Structure of PDB 3dkp Chain A Binding Site BS01

Receptor Information
>3dkp Chain A (length=240) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SMKINFLRNKHKIHVQGTDLPDPIATFQQLDQEYKINSRLLQNILDAGFQ
MPTPIQMQAIPVMLHGRELLASAPTGSGKTLAFSIPILMQLKQPANKGFR
ALIISPTRELASQIHRELIKISEGTGFRIHMIHKAAVAAKKFGPKSSKKF
DILVTTPNRLIYLLKQDPPGIDLASVEWLVVDESDKLFEDGGFRDQLASI
FLACTSHKVRRAMFSATFAYDVEQWCKLNLDNVISVSIGA
Ligand information
Ligand IDADP
InChIInChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyXTWYTFMLZFPYCI-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
FormulaC10 H15 N5 O10 P2
NameADENOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL14830
DrugBankDB16833
ZINCZINC000012360703
PDB chain3dkp Chain A Residue 402 [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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PDB3dkp Comparative Structural Analysis of Human DEAD-Box RNA Helicases.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		F185 Q192 T211 G212 S213 G214 K215 T216
Binding residue
(residue number reindexed from 1)		F49 Q56 T75 G76 S77 G78 K79 T80
Annotation score5
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
Biological Process
GO:0030490 maturation of SSU-rRNA

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3dkp, PDBe:3dkp, PDBj:3dkp
PDBsum3dkp
PubMed20941364
UniProtQ9Y2R4|DDX52_HUMAN Probable ATP-dependent RNA helicase DDX52 (Gene Name=DDX52)

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