Ternary Complex of Macrophage Migration Inhibitory Factor (MIF) Bound Both to 4-hydroxyphenylpyruvate and to the Allosteric Inhibitor AV1013 (R-stereoisomer)

Experimental Data Snapshot

  • Resolution: 1.25 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.163 

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Allosteric inhibition of macrophage migration inhibitory factor revealed by ibudilast.

Cho, Y.Crichlow, G.V.Vermeire, J.J.Leng, L.Du, X.Hodsdon, M.E.Bucala, R.Cappello, M.Gross, M.Gaeta, F.Johnson, K.Lolis, E.J.

(2010) Proc Natl Acad Sci U S A 107: 11313-11318

  • DOI: https://doi.org/10.1073/pnas.1002716107
  • Primary Citation of Related Structures:  
    3IJG, 3IJJ

  • PubMed Abstract: 

    AV411 (ibudilast; 3-isobutyryl-2-isopropylpyrazolo-[1,5-a]pyridine) is an antiinflammatory drug that was initially developed for the treatment of bronchial asthma but which also has been used for cerebrovascular and ocular indications. It is a nonselective inhibitor of various phosphodiesterases (PDEs) and has varied antiinflammatory activity. More recently, AV411 has been studied as a possible therapeutic for the treatment of neuropathic pain and opioid withdrawal through its actions on glial cells. As described herein, the PDE inhibitor AV411 and its PDE-inhibition-compromised analog AV1013 inhibit the catalytic and chemotactic functions of the proinflammatory protein, macrophage migration inhibitory factor (MIF). Enzymatic analysis indicates that these compounds are noncompetitive inhibitors of the p-hydroxyphenylpyruvate (HPP) tautomerase activity of MIF and an allosteric binding site of AV411 and AV1013 is detected by NMR. The allosteric inhibition mechanism is further elucidated by X-ray crystallography based on the MIF/AV1013 binary and MIF/AV1013/HPP ternary complexes. In addition, our antibody experiments directed against MIF receptors indicate that CXCR2 is the major receptor for MIF-mediated chemotaxis of peripheral blood mononuclear cells.

  • Organizational Affiliation

    Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06510, 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 
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 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on AVR

Download Ideal Coordinates CCD File 
O [auth C](2R)-2-amino-1-[2-(1-methylethyl)pyrazolo[1,5-a]pyridin-3-yl]propan-1-one
C13 H17 N3 O
Query on ENO

Download Ideal Coordinates CCD File 
E [auth A],
J [auth B],
N [auth C]
C9 H8 O4
Query on EN1

Download Ideal Coordinates CCD File 
D [auth A],
I [auth B],
M [auth C]
(2E)-2-hydroxy-3-(4-hydroxyphenyl)prop-2-enoic acid
C9 H8 O4
Query on CL

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
K [auth B]
L [auth B]
F [auth A],
G [auth A],
H [auth A],
K [auth B],
L [auth B],
P [auth C],
Q [auth C],
R [auth C]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.25 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.163 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.236α = 90
b = 67.908β = 90
c = 87.329γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-06-16
    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