Structure of PDB 2db3 Chain D Binding Site BS02

Receptor Information
>2db3 Chain D (length=420) Species: 7227 (Drosophila melanogaster) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
YIPPEPSNDAIEIFSSGIASGIHFSKYNNIPVKVTGSDVPQPIQHFTSAD
LRDIIIDNVNKSGYKIPTPIQKCSIPVISSGRDLMACAQTGSGKTAAFLL
PILSKLLEDPHELELGRPQVVIVSPTRELAIQIFNEARKFAFESYLKIGI
VYGGTSFRHQNECITRGCHVVIATPGRLLDFVDRTFITFEDTRFVVLDEA
DRMLDMGFSEDMRRIMTHVTMRPEHQTLMFSATFPEEIQRMAGEFLKNYV
FVAIGIVGGACSDVKQTIYEVNKYAKRSKLIEILSEQADGTIVFVETKRG
ADFLASFLSEKEFPTTSIHGDRLQSQREQALRDFKNGSMKVLIATSVASR
GLDIKNIKHVINYDMPSKIDDYVHRIGRTGRVGNNGRATSFFDPEKDRAI
AADLVKILEGSGQTVPDFLR
Ligand information
Ligand IDANP
InChIInChI=1S/C10H17N6O12P3/c11-8-5-9(13-2-12-8)16(3-14-5)10-7(18)6(17)4(27-10)1-26-31(24,25)28-30(22,23)15-29(19,20)21/h2-4,6-7,10,17-18H,1H2,(H,24,25)(H2,11,12,13)(H4,15,19,20,21,22,23)/t4-,6-,7-,10-/m1/s1
InChIKeyPVKSNHVPLWYQGJ-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[CH](O)[CH]3O
CACTVS 3.370Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[C@@H](O)[C@H]3O
ACDLabs 12.01O=P(O)(O)NP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(NP(=O)(O)O)O)O)O)N
FormulaC10 H17 N6 O12 P3
NamePHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
ChEMBLCHEMBL1230989
DrugBank
ZINCZINC000008660410
PDB chain2db3 Chain D Residue 2904 [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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PDB2db3 Structural basis for RNA unwinding by the DEAD-box protein Drosophila Vasa.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		Y265 Q272 T291 G292 S293 G294 K295 T296 D554 R579 R582 V583
Binding residue
(residue number reindexed from 1)		Y64 Q71 T90 G91 S92 G93 K94 T95 D353 R378 R381 V382
Annotation score3
Enzymatic activity
Enzyme Commision number 3.6.4.13: RNA helicase.
Gene Ontology
Molecular Function
GO:0003676 nucleic acid binding
GO:0003724 RNA helicase activity
GO:0005524 ATP binding

View graph for
Molecular Function
External links
PDB RCSB:2db3, PDBe:2db3, PDBj:2db3
PDBsum2db3
PubMed16630817
UniProtP09052|VASA1_DROME ATP-dependent RNA helicase vasa (Gene Name=vas)

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