data_EOU
#
_chem_comp.id EOU
_chem_comp.name "dimethyl (~{E})-but-2-enedioate"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C6 H8 O4"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2020-01-17
_chem_comp.pdbx_modified_date 2020-07-31
_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 144.125
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code EOU
_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 6LRZ
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBJ
#
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
EOU C1 C1 C 0 1 N N N N N N -82.757 93.222 13.770 4.273 -0.147 -0.000 C1 EOU 1
EOU C2 C2 C 0 1 N N N N N N -86.114 93.626 10.894 -0.522 0.422 0.000 C2 EOU 2
EOU C C3 C 0 1 N N N N N N -89.521 94.900 10.022 -4.273 0.147 0.000 C EOU 3
EOU O O1 O 0 1 N N N N N N -87.509 95.145 12.028 -2.088 -1.308 -0.001 O EOU 4
EOU O1 O2 O 0 1 N N N N N N -83.844 91.928 10.740 2.088 1.308 0.001 O1 EOU 5
EOU C5 C4 C 0 1 N N N N N N -83.933 92.791 11.598 1.899 0.108 0.000 C5 EOU 6
EOU O3 O3 O 0 1 N N N N N N -82.741 93.171 12.344 2.947 -0.739 -0.000 O3 EOU 7
EOU C3 C5 C 0 1 N N N N N N -85.232 93.437 11.873 0.522 -0.422 -0.000 C3 EOU 8
EOU C4 C6 C 0 1 N N N N N N -87.412 94.274 11.176 -1.899 -0.108 -0.000 C4 EOU 9
EOU O2 O4 O 0 1 N N N N N N -88.604 93.892 10.435 -2.947 0.739 0.000 O2 EOU 10
EOU H1 H1 H 0 1 N N N N N N -81.766 93.528 14.138 4.396 0.471 -0.890 H1 EOU 11
EOU H2 H2 H 0 1 N N N N N N -83.512 93.950 14.102 4.396 0.470 0.890 H2 EOU 12
EOU H3 H3 H 0 1 N N N N N N -83.005 92.228 14.170 5.024 -0.937 -0.001 H3 EOU 13
EOU H4 H4 H 0 1 N N N N N N -85.880 93.305 9.890 -0.354 1.489 0.001 H4 EOU 14
EOU H5 H5 H 0 1 N N N N N N -90.357 94.435 9.479 -4.396 -0.470 -0.890 H5 EOU 15
EOU H6 H6 H 0 1 N N N N N N -89.907 95.429 10.906 -4.396 -0.471 0.890 H6 EOU 16
EOU H7 H7 H 0 1 N N N N N N -89.007 95.615 9.362 -5.024 0.937 0.001 H7 EOU 17
EOU H8 H8 H 0 1 N N N N N N -85.468 93.759 12.876 0.354 -1.489 -0.001 H8 EOU 18
#
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
EOU C O2 SING N N 1
EOU O2 C4 SING N N 2
EOU O1 C5 DOUB N N 3
EOU C2 C4 SING N N 4
EOU C2 C3 DOUB N E 5
EOU C4 O DOUB N N 6
EOU C5 C3 SING N N 7
EOU C5 O3 SING N N 8
EOU O3 C1 SING N N 9
EOU C1 H1 SING N N 10
EOU C1 H2 SING N N 11
EOU C1 H3 SING N N 12
EOU C2 H4 SING N N 13
EOU C H5 SING N N 14
EOU C H6 SING N N 15
EOU C H7 SING N N 16
EOU C3 H8 SING N N 17
#
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
EOU InChI InChI 1.03 InChI=1S/C6H8O4/c1-9-5(7)3-4-6(8)10-2/h3-4H,1-2H3/b4-3+
EOU InChIKey InChI 1.03 LDCRTTXIJACKKU-ONEGZZNKSA-N
EOU SMILES_CANONICAL CACTVS 3.385 COC(=O)/C=C/C(=O)OC
EOU SMILES CACTVS 3.385 COC(=O)C=CC(=O)OC
EOU SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 COC(=O)/C=C/C(=O)OC
EOU SMILES "OpenEye OEToolkits" 2.0.7 COC(=O)C=CC(=O)OC
#
_pdbx_chem_comp_identifier.comp_id EOU
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version 2.0.7
_pdbx_chem_comp_identifier.identifier "dimethyl (~{E})-but-2-enedioate"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
EOU 'Create component' 2020-01-17 PDBJ
EOU 'Initial release' 2020-08-05 RCSB
#
_pdbe_chem_comp_drugbank_details.comp_id EOU
_pdbe_chem_comp_drugbank_details.drugbank_id DB08908
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name 'Dimethyl fumarate'
_pdbe_chem_comp_drugbank_details.description
