8DBB | pdb_00008dbb

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 (Depositor), 0.156 (DCC) 
  • R-Value Work: 
    0.121 (Depositor), 0.121 (DCC) 
  • R-Value Observed: 
    0.123 (Depositor) 

Starting Model: experimental
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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 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.

Macromolecule Content 

  • Total Structure Weight: 38.87 kDa 
  • Atom Count: 3,192 
  • Modeled Residue Count: 351 
  • Deposited Residue Count: 354 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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 (Depositor), 0.156 (DCC) 
  • R-Value Work:  0.121 (Depositor), 0.121 (DCC) 
  • R-Value Observed: 0.123 (Depositor) 
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