6V8N

Crystal structure of the p300 acetyltransferase domain with AcCoA competitive inhibitor 17


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 

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
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • EP300 and CBP are two highly homologous, multidomain, epigenetic coregulators that play central roles in transcription via acetylation of lysine residues on histones and other proteins. Both enzymes have been implicated in human diseases, especially ...

    EP300 and CBP are two highly homologous, multidomain, epigenetic coregulators that play central roles in transcription via 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 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, AcCoA-competitive inhibitors, peptide-competitive inhibitors, and mixed/ allosteric inhibitors. The latter two classes of inhibitors have not been described before and the profiles of an exemplar 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 histone acetyltransferase inhibitors.


    Organizational Affiliation

    Constellation Pharmaceuticals, Lead Discovery, UNITED STATES.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone acetyltransferase p300
A
349Homo sapiensMutation(s): 0 
Gene Names: EP300P300
EC: 2.3.1.48 (PDB Primary Data), 2.3.1 (PDB Primary Data)
Find proteins for Q09472 (Homo sapiens)
Go to UniProtKB:  Q09472
NIH Common Fund Data Resources
PHAROS  Q09472
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
QS1
Query on QS1

Download CCD File 
A
(2R)-2-{[(2S)-2-(4-cyanophenyl)propyl]amino}-N-[5-(1-methyl-1H-pyrazol-4-yl)pyridin-2-yl]-2-phenylacetamide
C27 H26 N6 O
SEDFZSHSBUXKAC-NIYFSFCBSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ALY
Query on ALY
AL-PEPTIDE LINKINGC8 H16 N2 O3LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.65α = 90
b = 104.82β = 90
c = 169.12γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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