Structure of PDB 3llm Chain A Binding Site BS02

Receptor Information
>3llm Chain A (length=235) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VVPWSPPQSNWNPWTSSNIDEGPLAFATPEQISMDLKNELMYQLEQDHDL
QAILQERELLPVKKFESEILEAISQNSVVIIRGATGCGKTTQVPQFILDD
FIQNDRAAECNIVVTQPRRISAVSVAERVAFERGEEPGKSCGYSVRFESI
LPRPHASIMFCTVGVLLRKLEAGIRGISHVIVDEIHERDINTDFLLVVLR
DVVQAYPEVRIVLMSATIDTSMFCEYFFNCPIIEV
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 chain3llm Chain A Residue 565 [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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PDB3llm Crystal structure of human RNA helicase A (DHX9): structural basis for unselective nucleotide base binding in a DEAD-box variant protein.
Resolution2.8 Å
Binding residue
(original residue number in PDB)		T413 G414 C415 G416 K417 T418 T419 R456
Binding residue
(residue number reindexed from 1)		T85 G86 C87 G88 K89 T90 T91 R128
Annotation score5
Binding affinityPDBbind-CN: -logKd/Ki=4.74,Kd=18uM
Enzymatic activity
Enzyme Commision number 3.6.4.13: RNA helicase.
Gene Ontology
Molecular Function
GO:0003676 nucleic acid binding
GO:0005524 ATP binding
GO:0033679 3'-5' DNA/RNA helicase activity

View graph for
Molecular Function
External links
PDB RCSB:3llm, PDBe:3llm, PDBj:3llm
PDBsum3llm
PubMed20510246
UniProtQ08211|DHX9_HUMAN ATP-dependent RNA helicase A (Gene Name=DHX9)

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