Structure of PDB 7psa Chain D Binding Site BS02

Receptor Information
>7psa 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 ID88I
InChIInChI=1S/C37H68O6/c1-3-4-5-6-7-13-16-19-22-31(38)33-24-26-35(42-33)36-27-25-34(43-36)32(39)23-20-17-14-11-9-8-10-12-15-18-21-30-28-29(2)41-37(30)40/h29-36,38-39H,3-28H2,1-2H3/t29-,30-,31+,32+,33+,34+,35+,36+/m0/s1
InChIKeyTVBHUCPQEAPMPU-AFRALGOQSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CCCCCCCCCCC(C1CCC(O1)C2CCC(O2)C(CCCCCCCCCCCCC3CC(OC3=O)C)O)O
CACTVS 3.385CCCCCCCCCC[CH](O)[CH]1CC[CH](O1)[CH]2CC[CH](O2)[CH](O)CCCCCCCCCCCC[CH]3C[CH](C)OC3=O
CACTVS 3.385CCCCCCCCCC[C@@H](O)[C@H]1CC[C@@H](O1)[C@H]2CC[C@@H](O2)[C@H](O)CCCCCCCCCCCC[C@H]3C[C@H](C)OC3=O
OpenEye OEToolkits 2.0.7CCCCCCCCCC[C@H]([C@H]1CC[C@@H](O1)[C@H]2CC[C@@H](O2)[C@@H](CCCCCCCCCCCC[C@H]3C[C@@H](OC3=O)C)O)O
FormulaC37 H68 O6
Name(3~{S},5~{S})-5-methyl-3-[(13~{R})-13-oxidanyl-13-[(2~{R},5~{R})-5-[(2~{R},5~{R})-5-[(1~{R})-1-oxidanylundecyl]oxolan-2-yl]oxolan-2-yl]tridecyl]oxolan-2-one
ChEMBL
DrugBank
ZINC
PDB chain7psa Chain H Residue 402 [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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PDB7psa Cryo-electron microscopy reveals how acetogenins inhibit mitochondrial respiratory complex I.
Resolution3.4 Å
Binding residue
(original residue number in PDB)		H59 M152
Binding residue
(residue number reindexed from 1)		H59 M152
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:7psa, PDBe:7psa, PDBj:7psa
PDBsum7psa
PubMed35063503
UniProtQ91WD5|NDUS2_MOUSE NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial (Gene Name=Ndufs2)

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