Structure of PDB 8om1 Chain P Binding Site BS01

Receptor Information
>8om1 Chain P (length=342) Species: 10090 (Mus musculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LHHAVIPHGKGGRSSVSGVVATVFGATGFLGRYVVNHLGRMGSQVIIPYR
CDVYDIMHLRLMGDLGQLTFLEWDARDKDSIRKAVQHSNVVINLIGREWE
TRNFDFEDVFVNIPRAIAQASKEAGVERFIHVSHLNASMKSSSKSLRSKA
VGEKEVRSVFPEAIIIRPSDIFGREDRFLNHFANYRWFLAVPLVSLGFKT
VKQPVYVADVSKGIVNATKDPDAVGKTFAFTGPNRYLLFHLVKYIFGMTH
RTFIPYPLPLFVYSWIGKLFGLSPFEPWTTKDKVERIHISDVMPTDLPGL
EDLGVQPTPLELKSIEVLRRHRTYRWLSSEIEETKPAKTVNY
Ligand information
Ligand IDNDP
InChIInChI=1S/C21H30N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1,3-4,7-8,10-11,13-16,20-21,29-31H,2,5-6H2,(H2,23,32)(H,36,37)(H,38,39)(H2,22,24,25)(H2,33,34,35)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyACFIXJIJDZMPPO-NNYOXOHSSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)N5C=CCC(=C5)C(=O)N)O)O)O)OP(=O)(O)O)N
CACTVS 3.341NC(=O)C1=CN(C=CC1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O[P](O)(O)=O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
CACTVS 3.341NC(=O)C1=CN(C=CC1)[C@@H]2O[C@H](CO[P@@](O)(=O)O[P@](O)(=O)OC[C@H]3O[C@H]([C@H](O[P](O)(O)=O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)N5C=CCC(=C5)C(=O)N)O)O)O)OP(=O)(O)O)N
FormulaC21 H30 N7 O17 P3
NameNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
ChEMBLCHEMBL407009
DrugBankDB02338
ZINCZINC000008215411
PDB chain8om1 Chain P 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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PDB8om1 Investigation of hydrated channels and proton pathways in a high-resolution cryo-EM structure of mammalian complex I.
Resolution2.39 Å
Binding residue
(original residue number in PDB)		G25 T27 G28 F29 L30 R50 L94 I95 G96 R97 F104 V132 H134 K149 P168 S169 I171 R177
Binding residue
(residue number reindexed from 1)		G25 T27 G28 F29 L30 R50 L94 I95 G96 R97 F104 V132 H134 K149 P168 S169 I171 R177
Annotation score3
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003954 NADH dehydrogenase activity
GO:0005515 protein binding
GO:0044877 protein-containing complex binding
Biological Process
GO:0007623 circadian rhythm
GO:0009060 aerobic respiration
GO:0032981 mitochondrial respiratory chain complex I assembly
GO:0042776 proton motive force-driven mitochondrial ATP synthesis
Cellular Component
GO:0005739 mitochondrion
GO:0005743 mitochondrial inner membrane
GO:0005759 mitochondrial matrix
GO:0031966 mitochondrial 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:8om1, PDBe:8om1, PDBj:8om1
PDBsum8om1
PubMed37531432
UniProtQ9DC69|NDUA9_MOUSE NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial (Gene Name=Ndufa9)

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