D-Dopachrome tautomerase (D-DT)/ macrophage migration inhibitory factor 2 (MIF2) complexed with inhibitor 4-IPP

Experimental Data Snapshot

  • Resolution: 2.78 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.222 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.4 of the entry. See complete history


Targeting distinct tautomerase sites of D-DT and MIF with a single molecule for inhibition of neutrophil lung recruitment.

Rajasekaran, D.Zierow, S.Syed, M.Bucala, R.Bhandari, V.Lolis, E.J.

(2014) FASEB J 28: 4961-4971

  • DOI: https://doi.org/10.1096/fj.14-256636
  • Primary Citation of Related Structures:  
    3KAN, 3KER, 4Q3F

  • PubMed Abstract: 

    We report a new inflammatory activity for extracellular d-dopachrome tautomerase (D-DT), the recruitment of neutrophils to the lung on D-DT intratracheal installation of C57BL/6J mice with an EC50 of 5.6 μg. We also find that D-DT and macrophage migration inhibitory factor (MIF) have additive effects in neutrophil recruitment. Although the tautomerase site of D-DT and its homologue MIF are biophysically very different, 4-iodo-6-phenylpyrimidine (4-IPP) forms a covalent bond with Pro-1 of both proteins, resulting in a 6-phenylpyrimidine (6-PP) adduct. Recruitment of neutrophils to the lung for the 6-PP adducts of D-DT and MIF are reduced by ∼ 50% relative to the apo proteins, demonstrating that an unmodified Pro-1 is important for this activity, but there is no cooperativity in inhibition of the proteins together. The differences in the binding mode of the 6-PP adduct for D-DT was determined by crystallographic studies at 1.13 Å resolution and compared to the structure of the MIF-6-PP complex. There are major differences in the location of the 6-PP adduct to the D-DT and MIF active sites that provide insight into the lack of cooperativity by 4-IPP and into tuning the properties of the covalent inhibitors of D-DT and MIF that are necessary for the development of therapeutic small molecules against neutrophil damage from lung infections such as Pseudomonas aeruginosa in cystic fibrosis and immunocompromised patients.

  • Organizational Affiliation

    Department of Pharmacology.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
D-dopachrome decarboxylase
A, B, C, D
117Mus musculusMutation(s): 0 
Gene Names: Ddt
Find proteins for O35215 (Mus musculus)
Explore O35215 
Go to UniProtKB:  O35215
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO35215
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on RW1

Download Ideal Coordinates CCD File 
E [auth A],
J [auth B],
O [auth C],
T [auth D]
C10 H8 N2
Query on CL

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
I [auth A]
K [auth B]
L [auth B]
F [auth A],
G [auth A],
I [auth A],
K [auth B],
L [auth B],
N [auth B],
P [auth C],
Q [auth C],
S [auth C],
U [auth D],
V [auth D],
X [auth D]
Query on NA

Download Ideal Coordinates CCD File 
H [auth A],
M [auth B],
R [auth C],
W [auth D]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.78 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.222 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.172α = 90
b = 82.172β = 90
c = 144.253γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-10-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2020-10-21
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-09-06
    Changes: Data collection, Database references, Refinement description