Crystal structure of macrophage migration inhibitory factor (MIF) with phenylchromenone inhibitor at 1.94A resolution

Experimental Data Snapshot

  • Resolution: 1.94 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.197 

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Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


Fragment screening of inhibitors for MIF tautomerase reveals a cryptic surface binding site.

McLean, L.R.Zhang, Y.Li, H.Choi, Y.M.Han, Z.Vaz, R.J.Li, Y.

(2010) Bioorg Med Chem Lett 20: 1821-1824

  • DOI: https://doi.org/10.1016/j.bmcl.2010.02.009
  • Primary Citation of Related Structures:  
    3L5P, 3L5R, 3L5S, 3L5T, 3L5U, 3L5V

  • PubMed Abstract: 

    In the course of a fragment screening campaign by in silico docking followed by X-ray crystallography, a novel binding site for migration inhibitory factor (MIF) inhibitors was demonstrated. The site is formed by rotation of the side-chain of Tyr-36 to reveal a surface binding site in MIF that is hydrophobic and surrounded by aromatic side-chain residues. The crystal structures of two small inhibitors that bind to this site and of a quinolinone inhibitor, that spans the canonical deep pocket near Pro-1 and the new surface binding site, have been solved. These results suggest new opportunities for structure-based design of MIF inhibitors.

  • Organizational Affiliation

    Discovery Research, Sanofi-aventis, Bridgewater, NJ 08807, USA. Larry.Mclean@sanofi-aventis.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Macrophage migration inhibitory factor
A, B, C
122Homo sapiensMutation(s): 0 
EC: (PDB Primary Data), (PDB Primary Data)
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 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 47X

Download Ideal Coordinates CCD File 
D [auth A]3-(3,4-dihydroxyphenyl)-7-hydroxy-4H-chromen-4-one
C15 H10 O5
Query on SO4

Download Ideal Coordinates CCD File 
E [auth B],
F [auth B],
G [auth B],
I [auth B],
K [auth C]
O4 S
Query on GOL

Download Ideal Coordinates CCD File 
H [auth B],
J [auth C]
C3 H8 O3
Binding Affinity Annotations 
IDSourceBinding Affinity
47X BindingDB:  3L5R Ki: min: 38, max: 1.50e+4 (nM) from 2 assay(s)
IC50: 38 (nM) from 1 assay(s)
PDBBind:  3L5R IC50: 38 (nM) from 1 assay(s)
Binding MOAD:  3L5R IC50: 38 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.94 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.197 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.602α = 90
b = 67.694β = 90
c = 89.269γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
CrystalCleardata collection

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-03-09
    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: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description