Structure of PDB 9ema Chain A Binding Site BS02

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 IDA1H5V
InChIInChI=1S/C29H34ClFN4O5/c1-5-40-24-14-21(31)20(30)13-19(24)27(37)32-17-29(2,3)15-25(36)33-26-23(16-39-4)34-12-8-10-18-9-6-7-11-22(18)35(34)28(26)38/h6-7,9,11,13-14H,5,8,10,12,15-17H2,1-4H3,(H,32,37)(H,33,36)
InChIKeyVYCOZEBCSAQCES-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CCOc1cc(F)c(Cl)cc1C(=O)NCC(C)(C)CC(=O)NC2=C(COC)N3CCCc4ccccc4N3C2=O
OpenEye OEToolkits 2.0.7CCOc1cc(c(cc1C(=O)NCC(C)(C)CC(=O)NC2=C(N3CCCc4ccccc4N3C2=O)COC)Cl)F
FormulaC29 H34 Cl F N4 O5
Name5-chloranyl-2-ethoxy-4-fluoranyl-~{N}-[4-[[3-(methoxymethyl)-1-oxidanylidene-6,7-dihydro-5~{H}-pyrazolo[1,2-a][1,2]benzodiazepin-2-yl]amino]-2,2-dimethyl-4-oxidanylidene-butyl]benzamide
ChEMBL
DrugBank
ZINC
PDB chain9ema Chain A Residue 502 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB9ema Mechanism of allosteric inhibition of RUVBL1-RUVBL2 by the small-molecule CB-6644
Resolution2.4 Å
Binding residue
(original residue number in PDB)		M113 F116 R117 N280 R317 S321 I323 A324
Binding residue
(residue number reindexed from 1)		M101 F104 R105 N150 R187 S191 I193 A194
Annotation score1
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

View graph for
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)

[Back to BioLiP]