7VHY | pdb_00007vhy

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.250 (Depositor), 0.250 (DCC)
R-Value Work:
0.212 (Depositor), 0.210 (DCC)
R-Value Observed:
0.214 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

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 Search on PubMed
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.

Organizational Affiliation

Daiichi Sankyo Co., Ltd., 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan. Electronic address: kanada.ryutaro.nw@daiichisankyo.co.jp.

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

Find similar proteins by:

(by identity cutoff) | 3D Structure

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 (PDB Primary Data), 2.3.1 (UniProt)
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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q09472
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
6QI (Subject of Investigation/LOI) Query on 6QI Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	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		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain I [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B]	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		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B]