Structure of PDB 6saq Chain D Binding Site BS03

Receptor Information
>6saq Chain D (length=417) Species: 224324 (Aquifex aeolicus VF5) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SYPAIPRIYAETTLNMLLKRAKKPRVHSIDEYLKDGGYQALEKALNMSPE
EIIDWVDKSTLRGRGGAGFPTGKKWKFAVQNPGPRYFICNADESEPGTFK
DRIIIERDPHLLIEGIIISSYAIGANEAYIYIRGEYPAGYYILRDAIEEA
KKKGFLGKNILGSGFDLEIYVARGAGAYICGEETALIESLEGKRGHPRLK
PPYPVQKGLWGKPTVVNNVETIANVPFIISMGWEEYRYIGPSDYAGPKLF
PVSGKVKKPGVYELPMNTTLREVIFKYAGGTLGNKKVKAVFSGALDCFSS
EELDIPMDYSPLGFGGTGTVIVLTEEDDIVEAALKIAEFYEHETCGQCTP
CRVGCYEQANLLEKIYKGEATEQDWEGFDFVNRNIQPTSICGLGAVAGRL
IRQTLEKFPEEWEKYRK
Ligand information
Ligand IDL3W
InChIInChI=1S/C21H29N7O16P2/c22-17-12-19(25-6-24-17)28(7-26-12)21-16(34)14(32)11(43-21)5-41-46(38,39)44-45(36,37)40-4-10-13(31)15(33)20(42-10)27(8-29)3-1-2-9(30)18(23)35/h1-3,6-8,10-11,13-16,20-21,30-34H,4-5H2,(H2,23,35)(H,36,37)(H,38,39)(H2,22,24,25)/b3-1+,9-2-/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyQSTZUQWNOOUKGF-OTTADCDWSA-N
SMILES
SoftwareSMILES
CACTVS 3.385NC(=O)C(O)=CC=CN(C=O)[CH]1O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)n3cnc4c(N)ncnc34)[CH](O)[CH]1O
OpenEye OEToolkits 2.0.7c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)N(C=CC=C(C(=O)N)O)C=O)O)O)O)O)N
OpenEye OEToolkits 2.0.7c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)N(/C=C/C=C(/C(=O)N)\O)C=O)O)O)O)O)N
CACTVS 3.385NC(=O)\C(O)=C\C=C\N(C=O)[C@@H]1O[C@H](CO[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)n3cnc4c(N)ncnc34)[C@@H](O)[C@H]1O
FormulaC21 H29 N7 O16 P2
Name[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-[[(1~{E},3~{Z})-5-azanyl-4-oxidanyl-5-oxidanylidene-penta-1,3-dienyl]-methanoyl-amino]-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate
ChEMBL
DrugBank
ZINC
PDB chain6saq Chain D Residue 1003 [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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PDB6saq Structural Basis for Inhibition of ROS-Producing Respiratory Complex I by NADH-OH.
Resolution2.02 Å
Binding residue
(original residue number in PDB)
G67 G68 A69 F71 K76 F79 E95 E97 T100 E185 Y205 T319
Binding residue
(residue number reindexed from 1)
G65 G66 A67 F69 K74 F77 E93 E95 T98 E183 Y203 T317
Annotation score2
Enzymatic activity
Enzyme Commision number 7.1.1.-
Gene Ontology
Molecular Function
GO:0008137 NADH dehydrogenase (ubiquinone) activity
GO:0010181 FMN binding
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:6saq, PDBe:6saq, PDBj:6saq
PDBsum6saq
PubMed34612584
UniProtO66841|NUOF_AQUAE NADH-quinone oxidoreductase subunit F (Gene Name=nuoF)

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