9JUU | pdb_00009juu

X-ray crystal structure of Y16515 in CBP

• PDB DOI: https://doi.org/10.2210/pdb9JUU/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-10-08 Released: 2025-03-12 
• Deposition Author(s): Hu, J., Zhang, C., Luo, G., Tang, X., Wu, T., Shen, H., Zhao, X., Wu, X., Smaill, J., Zhang, Y., Xu, Y., Xiang, Q.
• Funding Organization(s): Ministry of Science and Technology (MoST, China)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free: 
  0.219 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: experimental

Literature

Discovery of 5-imidazole-3-methylbenz[d]isoxazole derivatives as potent and selective CBP/p300 bromodomain inhibitors for the treatment of acute myeloid leukemia.

Hu, J.K., Tang, X., Luo, G.L., Zhang, C., Wu, T.B., Wang, C., Shen, H., Zhao, X.F., Wu, X.S., Smaill, J.B., Xu, Y., Zhang, Y., Xiang, Q.P.

(2025) Acta Pharmacol Sin 46: 1706-1721

• PubMed: 39890943 
• DOI: https://doi.org/10.1038/s41401-025-01478-x
• Primary Citation of Related Structures:  
  9JUT, 9JUU, 9JUY


• PubMed Abstract: 
  

  Inhibition of the bromodomain of the cAMP response element binding protein (CREB)-binding protein (CBP) and its homologue p300 is an attractive therapeutic approach in oncology, particularly in acute myeloid leukemia (AML). In this study we describe the design, optimization, and evaluation of 5-imidazole-3-methylbenz[d]isoxazoles as novel, potent and selective CBP/p300 bromodomain inhibitors. Two of the representative compounds, 16t (Y16524) and 16u (Y16526), bound to the p300 bromodomain with IC ₅₀ values of 0.01 and 0.03 μM, respectively. Furthermore, 16t and 16u potently inhibited the growth of AML cell lines, particularly MV4;11 cells with IC ₅₀ values of 0.49 and 0.26 μM, respectively. The potent CBP/p300 bromodomain inhibitors represent a new class of compounds for the development of potential therapeutics against AML.

---

Organizational Affiliation: 
• China-New Zealand Joint Laboratory of Biomedicine and Health, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Biocomputing, Institute of Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences and Guangzhou Medical University, Guangzhou, 510530, China.
University of Chinese Academy of Sciences, Beijing, 100049, China.
Auckland Cancer Society Research Centre, School of Medical Sciences, The University of Auckland, Auckland, New Zealand.
Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland, New Zealand.
China-New Zealand Joint Laboratory of Biomedicine and Health, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Biocomputing, Institute of Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China. [e-mail].
China-New Zealand Joint Laboratory of Biomedicine and Health, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Biocomputing, Institute of Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China. [e-mail].
Guoke Ningbo Life Science and Health Industry Research Institute, Ningbo No. 2 Hospital, Ningbo, 315010, China. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 16.6 kDa 
• Atom Count: 1,075 
• Modeled Residue Count: 113 
• Deposited Residue Count: 133 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CREB-binding protein	A	133	Homo sapiens	Mutation(s): 0  Gene Names: CREBBP, CBP EC: 2.3.1.48 (PDB Primary Data), 2.3.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q92793 (Homo sapiens) Explore Q92793  Go to UniProtKB:  Q92793
PHAROS:  Q92793 GTEx:  ENSG00000005339

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1EDN (Subject of Investigation/LOI)	B [auth A]	(5~{S})-1-(3-chloranyl-4-methoxy-phenyl)-5-[4-(3-methyl-1,2-benzoxazol-5-yl)-1-[(2~{R})-2-morpholin-4-ylpropyl]imidazol-2-yl]pyrrolidin-2-one C29 H32 Cl N5 O4 KUECYLYQFQZBBX-CJAUYULYSA-N
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free:  0.219 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.53	α = 90
b = 55.87	β = 90
c = 113.4	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
iMOSFLM	data reduction
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-03-12 
Deposition Author(s): Hu, J., Zhang, C., Luo, G., Tang, X., Wu, T., Shen, H., Zhao, X., Wu, X., Smaill, J., Zhang, Y., Xu, Y., Xiang, Q.

---

Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2022YFE0210600

Revision History  

• Version 1.0: 2025-03-12
  Type: Initial release
  
• Version 1.1: 2025-06-04
  Changes: Database references