Structure of PDB 2r6h Chain B Binding Site BS01

Receptor Information
>2r6h Chain B (length=286) Species: 242619 (Porphyromonas gingivalis W83) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VFGVKEWECEVLSNKNVSTFIKEFVVKLPEGETMNFKSGSYAQIKIPKYN
IRYADYDIQDRFRGDWDKMDAWSLTCKNEEETVRAYSMANYPAEGNIITL
NVRIATPPFDRAANKWKAGIKPGISSSYIFSLKPGDKVMMSGPYGDFHIQ
DTDAEMLYIGGGAGMAPLRAQILHLFRTLKTGRKVSYWYGARSKNEIFYE
EDFREIEREFPNFKFHIALSDPQPEDNWTGYVGFIHQVIYDNYLKDHDAP
EDIEYYMCGPGPMANAVKGMLENLGVPRNMLFFDDF
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 chain2r6h Chain B Residue 2 [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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PDB2r6h Crystal Structure of the Domain Comprising the Regions Binding NAD and FAD from the NADH:Ubiquinone Oxidoreductase, Na Translocating, F Subunit from Porphyromonas gingivalis.
Resolution2.95 Å
Binding residue
(original residue number in PDB)		Y166 R209 A210 Y211 S212 N226 A230 T231 K246 P247 G248 I249 S250 S251 D410 F411
Binding residue
(residue number reindexed from 1)		Y41 R84 A85 Y86 S87 N101 A105 T106 K121 P122 G123 I124 S125 S126 D285 F286
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) C383
Catalytic site (residue number reindexed from 1) C258
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

View graph for
Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2r6h, PDBe:2r6h, PDBj:2r6h
PDBsum2r6h
PubMed
UniProtQ7MT22

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