6CBG

Macrophage Migration Inhibitory Factor in Complex with a Pyrazole Inhibitor (5)

• PDB DOI: https://doi.org/10.2210/pdb6CBG/pdb

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


• Deposited: 2018-02-02 Released: 2018-04-04 
• Deposition Author(s): Robertson, M.J., Krimmer, S.G., Jorgensen, W.L.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.205 
• R-Value Work: 0.168 
• R-Value Observed: 0.172 

Starting Model: experimental

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

• PubMed: 29575754 
• DOI: https://doi.org/10.1002/cmdc.201800158
• Primary Citation of Related Structures:  
  6CB5, 6CBF, 6CBG, 6CBH


• 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 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 38.85 kDa 
• Atom Count: 2,909 
• Modelled Residue Count: 342 
• Deposited Residue Count: 342 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Macrophage migration inhibitory factor	A, B, C	114	Homo sapiens	Mutation(s): 0  Gene Names: MIF, GLIF, MMIF 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) Go to UniProtKB:  P14174
PHAROS:  P14174 GTEx:  ENSG00000240972

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EWG (Subject of Investigation/LOI)	L [auth B], Q [auth C]	3-(1H-pyrazol-4-yl)benzoic acid C10 H8 N2 O2 BXSUQWZHUHROLP-UHFFFAOYSA-N
SO4	D [auth A], J [auth B], K [auth B], N [auth C], O [auth C], P [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	E [auth A], F [auth A], G [auth A], H [auth A], I [auth B], M [auth B], R [auth C], S [auth C], T [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
EWG	BindingDB:  6CBG	Ki: 1.13e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.205 
• R-Value Work: 0.168 
• R-Value Observed: 0.172 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.331	α = 90
b = 68.258	β = 90
c = 86.753	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-04-04 
Deposition Author(s): Robertson, M.J., Krimmer, S.G., Jorgensen, W.L.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM32136
National Science Foundation (NSF, United States)	United States	DGE-1122492

Revision History  

• Version 1.0: 2018-04-04
  Type: Initial release
  
• Version 1.1: 2018-06-20
  Changes: Data collection, Database references
• Version 1.2: 2019-02-20
  Changes: Author supporting evidence, Data collection
• Version 1.3: 2019-11-27
  Changes: Author supporting evidence
• Version 1.4: 2023-10-04
  Changes: Data collection, Database references, Refinement description