5LVR

Crystal structure of human PCAF bromodomain in complex with compound-E (CPD-E)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.176 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Discovery of New Bromodomain Scaffolds by Biosensor Fragment Screening.

Navratilova, I.Aristotelous, T.Picaud, S.Chaikuad, A.Knapp, S.Filappakopoulos, P.Hopkins, A.L.

(2016) ACS Med Chem Lett 7: 1213-1218

  • DOI: 10.1021/acsmedchemlett.6b00154
  • Primary Citation of Related Structures:  
    5TB6, 5LUU, 5LVR, 5LVQ

  • PubMed Abstract: 
  • The discovery of novel bromodomain inhibitors by fragment screening is complicated by the presence of dimethyl sulfoxide (DMSO), an acetyl-lysine mimetic, that can compromise the detection of low affinity fragments. We demonstrate surface plasmon resonance as a primary fragment screening approach for the discovery of novel bromodomain scaffolds, by describing a protocol to overcome the DMSO interference issue ...

    The discovery of novel bromodomain inhibitors by fragment screening is complicated by the presence of dimethyl sulfoxide (DMSO), an acetyl-lysine mimetic, that can compromise the detection of low affinity fragments. We demonstrate surface plasmon resonance as a primary fragment screening approach for the discovery of novel bromodomain scaffolds, by describing a protocol to overcome the DMSO interference issue. We describe the discovery of several novel small molecules scaffolds that inhibit the bromodomains PCAF, BRD4, and CREBBP, representing canonical members of three out of the seven subfamilies of bromodomains. High-resolution crystal structures of the complexes of key fragments binding to BRD4(1), CREBBP, and PCAF were determined to provide binding mode data to aid the development of potent and selective inhibitors of PCAF, CREBBP, and BRD4.


    Organizational Affiliation

    Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee , Dow Street, Dundee DD1 5EH, United Kingdom.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone acetyltransferase KAT2B AB119Homo sapiensMutation(s): 0 
Gene Names: KAT2BPCAF
EC: 2.3.1.48 (PDB Primary Data), 2.3.1.57 (UniProt)
Find proteins for Q92831 (Homo sapiens)
Explore Q92831 
Go to UniProtKB:  Q92831
NIH Common Fund Data Resources
PHAROS:  Q92831
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
78YKd:  660000   nM  BindingDB
78YKd:  360000   nM  BindingDB
78YKd:  1080000   nM  BindingDB
78YKd:  250000   nM  Binding MOAD
78YKd:  250000   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.176 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.659α = 90
b = 99.659β = 90
c = 100.354γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-26
    Type: Initial release
  • Version 1.1: 2017-01-11
    Changes: Database references