7VHY

Crystal structure of EP300 HAT domain in complex with compound (+)-3

• PDB DOI: https://doi.org/10.2210/pdb7VHY/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2021-09-24 Released: 2022-04-27 
• Deposition Author(s): Takahashi, M., Hanzawa, H.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.250 
• R-Value Work: 0.212 
• R-Value Observed: 0.214 

Starting Model: experimental

Literature

Discovery of EP300/CBP histone acetyltransferase inhibitors through scaffold hopping of 1,4-oxazepane ring.

Kanada, R., Kagoshima, Y., Asano, M., Suzuki, T., Murata, T., Haruta, M., Takahashi, M., Ubukata, O., Hashimoto, K., Obata, K., Kihara, K., Kuroha, M., Banjo, T., Togashi, N., Sato, K., Yamamoto, Y., Suzuki, K., Isoyama, T., Tominaga, Y., Higuchi, S., Naito, H.

(2022) Bioorg Med Chem Lett 66: 128726-128726

• PubMed: 35413416 
• DOI: https://doi.org/10.1016/j.bmcl.2022.128726
• Primary Citation of Related Structures:  
  7VHY, 7VHZ, 7VI0


• PubMed Abstract: 
  

  EP300 and its paralog CBP play an important role in post-translational modification as histone acetyltransferases (HATs). EP300/CBP inhibition has been gaining attention as an anticancer treatment target in recent years. Herein, we describe the identification of a novel, highly selective EP300/CBP inhibitor, compound 11 (DS17701585), by scaffold hopping and structure-based optimization of a high-throughput screening hit 1. Compound 11 (DS17701585) shows dose-dependent inhibition of SRY-box transcription factor 2 (SOX2) mRNA expression in a human lung squamous cell carcinoma cell line LK2-xenografted mouse model.

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Organizational Affiliation: 

Daiichi Sankyo Co., Ltd., 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan. Electronic address: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 105.64 kDa 
• Atom Count: 7,299 
• Modelled Residue Count: 876 
• Deposited Residue Count: 908 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone acetyltransferase p300	A, B	454	Homo sapiens	Mutation(s): 1  Gene Names: EP300, P300 EC: 2.3.1.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q09472 (Homo sapiens) Go to UniProtKB:  Q09472
PHAROS:  Q09472 GTEx:  ENSG00000100393

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6QI (Subject of Investigation/LOI)	F [auth A]	[(6R)-6-(1H-indazol-4-ylmethyl)-1,4-oxazepan-4-yl]-[1-(4-methoxyphenyl)cyclopentyl]methanone C26 H31 N3 O3 DUYFMLONWKDSAB-LJQANCHMSA-N
ZN	C [auth A], D [auth A], E [auth A], G [auth B], H [auth B], I [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
6QI	BindingDB:  7VHY	IC50: min: 130, max: 2.50e+4 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.250 
• R-Value Work: 0.212 
• R-Value Observed: 0.214 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.49	α = 116.58
b = 88.781	β = 99.44
c = 89.949	γ = 85.3

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
CrystalClear	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-04-27 
Deposition Author(s): Takahashi, M., Hanzawa, H.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-04-27
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description