9KPI | pdb_00009kpi

Aromatic acetyl piperidine derivatives as soluble epoxide hydrolase inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.238 (Depositor), 0.239 (DCC) 
  • R-Value Work: 
    0.180 (Depositor), 0.181 (DCC) 
  • R-Value Observed: 
    0.185 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Discovery of Phenylacylpiperidine as Novel sEH Inhibitors through Scaffold Hopping of Natural Stilbene.

Ding, J.Zhu, M.Z.Du, X.Y.Liu, S.M.Wang, H.Liu, X.Z.Xie, W.S.Ma, H.L.Feng, Y.Zhu, X.H.Liang, J.H.

(2025) J Med Chem 68: 8980-9013

  • DOI: https://doi.org/10.1021/acs.jmedchem.5c00685
  • Primary Citation of Related Structures:  
    9KPI

  • PubMed Abstract: 

    Despite the development of soluble epoxide hydrolase (sEH) inhibitors as a promising therapeutic approach, no drug candidate has successfully progressed beyond clinical phase II, highlighting the need for a novel chemotype with improved in vivo potency, pharmacokinetics and safety. In this study, we discovered a phenylacetylpiperidine-based compound, 77 (lab code: DJ-89 ; IC 50 : 0.51 nM), through strategic scaffold hopping from previously reported styrene-based sEH inhibitors. Resolving the cocrystal structure and mode-of-action studies revealed a distinct profile compared to well-known sEH inhibitors TPPU and EC5026 (IC 50 : 44, 19 nM). Notably, 77 demonstrated additional interactions with sEH compared to TPPU , and uniquely enhanced anti-inflammatory factors, including EET levels and IL-10, a capability not observed with EC5026 . Moreover, 77 showed excellent pharmacokinetics and safety, positioning it as a promising candidate for treating both acute and chronic inflammatory diseases, including rheumatoid arthritis, leveraging phenylacylpiperidine scaffolds in sEH-targeted therapies.


  • Organizational Affiliation
    • Key Laboratory of Medicinal Molecule Science and Pharmaceutical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 102488, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bifunctional epoxide hydrolase 2555Homo sapiensMutation(s): 0 
Gene Names: EPHX2
EC: 3.3.2.10 (PDB Primary Data), 3.1.3.76 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P34913 (Homo sapiens)
Explore P34913 
Go to UniProtKB:  P34913
PHAROS:  P34913
GTEx:  ENSG00000120915 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP34913
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.238 (Depositor), 0.239 (DCC) 
  • R-Value Work:  0.180 (Depositor), 0.181 (DCC) 
  • R-Value Observed: 0.185 (Depositor) 
Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.507α = 90
b = 91.507β = 90
c = 242.802γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
Aimlessdata scaling
PHENIXphasing
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China--

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-16
    Type: Initial release
  • Version 1.1: 2025-10-01
    Changes: Database references