8IDH | pdb_00008idh

Bromodomain and Extra-terminal Domain (BET) BRD4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 
    0.252 (Depositor), 0.253 (DCC) 
  • R-Value Work: 
    0.221 (Depositor), 0.222 (DCC) 
  • R-Value Observed: 
    0.225 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

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 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.

Macromolecule Content 

  • Total Structure Weight: 13.58 kDa 
  • Atom Count: 1,026 
  • Modeled Residue Count: 112 
  • Deposited Residue Count: 112 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
PHAROS:  O60885
GTEx:  ENSG00000141867 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60885
Sequence Annotations
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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
RPWDTXPUVLCSDW-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CME
Query on CME
A
L-PEPTIDE LINKINGC5 H11 N O3 S2CYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free:  0.252 (Depositor), 0.253 (DCC) 
  • R-Value Work:  0.221 (Depositor), 0.222 (DCC) 
  • R-Value Observed: 0.225 (Depositor) 
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
PHENIXrefinement
Aimlessdata scaling
PHENIXphasing
HKL-3000data collection

Structure Validation

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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
  • Version 1.1: 2024-11-20
    Changes: Structure summary