'Dimethyl fumarate is an agent indicated for the treatment of relapsing forms of multiple sclerosis.[A253942,L43752] The mechanism of action of dimethyl fumarate in multiple sclerosis is not well understood. It is thought to involve dimethyl fumarate degradation to its active metabolite monomethyl fumarate (MMF) then MMF up-regulates the Nuclear factor (erythroid-derived 2)-like 2 (Nrf2) pathway that is activated in response to oxidative stress.[L43752] Dimethyl fumarate is marketed under the brand name Tecfidera, and it was the third oral disease-modifying agent for multiple sclerosis approved by the FDA, following [fingolimod] and [teriflunomide].[A253917] Prior to its FDA approval, dimethyl fumarate had been used in Germany for treatment of psoriasis.[A253917]'
_pdbe_chem_comp_drugbank_details.cas_number 624-49-7
_pdbe_chem_comp_drugbank_details.mechanism_of_action
'The mechanism of action of dimethyl fumarate in multiple sclerosis is not well understood. It is thought to involve dimethyl fumarate degradation to its active metabolite, monomethyl fumarate (MMF). Both dimethyl fumarate and MMF up-regulate the Nuclear factor (erythroid-derived 2)-like 2 (Nrf2) pathway that is activated in response to oxidative stress. Dimethyl fumarate also suppresses pro-inflammatory genes through nuclear factor kappa B inhibition. Additionally, MMF acts as an agonist at the nicotinic acid receptor, but the relevance of this is unknown.[A253917,L43752]  It has been suggested that dimethyl fumarate exerts its immunomodulatory effects through changes in the composition and phenotype of immune cells. It reduces CNS infiltration and alters the composition of all lymphocyte subpopulations, especially for cytotoxic and effector T cells. This causes a shift from a mainly pro-inflammatory phenotype to an anti-inflammatory one.[A253942]'
#
loop_
_pdbe_chem_comp_synonyms.comp_id
_pdbe_chem_comp_synonyms.name
_pdbe_chem_comp_synonyms.provenance
_pdbe_chem_comp_synonyms.type
EOU '(E)-But-2-enedioic acid dimethyl ester' DrugBank ?
EOU 1,2-bis(methoxycarbonyl)-trans-ethylene DrugBank ?
EOU 'Dimethyl fumarate' DrugBank ?
EOU 'Dimethyl trans-ethylenedicarboxylate' DrugBank ?
EOU 'Fumaric acid, dimethyl ester' DrugBank ?
EOU 'trans-1,2-Ethylenedicarboxylic acid dimethyl ester' DrugBank ?
EOU 'trans-Butenedioic acid dimethyl ester' DrugBank ?
#
_pdbe_chem_comp_drugbank_classification.comp_id EOU
_pdbe_chem_comp_drugbank_classification.drugbank_id DB08908
_pdbe_chem_comp_drugbank_classification.parent 'Fatty acid esters'
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class 'Fatty Acyls'
_pdbe_chem_comp_drugbank_classification.superclass 'Lipids and lipid-like molecules'
_pdbe_chem_comp_drugbank_classification.description
'This compound belongs to the class of organic compounds known as fatty acid esters. These are carboxylic ester derivatives of a fatty acid.'
#
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
EOU DB08908 'Kelch-like ECH-associated protein 1' Humans Q14145 yes 1
EOU DB08908 'Transcription factor p65' Humans Q04206 unknown 2
#
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
EOU C1 C 3.000 -0.375 1
EOU C2 C 8.196 -0.375 2
EOU C C 12.093 0.375 3
EOU O O 9.495 1.875 4
EOU O1 O 5.598 -1.875 5
EOU C5 C 5.598 -0.375 6
EOU O3 O 4.299 0.375 7
EOU C3 C 6.897 0.375 8
EOU C4 C 9.495 0.375 9
EOU O2 O 10.794 -0.375 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
EOU C O2 SINGLE NONE 1
EOU O2 C4 SINGLE NONE 2
EOU O1 C5 DOUBLE NONE 3
EOU C2 C4 SINGLE ENDDOWNRIGHT 4
EOU C2 C3 DOUBLE NONE 5
EOU C4 O DOUBLE NONE 6
EOU C5 C3 SINGLE ENDDOWNRIGHT 7
EOU C5 O3 SINGLE NONE 8
EOU O3 C1 SINGLE NONE 9
#
#
#
_pdbe_chem_comp_rdkit_properties.comp_id EOU
_pdbe_chem_comp_rdkit_properties.exactmw 144.042
_pdbe_chem_comp_rdkit_properties.amw 144.126
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 4
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 0
