data_MSE
#
_chem_comp.id MSE
_chem_comp.name SELENOMETHIONINE
_chem_comp.type "L-PEPTIDE LINKING"
_chem_comp.pdbx_type ATOMP
_chem_comp.formula "C5 H11 N O2 Se"
_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 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 196.106
_chem_comp.one_letter_code M
_chem_comp.three_letter_code MSE
_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
MSE N N N 0 1 N N N Y Y N 11.285 -7.474 19.929 1.869 0.121 -1.981 N MSE 1
MSE CA CA C 0 1 N N S Y N N 10.307 -8.472 19.503 0.520 -0.459 -1.960 CA MSE 2
MSE C C C 0 1 N N N Y N Y 8.897 -8.150 19.998 -0.232 -0.028 -3.192 C MSE 3
MSE O O O 0 1 N N N Y N Y 8.742 -7.166 20.755 0.011 1.037 -3.706 O MSE 4
MSE OXT OXT O 0 1 N Y N Y N Y 7.964 -8.893 19.623 -1.173 -0.828 -3.717 OXT MSE 5
MSE CB CB C 0 1 N N N N N N 10.721 -9.857 20.004 -0.222 0.023 -0.713 CB MSE 6
MSE CG CG C 0 1 N N N N N N 12.078 -10.319 19.497 0.541 -0.414 0.538 CG MSE 7
MSE SE SE SE 0 0 N N N N N N 12.537 -11.948 20.120 -0.410 0.204 2.135 SE MSE 8
MSE CE CE C 0 1 N N N N N N 13.416 -11.501 21.616 0.876 -0.552 3.405 CE MSE 9
MSE H H H 0 1 N N N Y Y N 12.225 -7.688 19.598 1.753 1.123 -1.999 H MSE 10
MSE H2 HN2 H 0 1 N Y N Y Y N 11.269 -7.351 20.941 2.297 -0.105 -1.096 HN2 MSE 11
MSE HA HA H 0 1 N N N Y N N 10.286 -8.458 18.388 0.593 -1.547 -1.940 HA MSE 12
MSE HXT HXT H 0 1 N Y N Y N Y 7.087 -8.692 19.930 -1.656 -0.551 -4.508 HXT MSE 13
MSE HB2 HB2 H 0 1 N N N N N N 10.685 -9.896 21.117 -1.223 -0.408 -0.696 HB2 MSE 14
MSE HB3 HB3 H 0 1 N N N N N N 9.935 -10.611 19.762 -0.296 1.110 -0.732 HB3 MSE 15
MSE HG2 HG2 H 0 1 N N N N N N 12.119 -10.290 18.383 1.542 0.016 0.521 HG2 MSE 16
MSE HG3 HG3 H 0 1 N N N N N N 12.867 -9.566 19.726 0.614 -1.501 0.557 HG3 MSE 17
MSE HE1 HE1 H 0 1 N N N N N N 13.699 -12.508 22.001 0.554 -0.332 4.423 HE1 MSE 18
MSE HE2 HE2 H 0 1 N N N N N N 14.258 -10.783 21.481 0.931 -1.632 3.267 HE2 MSE 19
MSE HE3 HE3 H 0 1 N N N N N N 12.852 -10.855 22.329 1.858 -0.113 3.231 HE3 MSE 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
MSE N CA SING N N 1
MSE N H SING N N 2
MSE N H2 SING N N 3
MSE CA C SING N N 4
MSE CA CB SING N N 5
MSE CA HA SING N N 6
MSE C O DOUB N N 7
MSE C OXT SING N N 8
MSE OXT HXT SING N N 9
MSE CB CG SING N N 10
MSE CB HB2 SING N N 11
MSE CB HB3 SING N N 12
MSE CG SE SING N N 13
MSE CG HG2 SING N N 14
MSE CG HG3 SING N N 15
MSE SE CE SING N N 16
MSE CE HE1 SING N N 17
MSE CE HE2 SING N N 18
MSE CE HE3 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
MSE SMILES ACDLabs 10.04 O=C(O)C(N)CC[Se]C
MSE SMILES_CANONICAL CACTVS 3.341 C[Se]CC[C@H](N)C(O)=O
MSE SMILES CACTVS 3.341 C[Se]CC[CH](N)C(O)=O
MSE SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C[Se]CC[C@@H](C(=O)O)N
MSE SMILES "OpenEye OEToolkits" 1.5.0 C[Se]CCC(C(=O)O)N
