3U18

Chicago Sky Blue 6B, A Novel Inhibitor for Macrophage Migration Inhibitory Factor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.143 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

A Novel Allosteric Inhibitor of Macrophage Migration Inhibitory Factor (MIF).

Bai, F.Asojo, O.A.Cirillo, P.Ciustea, M.Ledizet, M.Aristoff, P.A.Leng, L.Koski, R.A.Powell, T.J.Bucala, R.Anthony, K.G.

(2012) J Biol Chem 287: 30653-30663

  • DOI: https://doi.org/10.1074/jbc.M112.385583
  • Primary Citation of Related Structures:  
    3U18

  • PubMed Abstract: 

    Macrophage migration inhibitory factor (MIF) is a catalytic cytokine and an upstream mediator of the inflammatory pathway. MIF has broad regulatory properties, dysregulation of which has been implicated in the pathology of multiple immunological diseases. Inhibition of MIF activity with small molecules has proven beneficial in a number of disease models. Known small molecule MIF inhibitors typically bind in the tautomerase site of the MIF trimer, often covalently modifying the catalytic proline. Allosteric MIF inhibitors, particularly those that associate with the protein by noncovalent interactions, could reveal novel ways to block MIF activity for therapeutic benefit and serve as chemical probes to elucidate the structural basis for the diverse regulatory properties of MIF. In this study, we report the identification and functional characterization of a novel allosteric MIF inhibitor. Identified from a high throughput screening effort, this sulfonated azo compound termed p425 strongly inhibited the ability of MIF to tautomerize 4-hydroxyphenyl pyruvate. Furthermore, p425 blocked the interaction of MIF with its receptor, CD74, and interfered with the pro-inflammatory activities of the cytokine. Structural studies revealed a unique mode of binding for p425, with a single molecule of the inhibitor occupying the interface of two MIF trimers. The inhibitor binds MIF mainly on the protein surface through hydrophobic interactions that are stabilized by hydrogen bonding with four highly specific residues from three different monomers. The mode of p425 binding reveals a unique way to block the activity of the cytokine for potential therapeutic benefit in MIF-associated diseases.


  • Organizational Affiliation

    L2 Diagnostics, LLC, New Haven, CT 06511, USA.


Macromolecules
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: MIFGLIFMMIF
EC: 5.3.2.1 (PDB Primary Data), 5.3.3.12 (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
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Y0X
Query on Y0X

Download Ideal Coordinates CCD File 
D [auth A]6,6'-[(3,3'-dimethoxybiphenyl-4,4'-diyl)di(E)diazene-2,1-diyl]bis(4-amino-5-hydroxynaphthalene-1,3-disulfonic acid)
C34 H28 N6 O16 S4
OHMJKMNGYYWCHB-HVMBLDELSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
O [auth B],
W [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
K [auth A]
M [auth B]
Q [auth B]
F [auth A],
G [auth A],
K [auth A],
M [auth B],
Q [auth B],
S [auth B],
V [auth C],
X [auth C],
Y [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
H [auth A],
N [auth B],
R [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
IPA
Query on IPA

Download Ideal Coordinates CCD File 
E [auth A],
T [auth B],
U [auth C],
Z [auth C]
ISOPROPYL ALCOHOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
I [auth A],
J [auth A],
L [auth A],
P [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
Y0X PDBBind:  3U18 IC50: 810 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.143 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.857α = 90
b = 67.907β = 90
c = 86.572γ = 90
Software Package:
Software NamePurpose
CrysalisProdata collection
PHASERphasing
REFMACrefinement
CrysalisProdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2012-07-18 
  • Deposition Author(s): Asojo, O.A.

Revision History  (Full details and data files)

  • Version 1.0: 2012-07-18
    Type: Initial release
  • Version 1.1: 2012-10-17
    Changes: Database references
  • Version 1.2: 2017-11-08
    Changes: Refinement description
  • Version 1.3: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description