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 4
_pdbe_chem_comp_rdkit_properties.NumHBD 0
_pdbe_chem_comp_rdkit_properties.NumHBA 4
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 10
_pdbe_chem_comp_rdkit_properties.NumAtoms 18
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 4
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.333
_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 0
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 69.664
_pdbe_chem_comp_rdkit_properties.tpsa 52.600
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.111
_pdbe_chem_comp_rdkit_properties.CrippenMR 33.172
_pdbe_chem_comp_rdkit_properties.chi0v 4.633
_pdbe_chem_comp_rdkit_properties.chi1v 1.975
_pdbe_chem_comp_rdkit_properties.chi2v 0.452
_pdbe_chem_comp_rdkit_properties.chi3v 0.452
_pdbe_chem_comp_rdkit_properties.chi4v 0.153
_pdbe_chem_comp_rdkit_properties.chi0n 12.633
_pdbe_chem_comp_rdkit_properties.chi1n 5.975
_pdbe_chem_comp_rdkit_properties.chi2n 0.452
_pdbe_chem_comp_rdkit_properties.chi3n 0.452
_pdbe_chem_comp_rdkit_properties.chi4n 0.153
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.320
_pdbe_chem_comp_rdkit_properties.kappa1 2.082
_pdbe_chem_comp_rdkit_properties.kappa2 4.549
_pdbe_chem_comp_rdkit_properties.kappa3 3.654
_pdbe_chem_comp_rdkit_properties.Phi 0.947
#
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
EOU UniChem ChEMBL CHEMBL2107333
EOU UniChem DrugBank DB08908
EOU UniChem PDBe EOU
EOU UniChem 'Guide to Pharmacology' 7045
EOU UniChem 'PubChem DOTF' 99431554
EOU UniChem ChEBI 76004
EOU UniChem ZINC ZINC000003843378
EOU UniChem fdasrs FO2303MNI2
EOU UniChem PharmGKB PA166152838
EOU UniChem HMDB HMDB0031257
EOU UniChem Selleck dimethyl-Fumarate
EOU UniChem 'PubChem TPHARMA' 15146755
EOU UniChem NMRShiftDB 74928
EOU UniChem LINCS LSM-45569
EOU UniChem ACTor 23055-10-9
EOU UniChem ACTor 624-49-7
EOU UniChem BindingDb 50504654
EOU UniChem DrugCentral 4757
EOU UniChem BRENDA 96414
EOU UniChem ChemicalBook CB4854003
EOU UniChem ChemicalBook CB6712800
EOU UniChem DailyMed 'DIMETHYL FUMARATE'
EOU UniChem ClinicalTrials 'BG 00012'
EOU UniChem ClinicalTrials 'BG 12'
EOU UniChem ClinicalTrials BG-00012
EOU UniChem ClinicalTrials BG-12
EOU UniChem ClinicalTrials BG00012
EOU UniChem ClinicalTrials 'DIMETHYL FUMARATE'
EOU UniChem ClinicalTrials FAG-201
EOU UniChem ClinicalTrials FP-187
EOU UniChem ClinicalTrials FP187
EOU UniChem ClinicalTrials LAS-41008
EOU UniChem ClinicalTrials LAS41008
EOU UniChem ClinicalTrials TECFIDERA
EOU UniChem rxnorm 'DIMETHYL FUMARATE'
EOU UniChem rxnorm TECFIDERA
EOU UniChem MedChemExpress HY-17363
EOU UniChem 'Probes And Drugs' PD000183
EOU UniChem Nikkaji J502.486B
EOU UniChem eMolecules 491165
EOU UniChem SureChEMBL SCHEMBL41835
EOU UniChem PubChem 637568
EOU UniChem Mcule MCULE-4208733984
EOU UniChem ACTor 624-48-6
EOU UniChem Nikkaji J45.019G
#
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
EOU C1 3.936 0.296 -0.018 ETKDGv3 1
EOU C2 -0.362 -0.054 -0.095 ETKDGv3 2
EOU C -3.986 1.095 -0.072 ETKDGv3 3
EOU O -2.426 -1.233 -0.192 ETKDGv3 4
EOU O1 2.547 -2.136 -0.182 ETKDGv3 5
EOU C5 1.875 -1.070 -0.127 ETKDGv3 6
EOU O3 2.519 0.169 -0.044 ETKDGv3 7
EOU C3 0.406 -1.148 -0.150 ETKDGv3 8
EOU C4 -1.833 -0.122 -0.117 ETKDGv3 9
EOU O2 -2.564 1.068 -0.056 ETKDGv3 10
EOU H1 4.373 -0.126 -0.948 ETKDGv3 11
EOU H2 4.204 1.371 0.050 ETKDGv3 12
EOU H3 4.349 -0.234 0.866 ETKDGv3 13
EOU H4 0.093 0.926 -0.030 ETKDGv3 14
EOU H5 -4.331 2.148 -0.014 ETKDGv3 15
EOU H6 -4.364 0.645 -1.014 ETKDGv3 16
EOU H7 -4.387 0.536 0.799 ETKDGv3 17
EOU H8 -0.049 -2.129 -0.215 ETKDGv3 18
#