Structure of PDB 8rgr Chain D Binding Site BS02

Receptor Information
>8rgr Chain D (length=430) Species: 10090 (Mus musculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ARQWQPDIEWAEQFSGAVMYPSKETAHWKPPPWNDVDILKEKAVTNMTLN
FGPQHPAAHGVLRLVLELSGEMVRKCDPHIGLLHRGTEKLIEYKTYLQAL
PYFDRLDYVSMMCNEQAYSIAVEKLLNIQPPPRAQWIRVLFGEITRILNH
IMAVTTHALDIGAMTPFFWMFEEREKMFEFYERVSGARMHAAYIRPGGVH
QDLPLGLLDDIYEFSKNFSLRIDEVEEMLTNNRIWRNRTVDIGVVTAEDA
LNYGFSGVMLRGSGIQWDLRKTQPYDVYDQVEFDVPIGSRGDCYDRYLCR
VEEMRQSLRIIEQCLNKMPPGEIKVDDAKVSPPKRAEMKTSMESLIHHFK
LYTEGYQVPPGATYTAIEAPKGEFGVYLVSDGSSRPYRCKIKAPGFAHLA
GLDKMSKGHMLADVVAIIGTQDIVFGEIDR
Ligand information
Ligand IDUQ
InChIInChI=1S/C59H90O4/c1-44(2)24-15-25-45(3)26-16-27-46(4)28-17-29-47(5)30-18-31-48(6)32-19-33-49(7)34-20-35-50(8)36-21-37-51(9)38-22-39-52(10)40-23-41-53(11)42-43-55-54(12)56(60)58(62-13)59(63-14)57(55)61/h24,26,28,30,32,34,36,38,40,42H,15-23,25,27,29,31,33,35,37,39,41,43H2,1-14H3/b45-26?,46-28?,47-30-,48-32+,49-34+,50-36+,51-38-,52-40+,53-42-
InChIKeyACTIUHUUMQJHFO-RECDIHICSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC1=C(C(=O)C(=C(C1=O)OC)OC)C\C=C(\C)/CCC=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)CCC=C(C)CCC=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)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)CC\C=C(/C)C
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)CCC=C(C)CCC=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)CCC=C(C)C
FormulaC59 H90 O4
NameCoenzyme Q10, (2Z,6E,10Z,14E,18E,22E,26Z)-isomer
ChEMBL
DrugBank
ZINC
PDB chain8rgr Chain D Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB8rgr SCAF1 drives the compositional diversity of mammalian respirasomes.
Resolution2.9 Å
Binding residue
(original residue number in PDB)		H59 Y108 T156 F167
Binding residue
(residue number reindexed from 1)		H59 Y108 T156 F167
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:0005515 protein binding
GO:0008137 NADH dehydrogenase (ubiquinone) activity
GO:0016491 oxidoreductase activity
GO:0016651 oxidoreductase activity, acting on NAD(P)H
GO:0019826 oxygen sensor activity
GO:0031625 ubiquitin protein ligase binding
GO:0046872 metal ion binding
GO:0048038 quinone binding
GO:0051287 NAD binding
GO:0051539 4 iron, 4 sulfur cluster binding
Biological Process
GO:0006120 mitochondrial electron transport, NADH to ubiquinone
GO:0009060 aerobic respiration
GO:0022008 neurogenesis
GO:0032981 mitochondrial respiratory chain complex I assembly
GO:0042063 gliogenesis
GO:0042775 mitochondrial ATP synthesis coupled electron transport
GO:0042776 proton motive force-driven mitochondrial ATP synthesis
GO:0061351 neural precursor cell proliferation
GO:0071453 cellular response to oxygen levels
GO:1902600 proton transmembrane transport
Cellular Component
GO:0005654 nucleoplasm
GO:0005739 mitochondrion
GO:0005743 mitochondrial inner 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:8rgr, PDBe:8rgr, PDBj:8rgr
PDBsum8rgr
PubMed38575788
UniProtQ91WD5|NDUS2_MOUSE NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial (Gene Name=Ndufs2)

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