Structure of PDB 8ad4 Chain A Binding Site BS01

Receptor Information
>8ad4 Chain A (length=279) Species: 666 (Vibrio cholerae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MVKKWECTVISNDNKATFIKELKLAIPDGESVPFRAGGYIQIEAPAHHVK
YADFDVPEKYRGDWDKFNLFRYESKVDEPIIRAYSMANYPEEFGIIMLNV
RIATPPPNNPNVPPGQMSSYIWSLKAGDKCTISGPFGEFFAKDTDAEMVF
IGGGAGMAPMRSHIFDQLKRLKSKRKMSYWYGARSKREMFYVEDFDGLAA
ENDNFVWHCALSDPQPEDNWTGYTGFIHNVLYENYLKDHEAPEDCEYYMC
GPPMMNAAVINMLKNLGVEEENILLDDFG
Ligand information
Ligand IDFAD
InChIInChI=1S/C27H33N9O15P2/c1-10-3-12-13(4-11(10)2)35(24-18(32-12)25(42)34-27(43)33-24)5-14(37)19(39)15(38)6-48-52(44,45)51-53(46,47)49-7-16-20(40)21(41)26(50-16)36-9-31-17-22(28)29-8-30-23(17)36/h3-4,8-9,14-16,19-21,26,37-41H,5-7H2,1-2H3,(H,44,45)(H,46,47)(H2,28,29,30)(H,34,42,43)/t14-,15+,16+,19-,20+,21+,26+/m0/s1
InChIKeyVWWQXMAJTJZDQX-UYBVJOGSSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[C@H](O)[C@H](O)[C@H](O)CO[P@](O)(=O)O[P@@](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6c(N)ncnc56)c2cc1C
OpenEye OEToolkits 1.5.0Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)O
OpenEye OEToolkits 1.5.0Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]([C@@H]([C@@H](CO[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)O)O)O
CACTVS 3.341Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[CH](O)[CH](O)[CH](O)CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)c2cc1C
ACDLabs 10.04O=C2C3=Nc1cc(c(cc1N(C3=NC(=O)N2)CC(O)C(O)C(O)COP(=O)(O)OP(=O)(O)OCC6OC(n5cnc4c(ncnc45)N)C(O)C6O)C)C
FormulaC27 H33 N9 O15 P2
NameFLAVIN-ADENINE DINUCLEOTIDE
ChEMBLCHEMBL1232653
DrugBankDB03147
ZINCZINC000008215434
PDB chain8ad4 Chain A Residue 500 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8ad4 Conformational coupling of redox-driven Na + -translocation in Vibrio cholerae NADH:quinone oxidoreductase.
Resolution1.5 Å
Binding residue
(original residue number in PDB)		Y167 R210 A211 Y212 S213 N227 A231 V240 P241 P242 G243 Q244 M245 S246 F406
Binding residue
(residue number reindexed from 1)		Y39 R82 A83 Y84 S85 N99 A103 V112 P113 P114 G115 Q116 M117 S118 F278
Annotation score2
Enzymatic activity
Enzyme Commision number 7.2.1.1: NADH:ubiquinone reductase (Na(+)-transporting).
Gene Ontology
Molecular Function
GO:0016491 oxidoreductase activity
GO:0016655 oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor
GO:0051537 2 iron, 2 sulfur cluster binding
Biological Process
GO:0006814 sodium ion transport
Cellular Component
GO:0016020 membrane

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8ad4, PDBe:8ad4, PDBj:8ad4
PDBsum8ad4
PubMed37710014
UniProtA5F5Y4|NQRF_VIBC3 Na(+)-translocating NADH-quinone reductase subunit F (Gene Name=nqrF)

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