Structure of PDB 8om1 Chain F Binding Site BS02

Receptor Information
>8om1 Chain F (length=430) Species: 10090 (Mus musculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KTSFGSLKDEDRIFTNLYGRHDWRLKGALRRGDWYKTKEILLKGPDWILG
EMKTSGLRGRGGAGFPTGLKWSFMNKPSDGRPKYLVVNADEGEPGTCKDR
EIMRHDPHKLVEGCLVGGRAMGARAAYIYIRGEFYNEASNLQVAIREAYE
AGLIGKNACGSDYDFDVFVVRGAGAYICGEETALIESIEGKQGKPRLKPP
FPADVGVFGCPTTVANVETVAVSPTICRRGGTWFAGFGRERNSGTKLFNI
SGHVNHPCTVEEEMSVPLKELIEKHAGGVTGGWDNLLAVIPGGSSTPLIP
KSVCETVLMDFDALVQAQTGLGTAAVIVMDRSTDIVKAIARLIEFYKHES
CGQCTPCREGVDWMNKVMARFVKGDARPAEIDSLWEISKQIEGHTICALG
DGAAWPVQGLIRHFRPELEDRMQRFAQQHR
Ligand information
Ligand IDFMN
InChIInChI=1S/C17H21N4O9P/c1-7-3-9-10(4-8(7)2)21(15-13(18-9)16(25)20-17(26)19-15)5-11(22)14(24)12(23)6-30-31(27,28)29/h3-4,11-12,14,22-24H,5-6H2,1-2H3,(H,20,25,26)(H2,27,28,29)/t11-,12+,14-/m0/s1
InChIKeyFVTCRASFADXXNN-SCRDCRAPSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)O)O)O)O
OpenEye OEToolkits 1.7.6Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]([C@@H]([C@@H](COP(=O)(O)O)O)O)O
ACDLabs 12.01N=2C(=O)NC(=O)C3=Nc1cc(C)c(C)cc1N(C=23)CC(O)C(O)C(O)COP(=O)(O)O
CACTVS 3.385Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[CH](O)[CH](O)[CH](O)CO[P](O)(O)=O)c2cc1C
CACTVS 3.385Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[C@H](O)[C@H](O)[C@H](O)CO[P](O)(O)=O)c2cc1C
FormulaC17 H21 N4 O9 P
NameFLAVIN MONONUCLEOTIDE;
RIBOFLAVIN MONOPHOSPHATE
ChEMBLCHEMBL1201794
DrugBankDB03247
ZINCZINC000003831425
PDB chain8om1 Chain F Residue 502 [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)		G67 G69 K78 N96 D98 E99 Y184 G187 E188 E189 A223 N224 A406 L407
Binding residue
(residue number reindexed from 1)		G59 G61 K70 N88 D90 E91 Y176 G179 E180 E181 A215 N216 A398 L399
Annotation score1
Enzymatic activity
Enzyme Commision number 7.1.1.2: NADH:ubiquinone reductase (H(+)-translocating).
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0008137 NADH dehydrogenase (ubiquinone) activity
GO:0010181 FMN binding
GO:0016491 oxidoreductase activity
GO:0046872 metal ion 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:0042775 mitochondrial ATP synthesis coupled electron transport
GO:0042776 proton motive force-driven mitochondrial ATP synthesis
GO:1902600 proton transmembrane transport
Cellular Component
GO:0005739 mitochondrion
GO:0005743 mitochondrial inner membrane
GO:0005829 cytosol
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
UniProtQ91YT0|NDUV1_MOUSE NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial (Gene Name=Ndufv1)

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