Structure of PDB 6rfr Chain 1 Binding Site BS01

Receptor Information
>6rfr Chain 1 (length=340) Species: 4952 (Yarrowia lipolytica) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MIINIVEILIFLVCVLFSVAYLTVAERKTLAYMQRRLGPNFVGYYGLLQA
FADAVKLLLKEIVLPKESNYIILVISPLITLITALIGWVVIPLGPGITLG
ELNLGILFSLAIGSLGVFGSLLSGWSSNSKYSLLGSIRSTAQLISYELIL
TSIFIIIIMFVSSLNITTIIETQRVVWYCIPLLPLLLIFFIASVAETARP
PFDLTESESELVAGYFTEYSGSPFVFFFLAEYSNIILISAFNGYLLLGGY
LSFNYSYLFNILFNDYSYVSFLFEGLINSSAYAIKLVFLMFSFIWVRAAF
PRFTYDNLINFCWIILLPLLFGIFLIIPSTLYIFDSFPTL
Ligand information
Ligand IDUQ9
InChIInChI=1S/C54H82O4/c1-40(2)22-14-23-41(3)24-15-25-42(4)26-16-27-43(5)28-17-29-44(6)30-18-31-45(7)32-19-33-46(8)34-20-35-47(9)36-21-37-48(10)38-39-50-49(11)51(55)53(57-12)54(58-13)52(50)56/h22,24,26,28,30,32,34,36,38H,14-21,23,25,27,29,31,33,35,37,39H2,1-13H3/b41-24-,42-26+,43-28+,44-30+,45-32-,46-34+,47-36+,48-38+
InChIKeyUUGXJSBPSRROMU-YJKFELPISA-N
SMILES
SoftwareSMILES
CACTVS 3.341COC1=C(OC)C(=O)C(=C(C)C1=O)C/C=C(C)/CC\C=C(C)\CC/C=C(C)/CC\C=C(C)/CC/C=C(C)/CC\C=C(C)\CC/C=C(C)/CC\C=C(C)/CCC=C(C)C
CACTVS 3.341COC1=C(OC)C(=O)C(=C(C)C1=O)CC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)C
OpenEye OEToolkits 1.5.0CC1=C(C(=O)C(=C(C1=O)OC)OC)C\C=C(/C)\CC\C=C(/C)\CC\C=C(/C)\CC\C=C(\C)/CC\C=C(/C)\CC\C=C(/C)\CC\C=C(/C)\CC\C=C(\C)/CCC=C(C)C
ACDLabs 10.04O=C1C(=C(C(=O)C(OC)=C1OC)C)C\C=C(/C)CC\C=C(/C)CC\C=C(/C)CC/C=C(/C)CC\C=C(/C)CC\C=C(/C)CC\C=C(/C)CC/C=C(/C)CC\C=C(/C)C
OpenEye OEToolkits 1.5.0CC1=C(C(=O)C(=C(C1=O)OC)OC)CC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)C
FormulaC54 H82 O4
NameUbiquinone-9;
2,3-dimethoxy-5-methyl-6-[(2E,6E,10E,14Z,18E,22E,26E,30Z)-3,7,11,15,19,23,27,31,35-nonamethylhexatriaconta-2,6,10,14,18 ,22,26,30,34-nonaen-1-yl]cyclohexa-2,5-diene-1,4-dione
ChEMBL
DrugBank
ZINCZINC000098209509
PDB chain6rfr Chain 1 Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6rfr High-resolution cryo-EM structures of respiratory complex I: Mechanism, assembly, and disease.
Resolution3.2 Å
Binding residue
(original residue number in PDB)		L16 F17 A20 A50 D53 A54 F228
Binding residue
(residue number reindexed from 1)		L16 F17 A20 A50 D53 A54 F228
Annotation score1
Enzymatic activity
Enzyme Commision number 7.1.1.2: NADH:ubiquinone reductase (H(+)-translocating).
Gene Ontology
Molecular Function
GO:0003954 NADH dehydrogenase activity
GO:0008137 NADH dehydrogenase (ubiquinone) activity
Biological Process
GO:0009060 aerobic respiration
GO:1902600 proton transmembrane transport
Cellular Component
GO:0005739 mitochondrion
GO:0005743 mitochondrial inner membrane
GO:0016020 membrane
GO:0045271 respiratory chain complex I

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6rfr, PDBe:6rfr, PDBj:6rfr
PDBsum6rfr
PubMed31844670
UniProtQ9B6E8|NU1M_YARLI NADH-ubiquinone oxidoreductase chain 1 (Gene Name=ND1)

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