Structure of PDB 8fkw Chain NI Binding Site BS02

Receptor Information
>8fkw Chain NI (length=647) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DGEFEIQRPLPTFPTSGGFQSMGLSYPVFKGIMKKGYKVPTPIQRKTIPV
ILDGKDVVAMARTGSGKTACFLLPMFERLKTHSAQTGARALILSPTRELA
LQTLKFTKELGKFTGLKTALILGGDRMEDQFAALHENPDIIIATPGRLVH
VAVEMSLKLQSVEYVVFDEADRLFEMGFAEQLQEIIARLPGGHQTVLFSA
TLPKLLVEFARAGLTEPVLIRLDVDTKLNEQLKTSFFLVREDTKAAVLLH
LLHNVVRPQDQTVVFVATKHHAEYLTELLTTQRVSCAHIYSALDPTARKI
NLAKFTLGKCSTLIVTDLAARGLDIPLLDNVINYSFPAKGKLFLHRVGRV
ARAGRSGTAYSLVAPDEIPYLLDLHLFLGRSLTLARPLKEPSGVAGVDGM
LGRVPQSVVDEEDSGLQSTLEASLELRGLARVADNAQQQYVRSRPAPSPE
SIKRAKEMDLVGLGLHPLFSSRFEEEELQRLRLVDSIKNYRSRATIFEIN
ASSRDLCSQVMRAKRQKDRKAIARFQQGQQGRQEQQEGPDQEFYIPYRPK
AFEQQAAGAVLDLMGDEAQNLTRGRQQLKWDRKKKRFKKIKTESGRYISS
SYKRDLYQKWKQKQKIDDRDSRPELKTKQQILKQRRRAQKLHFLQRG
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 chain8fkw Chain NI 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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PDB8fkw Principles of human pre-60 S biogenesis.
Resolution2.5 Å
Binding residue
(original residue number in PDB)		Y116 T120 Q123 T142 G143 G145 K146 T147
Binding residue
(residue number reindexed from 1)		Y37 T41 Q44 T63 G64 G66 K67 T68
Annotation score5
Enzymatic activity
Enzyme Commision number 3.6.4.13: RNA helicase.
Gene Ontology
Molecular Function
GO:0003676 nucleic acid binding
GO:0003714 transcription corepressor activity
GO:0003723 RNA binding
GO:0003724 RNA helicase activity
GO:0004386 helicase activity
GO:0005102 signaling receptor binding
GO:0005524 ATP binding
GO:0016787 hydrolase activity
GO:0016887 ATP hydrolysis activity
GO:0030331 nuclear estrogen receptor binding
Biological Process
GO:0006364 rRNA processing
GO:0006396 RNA processing
GO:0016070 RNA metabolic process
GO:0030520 estrogen receptor signaling pathway
GO:0045892 negative regulation of DNA-templated transcription
Cellular Component
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus
GO:0005794 Golgi apparatus
GO:0016020 membrane

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8fkw, PDBe:8fkw, PDBj:8fkw
PDBsum8fkw
PubMed37410842
UniProtQ8TDD1|DDX54_HUMAN ATP-dependent RNA helicase DDX54 (Gene Name=DDX54)

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