8DBB image
Deposition Date 2022-06-14
Release Date 2023-03-08
Last Version Date 2023-10-25
Entry Detail
PDB ID:
8DBB
Keywords:
Title:
Crystal structure of DDT with the selective inhibitor 2,5-Pyridinedicarboxylic Acid
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Host Organism:
Method Details:
Experimental Method:
Resolution:
1.30 Å
R-Value Free:
0.15
R-Value Work:
0.12
R-Value Observed:
0.12
Space Group:
P 3
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:D-dopachrome decarboxylase
Gene (Uniprot):DDT
Chain IDs:A, B, C
Chain Length:118
Number of Molecules:3
Biological Source:Homo sapiens
Primary Citation
2,5-Pyridinedicarboxylic acid is a bioactive and highly selective inhibitor of D-dopachrome tautomerase.
Structure 31 355 ? (2023)
PMID: 36805127 DOI: 10.1016/j.str.2023.01.008

Abstact

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.

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Primary Citation of related structures