Structure of PDB 9ema Chain A Binding Site BS03

Receptor Information
>9ema Chain A (length=326) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QRIASHSHVKGLGLDESGLAKQAASGLVGQENAREACGVIVELIKSKKMA
GRAVLLAGPPGTGKTALALAIAQELGSKVPFCPMVGSEVYSTEIKKTEVL
MENFRRAIGLRIKIQDVTLHDLDVANARPMGQLMKPKKTEITDKLRGEIN
KVVNKYIDQGIAELVPGVLFVDEVHMLDIECFTYLHRALESSIAPIVIFA
SNRGNCVIRGTEDITSPHGIPLDLLDRVMIIRTMLYTPQEMKQIIKIRAQ
TEGINISEEALNHLGEIGTKTTLRYSVQLLTPANLLAKINGKDSIEKEHV
EEISELFYDAKSSAKILADQQDKYMK
Ligand information
Ligand IDATP
InChIInChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyZKHQWZAMYRWXGA-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=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[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
FormulaC10 H16 N5 O13 P3
NameADENOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL14249
DrugBankDB00171
ZINCZINC000004261765
PDB chain9ema Chain D Residue 801 [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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PDB9ema Mechanism of allosteric inhibition of RUVBL1-RUVBL2 by the small-molecule CB-6644
Resolution2.4 Å
Binding residue
(original residue number in PDB)		E320 R357
Binding residue
(residue number reindexed from 1)		E190 R227
Annotation score5
Enzymatic activity
Enzyme Commision number 3.6.4.12: DNA helicase.
Gene Ontology
Molecular Function
GO:0001094 TFIID-class transcription factor complex binding
GO:0003678 DNA helicase activity
GO:0003713 transcription coactivator activity
GO:0004386 helicase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0008094 ATP-dependent activity, acting on DNA
GO:0016787 hydrolase activity
GO:0016887 ATP hydrolysis activity
GO:0017025 TBP-class protein binding
GO:0043531 ADP binding
GO:0045296 cadherin binding
GO:0051117 ATPase binding
Biological Process
GO:0000492 box C/D snoRNP assembly
GO:0000723 telomere maintenance
GO:0006275 regulation of DNA replication
GO:0006281 DNA repair
GO:0006282 regulation of DNA repair
GO:0006310 DNA recombination
GO:0006325 chromatin organization
GO:0006338 chromatin remodeling
GO:0006355 regulation of DNA-templated transcription
GO:0006357 regulation of transcription by RNA polymerase II
GO:0007283 spermatogenesis
GO:0032508 DNA duplex unwinding
GO:0033044 regulation of chromosome organization
GO:0042981 regulation of apoptotic process
GO:0045739 positive regulation of DNA repair
GO:0045893 positive regulation of DNA-templated transcription
GO:0045995 regulation of embryonic development
GO:0050821 protein stabilization
GO:0051276 chromosome organization
GO:0051301 cell division
GO:0051726 regulation of cell cycle
GO:0060382 regulation of DNA strand elongation
GO:0090263 positive regulation of canonical Wnt signaling pathway
GO:0090671 telomerase RNA localization to Cajal body
GO:1904507 positive regulation of telomere maintenance in response to DNA damage
GO:1905168 positive regulation of double-strand break repair via homologous recombination
GO:2000779 regulation of double-strand break repair
Cellular Component
GO:0000786 nucleosome
GO:0000812 Swr1 complex
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005813 centrosome
GO:0005829 cytosol
GO:0005856 cytoskeleton
GO:0016020 membrane
GO:0016363 nuclear matrix
GO:0031011 Ino80 complex
GO:0035267 NuA4 histone acetyltransferase complex
GO:0070062 extracellular exosome
GO:0071339 MLL1 complex
GO:0097255 R2TP complex
GO:0101031 protein folding chaperone complex
GO:0120293 dynein axonemal particle
GO:1990062 RPAP3/R2TP/prefoldin-like complex
GO:1990904 ribonucleoprotein complex

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Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:9ema, PDBe:9ema, PDBj:9ema
PDBsum9ema
PubMed
UniProtQ9Y265|RUVB1_HUMAN RuvB-like 1 (Gene Name=RUVBL1)

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