6V90

Crystal structure of the p300 acetyltransferase domain with AcCoA competitive inhibitor 12


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Early Drug-Discovery Efforts towards the Identification of EP300/CBP Histone Acetyltransferase (HAT) Inhibitors.

Huhn, A.J.Gardberg, A.S.Poy, F.Brucelle, F.Vivat, V.Cantone, N.Patel, G.Patel, C.Cummings, R.Sims, R.Levell, J.Audia, J.E.Bommi-Reddy, A.Wilson, J.E.

(2020) ChemMedChem 15: 955-960

  • DOI: 10.1002/cmdc.202000007
  • Primary Citation of Related Structures:  
    6V8K, 6V90, 6V8N, 6V8B

  • PubMed Abstract: 
  • EP300 and CBP (KAT3A/3B) are two highly homologous, multidomain, epigenetic coregulators that play central roles in transcription through the acetylation of lysine residues on histones and other proteins. Both enzymes have been implicated in human diseases, especially cancer ...

    EP300 and CBP (KAT3A/3B) are two highly homologous, multidomain, epigenetic coregulators that play central roles in transcription through the acetylation of lysine residues on histones and other proteins. Both enzymes have been implicated in human diseases, especially cancer. From a high-throughput screen of 191 000 compounds searching for EP300/CBP histone acetyltransferase (HAT) inhibitors, 18 compounds were characterized by a suite of biochemical enzymatic assays and biophysical methods, including X-ray crystallography and native mass spectrometry. This work resulted in the discovery of three distinct mechanistic classes of EP300/CBP HAT inhibitors, including two classes not previously described. The profiles of an example of each class of inhibitor are described in detail. A subsequent medicinal chemistry effort led to the development of a novel class of orally bioavailable AcCoA-competitive EP300/CBP HAT inhibitors with in vivo activity. We believe that this work will prove to be a useful guide for other groups interested in the development of HAT inhibitors.


    Organizational Affiliation

    Constellation Pharmaceuticals, 215 First Street, Cambridge, MA 02142.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone acetyltransferase p300A349Homo sapiensMutation(s): 1 
Gene Names: EP300P300
EC: 2.3.1.48 (PDB Primary Data), 2.3.1 (PDB Primary Data)
Find proteins for Q09472 (Homo sapiens)
Explore Q09472 
Go to UniProtKB:  Q09472
NIH Common Fund Data Resources
PHAROS:  Q09472
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
QSD
Query on QSD

Download Ideal Coordinates CCD File 
B [auth A](2R)-2-{[2-(4-cyanophenyl)ethyl]amino}-N-[5-(1-methyl-1H-pyrazol-4-yl)pyridin-2-yl]-2-phenylacetamide
C26 H24 N6 O
ZJGMOHOOSGHFMJ-RUZDIDTESA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A], D [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
E [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.36α = 90
b = 104.639β = 90
c = 168.863γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2019-12-12 
  • Released Date: 2020-04-01 
  • Deposition Author(s): Gardberg, A.S.

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-01
    Type: Initial release
  • Version 1.1: 2020-06-17
    Changes: Database references