6CBH

Macrophage Migration Inhibitory Factor in Complex with a Pyrazole Inhibitor (8m)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Optimization of Pyrazoles as Phenol Surrogates to Yield Potent Inhibitors of Macrophage Migration Inhibitory Factor.

Trivedi-Parmar, V.Robertson, M.J.Cisneros, J.A.Krimmer, S.G.Jorgensen, W.L.

(2018) ChemMedChem 13: 1092-1097

  • DOI: 10.1002/cmdc.201800158
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Macrophage migration inhibitory factor (MIF) is a proinflammatory cytokine that is implicated in the regulation of inflammation, cell proliferation, and neurological disorders. MIF is also an enzyme that functions as a keto-enol tautomerase. Most pot ...

    Macrophage migration inhibitory factor (MIF) is a proinflammatory cytokine that is implicated in the regulation of inflammation, cell proliferation, and neurological disorders. MIF is also an enzyme that functions as a keto-enol tautomerase. Most potent MIF tautomerase inhibitors incorporate a phenol, which hydrogen bonds to Asn97 in the active site. Starting from a 113-μm docking hit, we report results of structure-based and computer-aided design that have provided substituted pyrazoles as phenol alternatives with potencies of 60-70 nm. Crystal structures of complexes of MIF with the pyrazoles highlight the contributions of hydrogen bonding with Lys32 and Asn97, and aryl-aryl interactions with Tyr36, Tyr95, and Phe113 to the binding.


    Organizational Affiliation

    Department of Chemistry, Yale University, New Haven, CT, 06520-8107, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Macrophage migration inhibitory factor
A, B, C
114Homo sapiensMutation(s): 0 
Gene Names: MIF (GLIF, MMIF)
EC: 5.3.2.1
Find proteins for P14174 (Homo sapiens)
Go to Gene View: MIF
Go to UniProtKB:  P14174
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
IPA
Query on IPA

Download SDF File 
Download CCD File 
A, C
ISOPROPYL ALCOHOL
2-PROPANOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
 Ligand Interaction
EWJ
Query on EWJ

Download SDF File 
Download CCD File 
C
5-(3-fluoro-1H-pyrazol-4-yl)-2-[(naphthalen-2-yl)oxy]benzoic acid
C20 H13 F N2 O3
DLVKEINOBWQQLX-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.173 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 68.149α = 90.00
b = 68.460β = 90.00
c = 88.699γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM32136
National Science Foundation (United States)United StatesDGE-1122492

Revision History 

  • Version 1.0: 2018-04-04
    Type: Initial release
  • Version 1.1: 2018-06-20
    Type: Data collection, Database references
  • Version 1.2: 2019-02-20
    Type: Author supporting evidence, Data collection