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Structure of PDB 9fdv Chain D Binding Site BS02

Receptor Information
>9fdv Chain D (length=418) Species: 224324 (Aquifex aeolicus VF5) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SYPAIPRIYAETTLNMLLKRAKKPRVHSIDEYLKDGGYQALEKALNMSPE
EIIDWVDKSTLRGGGGAGFPTGKKWKFAVQNPGPRYFICNADESEPGTFK
DRIIIERDPHLLIEGIIISSYAIGANEAYIYIRGEYPAGYYILRDAIEEA
KKKGFLGKNILGSGFDLEIYVARGAGAYICGEETALIESLEGKRGHPRLK
PPYPVQKGLWGKPTVVNNVETIANVPFIISMGWEEYRYIGPSDYAGPKLF
PVSGKVKKPGVYELPMNTTLREVIFKYAGGTLGNKKVKAVFSGALDCFSS
EELDIPMDYSPLGFGGTGTVIVLTEEDDIVEAALKIAEFYEHETCGQCTP
CRVGCYEQANLLEKIYKGEATEQDWEGFDFVNRNIQPTSICGLGAVAGRL
IRQTLEKFPEEWEKYRKK
Ligand information
Ligand IDFNR
InChIInChI=1S/C17H23N4O9P/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/h3-4,11-12,14,18,22-24H,5-6H2,1-2H3,(H2,27,28,29)(H2,19,20,25,26)/t11-,12+,14-/m0/s1
InChIKeyYTNIXZGTHTVJBW-SCRDCRAPSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cc1cc2NC3=C(NC(=O)NC3=O)N(C[C@H](O)[C@H](O)[C@H](O)CO[P](O)(O)=O)c2cc1C
OpenEye OEToolkits 1.7.6Cc1cc2c(cc1C)N(C3=C(N2)C(=O)NC(=O)N3)CC(C(C(COP(=O)(O)O)O)O)O
OpenEye OEToolkits 1.7.6Cc1cc2c(cc1C)N(C3=C(N2)C(=O)NC(=O)N3)C[C@@H]([C@@H]([C@@H](COP(=O)(O)O)O)O)O
CACTVS 3.385Cc1cc2NC3=C(NC(=O)NC3=O)N(C[CH](O)[CH](O)[CH](O)CO[P](O)(O)=O)c2cc1C
ACDLabs 12.01c23N(C=1NC(=O)NC(=O)C=1Nc2cc(C)c(C)c3)CC(O)C(O)C(O)COP(O)(=O)O
FormulaC17 H23 N4 O9 P
Name1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL;
TWO ELECTRON REDUCED FLAVIN MONONUCLEOTIDE
ChEMBL
DrugBank
ZINC
PDB chain9fdv Chain D 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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PDB9fdv Structural robustness of the NADH binding site in NADH:ubiquinone oxidoreductase (complex I).
Resolution1.986 Å
Binding residue
(original residue number in PDB)		G65 G67 K76 N92 E95 Y180 G183 E184 E185 V218 N219 N220 T223
Binding residue
(residue number reindexed from 1)		G63 G65 K74 N90 E93 Y178 G181 E182 E183 V216 N217 N218 T221
Annotation score1
Gene Ontology
Molecular Function
GO:0046872 metal ion binding
GO:0048038 quinone binding
GO:0051539 4 iron, 4 sulfur cluster binding
Biological Process
GO:1902600 proton transmembrane transport

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:9fdv, PDBe:9fdv, PDBj:9fdv
PDBsum9fdv
PubMed38960077
UniProtO66841|NUOF_AQUAE NADH-quinone oxidoreductase subunit F (Gene Name=nuoF)

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