAL CACTVS 3.341 'C[S](=O)(=O)CC[C@H](N)C(O)=O'
OMT SMILES CACTVS 3.341 'C[S](=O)(=O)CC[CH](N)C(O)=O'
OMT SMILES_CANONICAL 'OpenEye OEToolkits' 1.5.0 'CS(=O)(=O)CC[C@@H](C(=O)O)N'
OMT SMILES 'OpenEye OEToolkits' 1.5.0 'CS(=O)(=O)CCC(C(=O)O)N'
OMT InChI InChI 1.03 'InChI=1S/C5H11NO4S/c1-11(9,10)3-2-4(6)5(7)8/h4H,2-3,6H2,1H3,(H,7,8)/t4-/m0/s1'
OMT InChIKey InChI 1.03 UCUNFLYVYCGDHP-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
OMT 'SYSTEMATIC NAME' ACDLabs 10.04 '(2S)-2-amino-4-(methylsulfonyl)butanoic acid'
OMT 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 1.5.0 '(2S)-2-amino-4-methylsulfonyl-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
OMT 'Create component' 1999-07-08 RCSB
OMT 'Modify descriptor' 2011-06-04 RCSB
OMT 'Modify backbone' 2023-11-03 PDBE
OMT 'Modify PCM' 2024-09-27 PDBE
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id OMT
_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-0175
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ?
#
_pdbe_chem_comp_drugbank_details.comp_id OMT
_pdbe_chem_comp_drugbank_details.drugbank_id DB03790
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name 'L-methionine sulfone'
_pdbe_chem_comp_drugbank_details.description ?
_pdbe_chem_comp_drugbank_details.cas_number 7314-32-1
_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
OMT '(S)-Amino-4-(methylsulphonyl)butyric acid' DrugBank ?
OMT 'L-2-amino-4-(methylsulfonyl)butanoic acid' DrugBank ?
OMT 'L-methionine sulfone' DrugBank ?
OMT 'Methionine sulfone' DrugBank ?
OMT S-dioxymethionine DrugBank ?
#
_pdbe_chem_comp_drugbank_classification.comp_id OMT
_pdbe_chem_comp_drugbank_classification.drugbank_id DB03790
_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.'
#
_pdbe_chem_comp_drugbank_targets.comp_id OMT
_pdbe_chem_comp_drugbank_targets.drugbank_id DB03790
_pdbe_chem_comp_drugbank_targets.name Catalase
_pdbe_chem_comp_drugbank_targets.organism 'Proteus mirabilis'
_pdbe_chem_comp_drugbank_targets.uniprot_id P42321
_pdbe_chem_comp_drugbank_targets.pharmacologically_active unknown
_pdbe_chem_comp_drugbank_targets.ordinal 1
#
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
OMT N N 9.495 -0.851 1
OMT CA C 8.196 -0.101 2
OMT CB C 6.897 -0.851 3
OMT CG C 5.598 -0.101 4
OMT SD S 4.299 -0.851 5
OMT CE C 3.549 0.449 6
OMT C C 8.196 1.399 7
OMT O O 9.495 2.150 8
OMT OXT O 6.897 2.150 9
OMT OD1 O 5.049 -2.150 10
OMT OD2 O 3.000 -1.601 11
#
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
OMT CA N SINGLE BEGINWEDGE 1
OMT CA CB SINGLE NONE 2
OMT CA C SINGLE NONE 3
OMT CB CG SINGLE NONE 4
OMT CG SD SINGLE NONE 5
OMT SD CE SINGLE NONE 6
OMT SD OD1 DOUBLE NONE 7
OMT SD OD2 DOUBLE NONE 8
OMT C O DOUBLE NONE 9
OMT C OXT SINGLE NONE 10
#
_pdbe_chem_comp_substructure.comp_id OMT
_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
OMT O F1 1
OMT C F1 1