MSE InChI InChI 1.03 InChI=1S/C5H11NO2Se/c1-9-3-2-4(6)5(7)8/h4H,2-3,6H2,1H3,(H,7,8)/t4-/m0/s1
MSE InChIKey InChI 1.03 RJFAYQIBOAGBLC-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
MSE "SYSTEMATIC NAME" ACDLabs 10.04 "(2S)-2-amino-4-(methylselanyl)butanoic acid"
MSE "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2S)-2-amino-4-methylselanyl-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
MSE 'Create component' 1999-07-08 RCSB
MSE 'Modify descriptor' 2011-06-04 RCSB
MSE 'Modify backbone' 2023-11-03 PDBE
#
_pdbe_chem_comp_drugbank_details.comp_id MSE
_pdbe_chem_comp_drugbank_details.drugbank_id DB11142
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name Selenomethionine
_pdbe_chem_comp_drugbank_details.description
'Selenomethionine is a naturally occuring amino acid in some plant materials such as cereal grains, soybeans and enriched yeast but it cannot be synthesized from animals or humans. It can be produced from post-structural modifications. *In vivo*, selenomethionine plays an essential role in acting as an antioxidant, where it depletes reactive oxygen species (ROS) and aids in the formation and recycling of glutathione, another important antioxidant. In comparison to selenite, which is the inorganic form of selenium, the organic form of selenomethionine is more readily absorbed in the human body. Selenomethionin is used in biochemical laboratories where its incorporation into proteins that need to be visualized enhances the performance of X-ray crystallography.'
_pdbe_chem_comp_drugbank_details.cas_number 3211-76-5
_pdbe_chem_comp_drugbank_details.mechanism_of_action ?
#
_pdbe_chem_comp_drugbank_classification.comp_id MSE
_pdbe_chem_comp_drugbank_classification.drugbank_id DB11142
_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_
_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
MSE N N 4.299 1.875 1
MSE CA C 5.598 1.125 2
MSE C C 6.897 1.875 3
MSE O O 8.196 1.125 4
MSE OXT O 6.897 3.375 5
MSE CB C 5.598 -0.375 6
MSE CG C 4.299 -1.125 7
MSE SE Se 4.299 -2.625 8
MSE CE C 3.000 -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
MSE CA N SINGLE BEGINDASH 1
MSE CA C SINGLE NONE 2
MSE CA CB SINGLE NONE 3
MSE C O DOUBLE NONE 4
MSE C OXT SINGLE NONE 5
MSE CB CG SINGLE NONE 6
MSE CG SE SINGLE NONE 7
MSE SE CE SINGLE NONE 8
#
_pdbe_chem_comp_substructure.comp_id MSE
_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
MSE O F1 1
MSE C F1 1
MSE CA F1 1
MSE N F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id MSE
_pdbe_chem_comp_rdkit_properties.exactmw 196.995
_pdbe_chem_comp_rdkit_properties.amw 196.108
_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 3
_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 76.433
_pdbe_chem_comp_rdkit_properties.tpsa 63.320
