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)

• PDB DOI:  https://doi.org/10.2210/pdb5V84/pdb

• Classification: Transcription/Inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-03-21 Released: 2017-06-14 
• Deposition Author(s): Murray, J.M., Kiefer, J.R., Jayaran, H., Bellon, S., Boy, F.

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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 

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

• PubMed: 28740608 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 68.48 kDa 
• Atom Count: 3,517 
• Modelled Residue Count: 406 
• Deposited Residue Count: 560 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cat eye syndrome critical region protein 2	A, B, C, D	140	Homo sapiens	Mutation(s): 0  Gene Names: CECR2, KIAA1740
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BXF3 (Homo sapiens) Explore Q9BXF3  Go to UniProtKB:  Q9BXF3
PHAROS:  Q9BXF3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
96V	F [auth A], G [auth B], H [auth C], J [auth D]	N,2-dimethyl-7-oxo-N-{1-[(1S)-1-phenylethyl]piperidin-4-yl}-6-(prop-2-en-1-yl)-6,7-dihydro-1H-pyrrolo[2,3-c]pyridine-4- carboxamide C26 H32 N4 O2 WFCPQMAYBTUYAR-IBGZPJMESA-N
SO4	E [auth A], I [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
96V	BindingDB:  5V84	IC50: 190 (nM) from 1 assay(s)

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 = 101.184	α = 90
b = 116.488	β = 90
c = 132.93	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
BUSTER	refinement
PDB_EXTRACT	data extraction
PHASER	phasing
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-06-14 
Deposition Author(s): Murray, J.M., Kiefer, J.R., Jayaran, H., Bellon, S., Boy, F.

Revision History  

• Version 1.0: 2017-06-14
  Type: Initial release
  
• Version 1.1: 2017-08-09
  Changes: Database references