5LVQ

Crystal structure of human PCAF bromodomain in complex with compound-D (CPD-D), N-methyl-2-(tetrahydro-2H-pyran-4-yloxy)benzamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 

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
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2LX
Query on 2LX

Download Ideal Coordinates CCD File 
A
N-methyl-2-(tetrahydro-2H-pyran-4-yloxy)benzamide
C13 H17 N O3
WZBIMVSWUWZIHN-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

Download Ideal Coordinates CCD File 
B
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
A, B
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
2LXKd:  459000   nM  BindingDB
2LXKd:  104000   nM  BindingDB
2LXKd:  73000   nM  Binding MOAD
2LXKd:  166000   nM  BindingDB
2LXKd:  73000   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.859α = 90
b = 99.859β = 90
c = 100.762γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



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