OMT CA F1 1
OMT N F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id OMT
_pdbe_chem_comp_rdkit_properties.exactmw 181.041
_pdbe_chem_comp_rdkit_properties.amw 181.213
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 5
_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 5
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 11
_pdbe_chem_comp_rdkit_properties.NumAtoms 22
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 6
_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 80.778
_pdbe_chem_comp_rdkit_properties.tpsa 97.460
_pdbe_chem_comp_rdkit_properties.CrippenClogP -1.167
_pdbe_chem_comp_rdkit_properties.CrippenMR 39.939
_pdbe_chem_comp_rdkit_properties.chi0v 5.805
_pdbe_chem_comp_rdkit_properties.chi1v 3.607
_pdbe_chem_comp_rdkit_properties.chi2v 0.868
_pdbe_chem_comp_rdkit_properties.chi3v 0.868
_pdbe_chem_comp_rdkit_properties.chi4v 0.398
_pdbe_chem_comp_rdkit_properties.chi0n 15.988
_pdbe_chem_comp_rdkit_properties.chi1n 7.426
_pdbe_chem_comp_rdkit_properties.chi2n 0.497
_pdbe_chem_comp_rdkit_properties.chi3n 0.497
_pdbe_chem_comp_rdkit_properties.chi4n 0.167
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.620
_pdbe_chem_comp_rdkit_properties.kappa1 2.199
_pdbe_chem_comp_rdkit_properties.kappa2 3.679
_pdbe_chem_comp_rdkit_properties.kappa3 5.806
_pdbe_chem_comp_rdkit_properties.Phi 0.735
#
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
OMT UniChem ChEMBL CHEMBL442720
OMT UniChem ChEBI CHEBI:21363
OMT UniChem ChEBI CHEBI:87824
OMT UniChem BRENDA 106423
OMT UniChem BRENDA 135324
OMT UniChem BRENDA 3081
OMT UniChem BRENDA 69849
OMT UniChem BRENDA 9215
OMT UniChem MolPort Molport-003-938-154
OMT UniChem SureChEMBL 153635
OMT UniChem 'EPA CompTox Dashboard' DTXSID301350027
OMT UniChem fdasrs V3Z9QH81BX
OMT UniChem HMDB HMDB0062174
OMT UniChem PubChem 445282
OMT UniChem PubChem 6994316
OMT UniChem 'Probes And Drugs' PD059477
OMT UniChem CCDC IMIWUW
OMT UniChem DrugBank DB03790
#
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
OMT N -2.303 -1.036 -0.075 ETKDGv3 1
OMT CA -1.724 0.089 0.666 ETKDGv3 2
OMT CB -0.394 0.539 0.029 ETKDGv3 3
OMT CG 0.723 -0.496 0.207 ETKDGv3 4
OMT SD 2.278 0.137 -0.403 ETKDGv3 5
OMT CE 3.532 -1.110 -0.218 ETKDGv3 6
OMT C -2.689 1.242 0.676 ETKDGv3 7
OMT O -3.206 1.648 -0.400 ETKDGv3 8
OMT OXT -2.989 1.883 1.874 ETKDGv3 9
OMT OD1 2.147 0.495 -1.857 ETKDGv3 10
OMT OD2 2.674 1.357 0.379 ETKDGv3 11
OMT H -3.245 -1.250 0.329 ETKDGv3 12
OMT H2 -1.727 -1.888 0.109 ETKDGv3 13
OMT HA -1.540 -0.220 1.720 ETKDGv3 14
OMT HB2 -0.071 1.489 0.511 ETKDGv3 15
OMT HB3 -0.546 0.738 -1.054 ETKDGv3 16
OMT HG2 0.842 -0.750 1.282 ETKDGv3 17
OMT HG3 0.484 -1.422 -0.357 ETKDGv3 18
OMT HE1 3.247 -2.013 -0.797 ETKDGv3 19
OMT HE2 3.634 -1.378 0.854 ETKDGv3 20
OMT HE3 4.501 -0.722 -0.594 ETKDGv3 21
OMT HXT -3.629 2.668 1.897 ETKDGv3 22
#