6PEG

MIF with a allosteric inhibitor

  • Classification: ISOMERASE
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2019-06-20 Released: 2019-11-27 
  • Deposition Author(s): Asojo, O.A.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.145 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Inhibition of Macrophage Migration Inhibitory Factor by a Chimera of Two Allosteric Binders.

Cirillo, P.F.Asojo, O.A.Khire, U.Lee, Y.Mootien, S.Hegan, P.Sutherland, A.G.Peterson-Roth, E.Ledizet, M.Koski, R.A.Anthony, K.G.

(2020) ACS Med Chem Lett 11: 1843-1847

  • DOI: https://doi.org/10.1021/acsmedchemlett.9b00351
  • Primary Citation of Related Structures:  
    6PEG

  • PubMed Abstract: 

    Human Macrophage Migration Inhibitory Factor (MIF) is a trimeric cytokine implicated in a number of inflammatory and autoimmune diseases and cancer. We previously reported that the dye p425 (Chicago Sky Blue), which bound MIF at the interface of two MIF trimers covering the tautomerase and allosteric pockets, revealed a unique strategy to block MIF's pro-inflammatory activities. Structural liabilities, including the large size, precluded p425 as a medicinal chemistry lead for drug development. We report here a rational design strategy linking only the fragment of p425 that binds over the tautomerase pocket to the core of ibudilast, a known MIF allosteric site-specific inhibitor. The chimeric compound, termed L2-4048, was shown by X-ray crystallography to bind at the allosteric and tautomerase sites as anticipated. L2-4048 retained target binding and blocked MIF's tautomerase CD74 receptor binding, and pro-inflammatory activities. Our studies lay the foundation for the design and synthesis of smaller and more drug-like compounds that retain the MIF inhibitory properties of this chimera.


  • Organizational Affiliation

    L2 Diagnostics, LLC, 300 George Street, New Haven, Connecticut 06511, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Macrophage migration inhibitory factorA [auth D],
B [auth E],
C [auth F]
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 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
4FQ (Subject of Investigation/LOI)
Query on 4FQ

Download Ideal Coordinates CCD File 
H [auth E]4-amino-5-hydroxy-6-[(E)-(3-{[3-(2-methylpropanoyl)pyrazolo[1,5-a]pyridin-2-yl]methyl}phenyl)diazenyl]naphthalene-1,3-disulfonic acid
C28 H25 N5 O8 S2
DDUSPQQMFMSMNK-NVQSTNCTSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
G [auth D],
I [auth E],
O [auth F]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
PO4
Query on PO4

Download Ideal Coordinates CCD File 
J [auth E],
K [auth E]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth D],
L [auth F]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
D,
F [auth D],
M [auth F],
N [auth F]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Binding Affinity Annotations 
IDSourceBinding Affinity
4FQ BindingDB:  6PEG Kd: 6860 (nM) from 1 assay(s)
IC50: min: 930, max: 7590 (nM) from 3 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.145 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.89α = 90
b = 67.89β = 90
c = 88.59γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2019-11-27 
  • Deposition Author(s): Asojo, O.A.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States2R44AR056908-02A1

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-27
    Type: Initial release
  • Version 1.1: 2020-11-04
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description