Structure of PDB 5na1 Chain A Binding Site BS01

Receptor Information
>5na1 Chain A (length=398) Species: 93061 (Staphylococcus aureus subsp. aureus NCTC 8325) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RKKVLVLGAGYAGLQTVTKLQKAISTEEAEITLINKNEYHYEATWLHEAS
AGTLNYEDVLYPVESVLKKDKVNFVQAEVTKIDRDAKKVETNQGIYDFDI
LVVALGFVSETFGIEGMKDHAFQIENVITARELSRHIEDKFANYAASKEK
DDNDLSILVGGAGFTGVEFLGELTDRIPELCSKYGVDQNKVKITCVEAAP
KMLPMFSEELVNHAVSYLEDRGVEFKIATPIVACNEKGFVVEVDGEKQQL
NAGTSVWAAGVRGSKLMEESFEGVKRGRIVTKQDLTINGYDNIFVIGDCS
AFIPAGEERPLPTTAQIAMQQGESVAKNIKRILNGESTEEFEYVDRGTVC
SLGSHDGVGMVFGKPIAGKKAAFMKKVIDTRAVFKIGGIGLAFKKGKF
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 chain5na1 Chain A Residue 1001 [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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PDB5na1 The key role of glutamate 172 in the mechanism of type II NADH:quinone oxidoreductase of Staphylococcus aureus.
Resolution2.32 Å
Binding residue
(original residue number in PDB)		G14 Y15 A16 N39 K40 A47 T48 E82 V83 L109 G110 F111 F168 G301 D302 T317 T318 A319
Binding residue
(residue number reindexed from 1)		G10 Y11 A12 N35 K36 A43 T44 E78 V79 L105 G106 F107 F164 G297 D298 T313 T314 A315
Annotation score2
Enzymatic activity
Enzyme Commision number 1.6.5.9: NADH:ubiquinone reductase (non-electrogenic).
Gene Ontology
Molecular Function
GO:0003955 NAD(P)H dehydrogenase (quinone) activity
GO:0016491 oxidoreductase activity
GO:0050136 NADH:ubiquinone reductase (non-electrogenic) activity
Biological Process
GO:0019646 aerobic electron transport chain
Cellular Component
GO:0005886 plasma membrane

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5na1, PDBe:5na1, PDBj:5na1
PDBsum5na1
PubMed28801048
UniProtQ2FZV7|NDH_STAA8 Type II NADH:quinone oxidoreductase (Gene Name=SAOUHSC_00878)

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