MIF Bound to a Fluorinated OXIM Derivative

Experimental Data Snapshot

  • Resolution: 1.75 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.5 of the entry. See complete history


Alternative chemical modifications reverse the binding orientation of a pharmacophore scaffold in the active site of macrophage migration inhibitory factor.

Crichlow, G.V.Cheng, K.F.Dabideen, D.Ochani, M.Aljabari, B.Pavlov, V.A.Miller, E.J.Lolis, E.Al-Abed, Y.

(2007) J Biol Chem 282: 23089-23095

  • DOI: https://doi.org/10.1074/jbc.M701825200
  • Primary Citation of Related Structures:  
    2OOH, 2OOW, 2OOZ

  • PubMed Abstract: 

    Pharmacophores are chemical scaffolds upon which changes in chemical moieties (R-groups) at specific sites are made to identify a combination of R-groups that increases the therapeutic potency of a small molecule inhibitor while minimizing adverse effects. We developed a pharmacophore based on a carbonyloxime (OXIM) scaffold for macrophage migration inhibitory factor (MIF), a protein involved in the pathology of sepsis, to validate that inhibition of a catalytic site could produce therapeutic benefits. We studied the crystal structures of MIF.OXIM-based inhibitors and found two opposite orientations for binding to the active site that were dependent on the chemical structures of an R-group. One orientation was completely unexpected based on previous studies with hydroxyphenylpyruvate and (S,R)-3-(4-hydroxyphenyl)-4,5-dihydro-5-isoxazole acetic acid methyl ester (ISO-1). We further confirmed that the unexpected binding mode targets MIF in cellular studies by showing that one compound, OXIM-11, abolished the counter-regulatory activity of MIF on anti-inflammatory glucocorticoid action. OXIM-11 treatment of mice, initiated 24 h after the onset of cecal ligation and puncture-induced sepsis, significantly improved survival when compared with vehicle-treated controls, confirming that inhibition of the MIF catalytic site could produce therapeutic effects. The crystal structures of the MIF inhibitor complexes provide insight for further structure-based drug design efforts.

  • Organizational Affiliation

    Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Macrophage migration inhibitory factor
A, B, C
114Homo sapiensMutation(s): 0 
Gene Names: MIF
UniProt & NIH Common Fund Data Resources
Find proteins for P14174 (Homo sapiens)
Explore P14174 
Go to UniProtKB:  P14174
PHAROS:  P14174
GTEx:  ENSG00000240972 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14174
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on OX4

Download Ideal Coordinates CCD File 
F [auth A],
N [auth C]
C14 H16 F N O3
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
J [auth B],
L [auth C],
M [auth C]
O4 S
Query on GOL

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
K [auth B]
O [auth C]
G [auth A],
H [auth A],
I [auth A],
K [auth B],
O [auth C],
P [auth C]
C3 H8 O3
Query on IPA

Download Ideal Coordinates CCD File 
Q [auth C],
R [auth C],
S [auth C]
C3 H8 O
Experimental Data & Validation

Experimental Data

  • Resolution: 1.75 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.198 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.61α = 90
b = 67.794β = 90
c = 87.248γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
CrystalCleardata 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: 2007-06-05
    Type: Initial release
  • Version 1.1: 2008-02-06
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2012-06-13
    Changes: Other
  • Version 1.4: 2017-10-18
    Changes: Refinement description
  • Version 1.5: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description