5V84

CECR2 in complex with Cpd6 (6-allyl-N,2-dimethyl-7-oxo-N-(1-(1-phenylethyl)piperidin-4-yl)-6,7-dihydro-1H-pyrrolo[2,3-c]pyridine-4-carboxamide)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.207 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

GNE-886: A Potent and Selective Inhibitor of the Cat Eye Syndrome Chromosome Region Candidate 2 Bromodomain (CECR2).

Crawford, T.D.Audia, J.E.Bellon, S.Burdick, D.J.Bommi-Reddy, A.Cote, A.Cummings, R.T.Duplessis, M.Flynn, E.M.Hewitt, M.Huang, H.R.Jayaram, H.Jiang, Y.Joshi, S.Kiefer, J.R.Murray, J.Nasveschuk, C.G.Neiss, A.Pardo, E.Romero, F.A.Sandy, P.Sims, R.J.Tang, Y.Taylor, A.M.Tsui, V.Wang, J.Wang, S.Wang, Y.Xu, Z.Zawadzke, L.Zhu, X.Albrecht, B.K.Magnuson, S.R.Cochran, A.G.

(2017) ACS Med Chem Lett 8: 737-741

  • DOI: https://doi.org/10.1021/acsmedchemlett.7b00132
  • Primary Citation of Related Structures:  
    5V84

  • PubMed Abstract: 

    The biological function of bromodomains, epigenetic readers of acetylated lysine residues, remains largely unknown. Herein we report our efforts to discover a potent and selective inhibitor of the bromodomain of cat eye syndrome chromosome region candidate 2 (CECR2). Screening of our internal medicinal chemistry collection led to the identification of a pyrrolopyridone chemical lead, and subsequent structure-based drug design led to a potent and selective CECR2 bromodomain inhibitor (GNE-886) suitable for use as an in vitro tool compound.


  • Organizational Affiliation

    Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cat eye syndrome critical region protein 2
A, B, C, D
140Homo sapiensMutation(s): 0 
Gene Names: CECR2KIAA1740
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BXF3 (Homo sapiens)
Explore Q9BXF3 
Go to UniProtKB:  Q9BXF3
PHAROS:  Q9BXF3
GTEx:  ENSG00000099954 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BXF3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.207 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.184α = 90
b = 116.488β = 90
c = 132.93γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
BUSTERrefinement
PDB_EXTRACTdata extraction
PHASERphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-06-14
    Type: Initial release
  • Version 1.1: 2017-08-09
    Changes: Database references
  • Version 1.2: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary