9IZL

hVanin-1 complexed with X17


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 

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 Thiazole Carboxamides as Novel Vanin-1 Inhibitors for Inflammatory Bowel Disease Treatment.

Xie, T.Cao, G.Y.Zhang, S.Li, M.K.Jin, X.Liu, L.Wang, G.Zhen, L.

(2024) J Med Chem 67: 20372-20398

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c01838
  • Primary Citation of Related Structures:  
    9IZL

  • PubMed Abstract: 

    Inflammatory bowel disease (IBD) is a clinically heterogeneous disease demanding more therapeutic targets and intervention strategies. Vanin-1, an oxidative stress-regulating protein, has emerged as a promising target for alleviating inflammation and oxidative stress. In this study, a series of thiazole carboxamide derivatives as vanin-1 inhibitors were designed and synthesized. The preferred compound, X17 , demonstrated potent inhibition against vanin-1 at the protein, HT-29 cell, and tissue levels, whose binding mode with the target was confirmed via the cocrystal structure. X17 achieved a high bioavailability of 81% in rats, accompanied by concentration-dependent inhibition of serum vanin-1. In a DSS-induced mouse colitis model, X17 exhibited potent anti-inflammatory and antioxidant activities, repressing the inflammatory factor expressions and myeloperoxidase activity, elevating the colonic glutathione reserve, and restoring the intestinal barrier. Collectively, these findings depict the discovery of a potent vanin-1 inhibitor, providing an opportunity for further drug candidate development for treating IBD.


  • Organizational Affiliation

    Key Laboratory of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University, Nanjing, Jiangsu 210009, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pantetheinase
A, B
462Homo sapiensMutation(s): 1 
Gene Names: VNN1
EC: 3.5.1.92
UniProt & NIH Common Fund Data Resources
Find proteins for O95497 (Homo sapiens)
Explore O95497 
Go to UniProtKB:  O95497
PHAROS:  O95497
GTEx:  ENSG00000112299 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO95497
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1EAG (Subject of Investigation/LOI)
Query on A1EAG

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
8-oxa-2-azaspiro[4.5]decan-2-yl-[2-[(3~{S})-3-oxidanylpyrrolidin-1-yl]-1,3-thiazol-5-yl]methanone
C16 H23 N3 O3 S
PDHLSHPRWHXZMR-LBPRGKRZSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.823α = 90
b = 92.98β = 90
c = 218.923γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing

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)China82173686

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-04
    Type: Initial release
  • Version 1.1: 2024-12-11
    Changes: Database references