5JOH

CRYSTAL STRUCTURE OF CSN5(2-257) IN COMPLEX WITH CNS5i-1b


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.227 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Targeted inhibition of the COP9 signalosome for treatment of cancer.

Schlierf, A.Altmann, E.Quancard, J.Jefferson, A.B.Assenberg, R.Renatus, M.Jones, M.Hassiepen, U.Schaefer, M.Kiffe, M.Weiss, A.Wiesmann, C.Sedrani, R.Eder, J.Martoglio, B.

(2016) Nat Commun 7: 13166-13166

  • DOI: https://doi.org/10.1038/ncomms13166
  • Primary Citation of Related Structures:  
    5JOG, 5JOH

  • PubMed Abstract: 

    The COP9 signalosome (CSN) is a central component of the activation and remodelling cycle of cullin-RING E3 ubiquitin ligases (CRLs), the largest enzyme family of the ubiquitin-proteasome system in humans. CRLs are implicated in the regulation of numerous cellular processes, including cell cycle progression and apoptosis, and aberrant CRL activity is frequently associated with cancer. Remodelling of CRLs is initiated by CSN-catalysed cleavage of the ubiquitin-like activator NEDD8 from CRLs. Here we describe CSN5i-3, a potent, selective and orally available inhibitor of CSN5, the proteolytic subunit of CSN. The compound traps CRLs in the neddylated state, which leads to inactivation of a subset of CRLs by inducing degradation of their substrate recognition module. CSN5i-3 differentially affects the viability of tumour cell lines and suppresses growth of a human xenograft in mice. Our results provide insights into how CSN regulates CRLs and suggest that CSN5 inhibition has potential for anti-tumour therapy.


  • Organizational Affiliation

    Novartis Institutes for Biomedical Research, Novartis Pharma AG, 4002 Basel, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
COP9 signalosome complex subunit 5257Homo sapiensMutation(s): 0 
Gene Names: COPS5CSN5JAB1
EC: 3.4
UniProt & NIH Common Fund Data Resources
Find proteins for Q92905 (Homo sapiens)
Explore Q92905 
Go to UniProtKB:  Q92905
GTEx:  ENSG00000121022 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92905
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6M3
Query on 6M3

Download Ideal Coordinates CCD File 
C [auth A]2'-chloro-6-[(5S,6S)-6-hydroxy-6,7,8,9-tetrahydro-5H-imidazo[1,5-a]azepin-5-yl][1,1'-biphenyl]-3-carbonitrile
C21 H18 Cl N3 O
FKEZMHCTDJKGQH-SFTDATJTSA-N
MPD
Query on MPD

Download Ideal Coordinates CCD File 
D [auth A](4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.227 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.058α = 90
b = 102.058β = 90
c = 68.729γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling
BUSTERrefinement
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-11-02
    Type: Initial release
  • Version 1.1: 2024-01-10
    Changes: Data collection, Database references, Refinement description