8GZC

Crystal structure of EP300 HAT domain in complex with compound 10


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Discovery of DS-9300: A Highly Potent, Selective, and Once-Daily Oral EP300/CBP Histone Acetyltransferase Inhibitor.

Kanada, R.Kagoshima, Y.Suzuki, T.Nakamura, A.Funami, H.Watanabe, J.Asano, M.Takahashi, M.Ubukata, O.Suzuki, K.Aikawa, T.Sato, K.Goto, M.Setsu, G.Ito, K.Kihara, K.Kuroha, M.Kohno, T.Ogiwara, H.Isoyama, T.Tominaga, Y.Higuchi, S.Naito, H.

(2023) J Med Chem 66: 695-715

  • DOI: https://doi.org/10.1021/acs.jmedchem.2c01641
  • Primary Citation of Related Structures:  
    8GZC

  • PubMed Abstract: 

    Histone acetylation is a post-translational modification of histones that is catalyzed by histone acetyltransferases (HATs) and plays an essential role in cellular processes. The HAT domain of EP300/CBP has recently emerged as a potential drug target for cancer therapy. Here, we describe the identification of the novel, highly potent, and selective EP300/CBP HAT inhibitor DS-9300. Our optimization efforts using a structure-based drug design approach based on the cocrystal structures of the EP300 HAT domain in complex with compounds 2 and 3 led to the identification of compounds possessing low-nanomolar EP300 HAT inhibitory potency and the ability to inhibit cellular acetylation of histone H3K27. Optimization of the pharmacokinetic properties in this series resulted in compounds with excellent oral systemic exposure, and once-daily oral administration of 16 (DS-9300) demonstrated potent antitumor effects in a castrated VCaP xenograft mouse model without significant body weight loss.


  • Organizational Affiliation

    Daiichi Sankyo Co., Ltd., 1-2-58 Hiromachi, Shinagawa-ku, Tokyo140-8710, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone acetyltransferase p300
A, B
454Homo sapiensMutation(s): 1 
Gene Names: EP300P300
EC: 2.3.1.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q09472 (Homo sapiens)
Explore Q09472 
Go to UniProtKB:  Q09472
PHAROS:  Q09472
GTEx:  ENSG00000100393 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ09472
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
KQO (Subject of Investigation/LOI)
Query on KQO

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B]
(2~{R},4~{R})-4-fluoranyl-1-[1-(4-methoxyphenyl)cyclohexyl]carbonyl-~{N}-(1~{H}-pyrazolo[4,3-b]pyridin-5-yl)pyrrolidine-2-carboxamide
C25 H28 F N5 O3
CCRMEUSDGNVQDG-DYESRHJHSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
G [auth B]
H [auth B]
C [auth A],
D [auth A],
E [auth A],
G [auth B],
H [auth B],
I [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.5α = 116.6
b = 89.35β = 95.18
c = 91.6γ = 91.78
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-01-11
    Type: Initial release
  • Version 1.1: 2023-01-25
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description