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.041
_pdbe_chem_comp_rdkit_properties.CrippenMR 36.653
_pdbe_chem_comp_rdkit_properties.chi0v 5.885
_pdbe_chem_comp_rdkit_properties.chi1v 3.503
_pdbe_chem_comp_rdkit_properties.chi2v 0.842
_pdbe_chem_comp_rdkit_properties.chi3v 0.842
_pdbe_chem_comp_rdkit_properties.chi4v 0.435
_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 -0.051
_pdbe_chem_comp_rdkit_properties.kappa1 1.575
_pdbe_chem_comp_rdkit_properties.kappa2 4.793
_pdbe_chem_comp_rdkit_properties.kappa3 4.453
_pdbe_chem_comp_rdkit_properties.Phi 0.839
#
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
MSE UniChem ChEMBL CHEMBL113178
MSE UniChem DrugBank DB11142
MSE UniChem PDBe MSE
MSE UniChem 'KEGG LIGAND' C05335
MSE UniChem ChEBI 30021
MSE UniChem ChEBI 62621
MSE UniChem eMolecules 594273
MSE UniChem fdasrs 964MRK2PEL
MSE UniChem HMDB HMDB0003966
MSE UniChem 'PubChem TPHARMA' 16057472
MSE UniChem NMRShiftDB 60027566
MSE UniChem ACTor 3211-76-5
MSE UniChem Nikkaji J114.178C
MSE UniChem 'EPA CompTox Dashboard' DTXSID8046824
MSE UniChem DrugCentral 3544
MSE UniChem MetaboLights MTBLC30021
MSE UniChem MetaboLights MTBLC62621
MSE UniChem BRENDA 136323
MSE UniChem BRENDA 20345
MSE UniChem BRENDA 234217
MSE UniChem BRENDA 9266
MSE UniChem BRENDA 9267
MSE UniChem Rhea 62621
MSE UniChem ChemicalBook CB8183929
MSE UniChem DailyMed SELENOMETHIONINE
MSE UniChem ClinicalTrials SELENOMETHIONINE
MSE UniChem ClinicalTrials 'SELENOMETHIONINE (75 SE)'
MSE UniChem ClinicalTrials 'SELENOMETHIONINE (75SE)'
MSE UniChem ClinicalTrials 'SELENOMETHIONINE SE 75'
MSE UniChem ClinicalTrials 'SELENOMETHIONINE SE-75'
MSE UniChem ClinicalTrials SETHOTOPE
MSE UniChem rxnorm SELENOMETHIONINE
MSE UniChem rxnorm 'SELENOMETHIONINE SE 75'
MSE UniChem MedChemExpress HY-B1000A
MSE UniChem 'Probes And Drugs' PD000174
MSE UniChem SureChEMBL SCHEMBL63322
MSE UniChem 'PubChem TPHARMA' 15171614
MSE UniChem PubChem 105024
MSE UniChem PubChem 53262363
#
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
MSE N -2.302 -1.533 -1.079 ETKDGv3 1
MSE CA -1.244 -1.069 -0.180 ETKDGv3 2
MSE C -1.838 -0.347 1.002 ETKDGv3 3
MSE O -1.685 -0.809 2.165 ETKDGv3 4
MSE OXT -2.560 0.828 0.814 ETKDGv3 5
MSE CB -0.262 -0.171 -0.954 ETKDGv3 6
MSE CG 0.979 0.179 -0.128 ETKDGv3 7
MSE SE 2.204 1.259 -1.195 ETKDGv3 8
MSE CE 3.486 1.385 0.265 ETKDGv3 9
MSE H -2.928 -2.186 -0.553 ETKDGv3 10
MSE H2 -2.885 -0.719 -1.384 ETKDGv3 11
MSE HA -0.686 -1.963 0.182 ETKDGv3 12
MSE HXT -2.964 1.322 1.601 ETKDGv3 13
MSE HB2 -0.771 0.766 -1.272 ETKDGv3 14
MSE HB3 0.066 -0.707 -1.871 ETKDGv3 15
MSE HG2 0.688 0.757 0.775 ETKDGv3 16
MSE HG3 1.499 -0.751 0.187 ETKDGv3 17
MSE HE1 3.831 0.370 0.552 ETKDGv3 18
MSE HE2 4.358 1.985 -0.066 ETKDGv3 19
MSE HE3 3.015 1.879 1.139 ETKDGv3 20
#