4P7M

Crystal structure of Plasmodium falciparum MIF in complex with 3-[(2-methyl-6-phenylpyridin-4-yl)oxy]phenol

• PDB DOI: https://doi.org/10.2210/pdb4P7M/pdb

• Classification: CYTOKINE/INHIBITOR
• Organism(s): Plasmodium falciparum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-03-27 Released: 2014-10-15 
• Deposition Author(s): Pantouris, G., Lolis, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.02 Å
• R-Value Free: 0.324 
• R-Value Work: 0.247 
• R-Value Observed: 0.251 

Literature

Crystallographic and Receptor Binding Characterization of Plasmodium falciparum Macrophage Migration Inhibitory Factor Complexed to Two Potent Inhibitors.

Pantouris, G., Rajasekaran, D., Garcia, A.B., Ruiz, V.G., Leng, L., Jorgensen, W.L., Bucala, R., Lolis, E.J.

(2014) J Med Chem 57: 8652-8656

• PubMed: 25268646 
• DOI: https://doi.org/10.1021/jm501168q
• Primary Citation of Related Structures:  
  4P7M, 4P7S


• PubMed Abstract: 
  

  We report the crystal structures of two inhibitors of Plasmodium falciparum macrophage migration inhibitory factor (PfMIF) with nanomolar Ki's, analyze their interactions with the active site of PfMIF, and provide explanations regarding their selectivity of PfMIF versus human MIF. These inhibitors were also found to selectively inhibit interactions between PfMIF and the human MIF receptor CD74. The results of this study provide the framework for the development of new therapeutics that target PfMIF.

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Organizational Affiliation: 

Departments of Pharmacology, ‡Internal Medicine, §Chemistry, and the ∥Yale Cancer Center, Yale University , New Haven, Connecticut 06520-8066, United States.

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 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 38.28 kDa 
• Atom Count: 2,132 
• Modelled Residue Count: 297 
• Deposited Residue Count: 342 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Macrophage migration inhibitory factor-like protein	A, B, C	114	Plasmodium falciparum	Mutation(s): 0
UniProt
Find proteins for Q6Q3H7 (Plasmodium falciparum) Explore Q6Q3H7  Go to UniProtKB:  Q6Q3H7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2OE	D [auth A]	3-[(2-methyl-6-phenylpyridin-4-yl)oxy]phenol C18 H15 N O2 SJHYRSDSTDNDIP-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
2OE	BindingDB:  4P7M	Ki: 39 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.02 Å
• R-Value Free: 0.324 
• R-Value Work: 0.247 
• R-Value Observed: 0.251 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.036	α = 90
b = 79.75	β = 90
c = 97.082	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
PHASER	phasing
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-10-15 
Deposition Author(s): Pantouris, G., Lolis, E.

Revision History  

• Version 1.0: 2014-10-15
  Type: Initial release
  
• Version 1.1: 2014-11-05
  Changes: Database references
• Version 1.2: 2015-10-14
  Changes: Data collection
• Version 1.3: 2017-11-22
  Changes: Derived calculations, Refinement description
• Version 1.4: 2023-12-27
  Changes: Data collection, Database references, Refinement description