Structure of PDB 9fdj Chain D Binding Site BS03

Receptor Information
>9fdj 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]
MRSYPAIPRIYAETTLNMLLKRAKKPRVHSIDEYLKDGGYQALEKALNMS
PEEIIDWVDKSTLRGGGGAGFPTGKKWKFAVQNPGPRYFICNADESEPGT
FKDRIIIERDPHLLIEGIIISSYAIGANEAYIYIRGEYPAGYYILRDAIE
EAKKKGFLGKNILGSGFDLEIYVARGAGAYICGEETALIESLEGKRGHPR
LKPPYPVQKGLWGKPTVVNNVETIANVPFIISMGWEEYRYIGPSDYAGPK
LFPVSGKVKKPGVYELPMNTTLREVIFKYAGGTLGNKKVKAVFSGALDCF
SSEELDIPMDYSPLGFGGTGTVIVLTEEDDIVEAALKIAEFYEHETCGQC
TPCRVGCYEQANLLEKIYKGEATEQDWEGFDFVNRNIQPTSICGLGAVAG
RLIRQTLEKFPEEWEKYR
Ligand information
Ligand IDNAI
InChIInChI=1S/C21H29N7O14P2/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(32)14(30)11(41-21)6-39-44(36,37)42-43(34,35)38-5-10-13(29)15(31)20(40-10)27-3-1-2-9(4-27)18(23)33/h1,3-4,7-8,10-11,13-16,20-21,29-32H,2,5-6H2,(H2,23,33)(H,34,35)(H,36,37)(H2,22,24,25)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyBOPGDPNILDQYTO-NNYOXOHSSA-N
SMILES
SoftwareSMILES
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)O)N
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)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
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)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)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
FormulaC21 H29 N7 O14 P2
Name1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE;
NADH
ChEMBLCHEMBL1234616
DrugBankDB00157
ZINCZINC000008215403
PDB chain9fdj Chain D Residue 503 [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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PDB9fdj Structural robustness of the NADH binding site in NADH:ubiquinone oxidoreductase (complex I).
Resolution1.7 Å
Binding residue
(original residue number in PDB)		A69 F71 K76 E185
Binding residue
(residue number reindexed from 1)		A69 F71 K76 E185
Annotation score4
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

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Molecular Function
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Biological Process
External links
PDB RCSB:9fdj, PDBe:9fdj, PDBj:9fdj
PDBsum9fdj
PubMed38960077
UniProtO66841|NUOF_AQUAE NADH-quinone oxidoreductase subunit F (Gene Name=nuoF)

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