Structure of PDB 7xk7 Chain B Binding Site BS02

Receptor Information
>7xk7 Chain B (length=412) Species: 345073 (Vibrio cholerae O395) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GLKKFLEDIEHHFEPGGKHEKWFALYEAAATLFYTPGLVTKRSSHVRDSV
DLKRIMIMVWLAVFPAMFWGMYNAGGQAIAALNHLYSGDQLAAIVAGNWH
YWLTEMLGGTMSSDAGWGSKMLLGATYFLPIYATVFIVGGFWEVLFCMVR
KHEVNEGFFVTSILFALIVPPTLPLWQAALGITFGVVVAKEVFGGTGRNF
LNPALAGRAFLFFAYPAQISGDLVWTAADGYSGATALSQWAQGGAGALIN
NATGQTITWMDAFIGNIPGSIGEVSTLALMIGAAFIVYMGIASWRIIGGV
MIGMILLSTLFNVIGSDTNAMFNMPWHWHLVLGGFAFGMFFMATDPVSAS
FTNSGKWAYGILIGVMCVLIRVVNPAYPEGMMLAILFANLFAPLFDHVVV
ERNIKRRLARYG
Ligand information
Ligand IDRBF
InChIInChI=1S/C17H20N4O6/c1-7-3-9-10(4-8(7)2)21(5-11(23)14(25)12(24)6-22)15-13(18-9)16(26)20-17(27)19-15/h3-4,11-12,14,22-25H,5-6H2,1-2H3,(H,20,26,27)/t11-,12+,14-/m0/s1
InChIKeyAUNGANRZJHBGPY-SCRDCRAPSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[CH](O)[CH](O)[CH](O)CO)c2cc1C
OpenEye OEToolkits 1.7.6Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(CO)O)O)O
OpenEye OEToolkits 1.7.6Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]([C@@H]([C@@H](CO)O)O)O
CACTVS 3.385Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[C@H](O)[C@H](O)[C@H](O)CO)c2cc1C
ACDLabs 12.01N=2C(=O)NC(=O)C3=Nc1cc(C)c(C)cc1N(C=23)CC(O)C(O)C(O)CO
FormulaC17 H20 N4 O6
NameRIBOFLAVIN;
RIBOFLAVINE;
VITAMIN B2
ChEMBLCHEMBL1534
DrugBankDB00140
ZINCZINC000002036848
PDB chain7xk7 Chain B 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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PDB7xk7 Cryo-EM structures of Na + -pumping NADH-ubiquinone oxidoreductase from Vibrio cholerae.
Resolution2.9 Å
Binding residue
(original residue number in PDB)		V60 T162 L165 T197 N200 N203 P204 A205 F342 M343 T345 D346 P347 V348
Binding residue
(residue number reindexed from 1)		V59 T161 L164 T196 N199 N202 P203 A204 F341 M342 T344 D345 P346 V347
Annotation score1
Enzymatic activity
Enzyme Commision number 7.2.1.1: NADH:ubiquinone reductase (Na(+)-transporting).
Gene Ontology
Molecular Function
GO:0010181 FMN binding
GO:0016655 oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor
GO:1902444 riboflavin binding
Biological Process
GO:0006814 sodium ion transport
GO:0022904 respiratory electron transport chain
GO:0055085 transmembrane transport
Cellular Component
GO:0005886 plasma membrane
GO:0016020 membrane

View graph for
Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:7xk7, PDBe:7xk7, PDBj:7xk7
PDBsum7xk7
PubMed35882843
UniProtA5F5X0|NQRB_VIBC3 Na(+)-translocating NADH-quinone reductase subunit B (Gene Name=nqrB)

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