7EVJ | pdb_00007evj

Crystal structure of CBP bromodomain liganded with 9c

• PDB DOI: https://doi.org/10.2210/pdb7EVJ/pdb

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


• Deposited: 2021-05-21 Released: 2022-02-16 
• Deposition Author(s): Xiang, Q., Wang, C., Wu, T., Zhang, Y., Zhang, C., Luo, G., Wu, X., Shen, H., Xu, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.57 Å
• R-Value Free: 
  0.209 (Depositor), 0.217 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

Literature

Design, Synthesis, and Biological Evaluation of 1-(Indolizin-3-yl)ethan-1-ones as CBP Bromodomain Inhibitors for the Treatment of Prostate Cancer.

Xiang, Q., Wang, C., Wu, T., Zhang, C., Hu, Q., Luo, G., Hu, J., Zhuang, X., Zou, L., Shen, H., Wu, X., Zhang, Y., Kong, X., Liu, J., Xu, Y.

(2022) J Med Chem 65: 785-810

• PubMed: 34962793 
• DOI: https://doi.org/10.1021/acs.jmedchem.1c01864
• Primary Citation Related Structures: 
  7EVJ, 7XNE


• PubMed Abstract: 
  

  CREB (cyclic-AMP responsive element binding protein) binding protein (CBP) is a potential target for prostate cancer treatment. Herein, we report the structural optimization of a series of 1-(indolizin-3-yl)ethan-1-one compounds as new selective CBP bromodomain inhibitors, aiming to improve cellular potency and metabolic stability. This process led to compound 9g (Y08284), which possesses good liver microsomal stability and pharmacokinetic properties ( F = 25.9%). Furthermore, the compound is able to inhibit CBP bromodomain as well as the proliferation, colony formation, and migration of prostate cancer cells. Additionally, the new inhibitor shows promising antitumor efficacy in a 22Rv1 xenograft model (TGI = 88%). This study provides new lead compounds for further development of drugs for the treatment of prostate cancer.

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Organizational Affiliation: 
• Guangdong Provincial Key Laboratory of Biocomputing, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Guangzhou Medical University, Chinese Academy of Sciences, Guangzhou 510530, China.
University of Chinese Academy of Sciences, No. 19 Yuquan Road, Beijing 100049, China.
State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.
China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou 510530, 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: 16.6 kDa 
• Atom Count: 1,026 
• Modeled Residue Count: 111 
• 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
JE9 (Subject of Investigation/LOI)	B [auth A]	3-acetyl-1-((3-(1-cyclopropyl-1H-pyrazol-4-yl)-2-fluoro-5-(hydroxymethyl)phenyl)carbamoyl)indolizin-7-yl dimethylcarbamate C27 H26 F N5 O5 UMURGYUDULFAPH-UHFFFAOYSA-N
PO4	C [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.57 Å
• R-Value Free:  0.209 (Depositor), 0.217 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.45	α = 90
b = 79.45	β = 90
c = 45.11	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2022-02-16 
Deposition Author(s): Xiang, Q., Wang, C., Wu, T., Zhang, Y., Zhang, C., Luo, G., Wu, X., Shen, H., Xu, Y.

Revision History  

• Version 1.0: 2022-02-16
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description