Bromodomain and Extra-terminal Domain (BET) BRD4

Experimental Data Snapshot

  • Resolution: 1.57 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.225 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.0 of the entry. See complete history


Discovery of 1 H -Imidazo[4,5- b ]pyridine Derivatives as Potent and Selective BET Inhibitors for the Management of Neuropathic Pain.

Chen, X.Cao, D.Liu, C.Meng, F.Zhang, Z.Xu, R.Tong, Y.Xin, Y.Zhang, W.Kang, W.Bao, Q.Shen, J.Xiong, B.You, Q.Jiang, Z.

(2023) J Med Chem 66: 8725-8744

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c00372
  • Primary Citation of Related Structures:  
    8IBQ, 8IDH

  • PubMed Abstract: 

    Neuropathic pain (NP) is an intolerable pain syndrome that arises from continuous inflammation and excitability after nerve injury. Only a few NP therapeutics are currently available, and all of them do not provide adequate pain relief. Herein, we report the discovery of a selective and potent inhibitor of the bromodomain and extra-terminal (BET) proteins for reducing neuroinflammation and excitability to treat NP. Starting with the screening hit 1 from an in-house compound library, iterative optimization resulted in the potent BET inhibitor DDO-8926 with a unique binding mode and a novel chemical structure. DDO-8926 exhibits excellent BET selectivity and favorable drug-like properties. In mice with spared nerve injury, DDO-8926 significantly alleviated mechanical hypersensitivity by inhibiting pro-inflammatory cytokine expression and reducing excitability. Collectively, these results implicate that DDO-8926 is a promising agent for the treatment of NP.

  • Organizational Affiliation

    Jiang Su Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bromodomain-containing protein 4112Homo sapiensMutation(s): 0 
Gene Names: BRD4HUNK1
UniProt & NIH Common Fund Data Resources
Find proteins for O60885 (Homo sapiens)
Explore O60885 
Go to UniProtKB:  O60885
GTEx:  ENSG00000141867 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60885
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OWO (Subject of Investigation/LOI)
Query on OWO

Download Ideal Coordinates CCD File 
B [auth A]7-[2-fluoranyl-3-(1,3,5-trimethylpyrazol-4-yl)phenyl]-1~{H}-imidazo[4,5-b]pyridine
C18 H16 F N5
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on CME
Experimental Data & Validation

Experimental Data

  • Resolution: 1.57 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.225 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.591α = 90
b = 71.929β = 90
c = 32.044γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
HKL-3000data collection

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China82173680
National Natural Science Foundation of China (NSFC)China81930100

Revision History  (Full details and data files)

  • Version 1.0: 2023-10-04
    Type: Initial release