8DBB

Crystal structure of DDT with the selective inhibitor 2,5-Pyridinedicarboxylic Acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.157 
  • R-Value Work: 0.121 
  • R-Value Observed: 0.123 

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This is version 1.2 of the entry. See complete history


Literature

2,5-Pyridinedicarboxylic acid is a bioactive and highly selective inhibitor of D-dopachrome tautomerase.

Parkins, A.Das, P.Prahaladan, V.Rangel, V.M.Xue, L.Sankaran, B.Bhandari, V.Pantouris, G.

(2023) Structure 31: 355

  • DOI: https://doi.org/10.1016/j.str.2023.01.008
  • Primary Citation of Related Structures:  
    8DBB

  • PubMed Abstract: 

    Macrophage migration inhibitory factor (MIF) and D-dopachrome tautomerase (D-DT) are two pleotropic cytokines, which are coexpressed in various cell types to activate the cell surface receptor CD74. Via the MIF/CD74 and D-DT/CD74 axes, the two proteins exhibit either beneficial or deleterious effect on human diseases. In this study, we report the identification of 2,5-pyridinedicarboxylic acid (a.k.a. 1) that effectively blocks the D-DT-induced activation of CD74 and demonstrates an impressive 79-fold selectivity for D-DT over MIF. Crystallographic characterization of D-DT-1 elucidates the binding features of 1 and reveals previously unrecognized differences between the MIF and D-DT active sites that explain the ligand's functional selectivity. The commercial availability, low cost, and high selectivity make 1 the ideal tool for studying the pathophysiological functionality of D-DT in disease models. At the same time, our comprehensive biochemical, computational, and crystallographic analyses serve as a guide for generating highly potent and selective D-DT inhibitors.


  • Organizational Affiliation

    Department of Chemistry, University of the Pacific, Stockton, CA 95211, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
D-dopachrome decarboxylase
A, B, C
118Homo sapiensMutation(s): 0 
Gene Names: DDT
EC: 4.1.1.84
UniProt & NIH Common Fund Data Resources
Find proteins for P30046 (Homo sapiens)
Explore P30046 
Go to UniProtKB:  P30046
PHAROS:  P30046
GTEx:  ENSG00000099977 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP30046
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.157 
  • R-Value Work: 0.121 
  • R-Value Observed: 0.123 
  • Space Group: P 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.721α = 90
b = 83.721β = 90
c = 40.633γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-08
    Type: Initial release
  • Version 1.1: 2023-03-15
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description