Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 38.30 kDa 
• Atom Count: 2704 
• Modelled Residue Count: 315 
• Deposited Residue Count: 323 
• Unique protein chains: 1

6V8K

Crystal structure of the p300 acetyltransferase domain with peptide-competitive inhibitor 2

• DOI: 10.2210/pdb6V8K/pdb

• Classification: TRANSFERASE/INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2019-12-11 Released: 2020-04-01 
• Deposition Author(s): Gardberg, A.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free: 0.213 
• R-Value Work: 0.179 
• R-Value Observed: 0.180 

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

• PubMed: 32181984 
• 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone acetyltransferase p300	A	323	Homo sapiens	Mutation(s): 1  Gene Names: EP300, P300 EC: 2.3.1.48 (PDB Primary Data), 2.3.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q09472 (Homo sapiens) Explore Q09472  Go to UniProtKB:  Q09472
PHAROS:  Q09472 GTEx:  ENSG00000100393

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
COA	B [auth A]	COENZYME A C21 H36 N7 O16 P3 S RGJOEKWQDUBAIZ-IBOSZNHHSA-N
QS4	C [auth A]	1-(2-methyl-1H-indol-3-yl)-2-[(2R)-2-methylpiperidin-1-yl]ethan-1-one C17 H22 N2 O VMIOFZFIOOEUFH-GFCCVEGCSA-N
DMS	D [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free: 0.213 
• R-Value Work: 0.179 
• R-Value Observed: 0.180 
• Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.669	α = 90
b = 60.669	β = 90
c = 100.647	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2019-12-11 
• Released Date: 2020-04-01 
Deposition Author(s): Gardberg, A.S.

Revision History  

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