5FDZ

Crystal structure of human PCAF bromodomain in complex with compound BDOMB00091a (compound 14)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Structure-Based Identification of Inhibitory Fragments Targeting the p300/CBP-Associated Factor Bromodomain.

Chaikuad, A., Lang, S., Brennan, P.E., Temperini, C., Fedorov, O., Hollander, J., Nachane, R., Abell, C., Muller, S., Siegal, G., Knapp, S.

(2016) J Med Chem 59: 1648-1653

  • DOI: 10.1021/acs.jmedchem.5b01719
  • Primary Citation of Related Structures:  
    5FE1, 5FE0, 5FE3, 5FE2, 5FE5, 5FE4, 5FE7, 5FE6, 5FE9, 5FE8

  • PubMed Abstract: 

    • The P300/CBP-associated factor plays a central role in retroviral infection and cancer development, and the C-terminal bromodomain provides an opportunity for selective targeting. Here, we report several new classes of acetyl-lysine mimetic ligands ranging from mM to low micromolar affinity that were identified using fragment screening approaches ...

    The P300/CBP-associated factor plays a central role in retroviral infection and cancer development, and the C-terminal bromodomain provides an opportunity for selective targeting. Here, we report several new classes of acetyl-lysine mimetic ligands ranging from mM to low micromolar affinity that were identified using fragment screening approaches. The binding modes of the most attractive fragments were determined using high resolution crystal structures providing chemical starting points and structural models for the development of potent and selective PCAF inhibitors.

    Organizational Affiliation: 

    Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University and Buchmann Institute for Molecular Life Sciences , Max-von-Laue-Strasse 9, D-60438 Frankfurt am Main, Germany.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone acetyltransferase KAT2B A, B119Homo sapiensMutation(s): 0 
Gene Names: KAT2B, PCAF
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
GTEx:  ENSG00000114166
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5X0
Query on 5X0
Download Ideal Coordinates CCD File 
A, B
~{N}-methyl-2-(oxan-4-yloxy)-5-(2-oxidanylidene-2-phenylazanyl-ethoxy)benzamide
C21 H24 N2 O5
OLSMYKUQDJESEU-UHFFFAOYSA-N		 Ligand Interaction
EDO
Query on EDO
Download Ideal Coordinates CCD File 
B
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
5X0Kd:  6800   nM  Binding MOAD
5X0Kd:  6800   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.77α = 90
b = 99.77β = 90
c = 100.9γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-01-13
    Type: Initial release
  • Version 1.1: 2016-03-30
    Changes: Database references