9J6O | pdb_00009j6o

Crystal Structure of bromodomain of human CBP in complex with the inhibitor CZL-046

• PDB DOI: https://doi.org/10.2210/pdb9J6O/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2024-08-16 Released: 2024-10-16 
• Deposition Author(s): Zhang, Y., Zhang, C., Chen, Z., Yang, H., Huang, X., Li, Y., Xu, Y.
• Funding Organization(s): Ministry of Science and Technology (MoST, China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.67 Å
• R-Value Free: 
  0.290 (Depositor), 0.293 (DCC) 
• R-Value Work: 
  0.234 (Depositor), 0.238 (DCC) 
• R-Value Observed: 
  0.238 (Depositor) 

Starting Model: experimental

Literature

Discovery of CZL-046 with an ( S )-3-Fluoropyrrolidin-2-one Scaffold as a p300 Bromodomain Inhibitor for the Treatment of Multiple Myeloma.

Chen, Z., Yang, H., Zhang, Y., Lyu, X., Shi, Q., Zhang, C., Wang, X., Wang, Z., Zhang, Y., Deng, Y., Wang, Y., Huang, Y., Xu, Y., Huang, X., Li, Y.

(2024) J Med Chem 67: 18606-18628

• PubMed: 39356741 
• DOI: https://doi.org/10.1021/acs.jmedchem.4c01984
• Primary Citation of Related Structures:  
  9J6O


• PubMed Abstract: 
  

  E1A binding protein (p300) is a promising therapeutic target for the treatment of cancer. Herein, we report the discovery of a series of novel inhibitors with an ( S )-3-fluoropyrrolidin-2-one scaffold targeting p300 bromodomain. The best compound 29 (CZL-046) shows potent inhibitory activity of p300 bromodomain (IC ₅₀ = 3.3 nM) and antiproliferative activity in the multiple myeloma (MM) cell line (OPM-2 IC ₅₀ = 51.5 nM). 29 suppressed the mRNA levels of c-Myc and IRF4 and downregulated the expression of c-Myc and H3K27Ac. Compared to the lead compound 5 , 29 exhibits significantly improved in vitro and in vivo metabolic properties. Oral administration of 29 with 30 mg/kg achieved a TGI value of 44% in the OPM-2 xenograft model, accompanied by good tolerability. The cocrystal structure of CREB binding protein bromodomain with 29 provides an insight into the precise binding mode. The results demonstrate that 29 is a promising p300 bromodomain inhibitor for the treatment of MM.

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Organizational Affiliation: 
• Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China.
Lingang Laboratory, Shanghai 200031, P. R. China.
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.
Division of Antitumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, P. R. China.
School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
School of Pharmaceutical Sciences, Shanghai Jiao Tong University, Shanghai 200240, China.
School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, P. R. China.
Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai 200040, China.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 16.47 kDa 
• Atom Count: 1,038 
• Modeled Residue Count: 119 
• 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 (UniProt)
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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1L3S (Subject of Investigation/LOI)	B [auth A]	(3~{S},5~{S})-1-[3,4-bis(fluoranyl)phenyl]-5-[5-(3,5-dimethyl-1,2-oxazol-4-yl)-1-(4-methoxycyclohexyl)benzimidazol-2-yl]-3-fluoranyl-pyrrolidin-2-one C29 H29 F3 N4 O3 JLOJBSFFOSCKTK-BYHUZDBLSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.67 Å
• R-Value Free:  0.290 (Depositor), 0.293 (DCC) 
• R-Value Work:  0.234 (Depositor), 0.238 (DCC) 
• R-Value Observed: 0.238 (Depositor) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.379	α = 90
b = 60.637	β = 90
c = 61.177	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
XDS	data reduction
MERLOT	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-16 
Deposition Author(s): Zhang, Y., Zhang, C., Chen, Z., Yang, H., Huang, X., Li, Y., Xu, Y.

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

Revision History  

• Version 1.0: 2024-10-16
  Type: Initial release
  
• Version 1.1: 2024-11-06
  Changes: Database references