BRD4 in complex with Cpd2 (N,N-dimethyl-3-(6-methyl-7-oxo-6,7-dihydro-1H-pyrrolo[2,3-c]pyridin-4-yl)benzamide)

Experimental Data Snapshot

  • Resolution: 1.45 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.155 

wwPDB Validation   3D Report Full Report

This is version 1.0 of the entry. See complete history


Diving into the Water: Inducible Binding Conformations for BRD4, TAF1(2), BRD9, and CECR2 Bromodomains.

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

(2016) J Med Chem 59: 5391-5402

  • DOI: https://doi.org/10.1021/acs.jmedchem.6b00264
  • Primary Citation of Related Structures:  
    5I1Q, 5I29, 5I40, 5I7X, 5I7Y, 5I80, 5I88

  • PubMed Abstract: 

    The biological role played by non-BET bromodomains remains poorly understood, and it is therefore imperative to identify potent and highly selective inhibitors to effectively explore the biology of individual bromodomain proteins. A ligand-efficient nonselective bromodomain inhibitor was identified from a 6-methyl pyrrolopyridone fragment. Small hydrophobic substituents replacing the N-methyl group were designed directing toward the conserved bromodomain water pocket, and two distinct binding conformations were then observed. The substituents either directly displaced and rearranged the conserved solvent network, as in BRD4(1) and TAF1(2), or induced a narrow hydrophobic channel adjacent to the lipophilic shelf, as in BRD9 and CECR2. The preference of distinct substituents for individual bromodomains provided selectivity handles useful for future lead optimization efforts for selective BRD9, CECR2, and TAF1(2) inhibitors.

  • Organizational Affiliation

    Constellation Pharmaceuticals, Inc. 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bromodomain-containing protein 4126Homo sapiensMutation(s): 0 
Gene Names: BRD4HUNK1
UniProt & NIH Common Fund Data Resources
Find proteins for O60885 (Homo sapiens)
Explore O60885 
Go to UniProtKB:  O60885
PHAROS:  O60885
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60885
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
67B Binding MOAD:  5I80 Kd: 62 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.45 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.155 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.693α = 90
b = 48.67β = 90
c = 59.933γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

  • Released Date: 2016-10-12 
  • Deposition Author(s): Murray, J.M.

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-12
    Type: Initial release