3L5R

Crystal structure of macrophage migration inhibitory factor (MIF) with phenylchromenone inhibitor at 1.94A resolution

• PDB DOI: https://doi.org/10.2210/pdb3L5R/pdb

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


• Deposited: 2009-12-22 Released: 2010-03-09 
• Deposition Author(s): McLean, L., Zhang, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 0.233 
• R-Value Work: 0.196 
• R-Value Observed: 0.197 

Starting Model: experimental

Literature

Fragment screening of inhibitors for MIF tautomerase reveals a cryptic surface binding site.

McLean, L.R., Zhang, Y., Li, H., Choi, Y.M., Han, Z., Vaz, R.J., Li, Y.

(2010) Bioorg Med Chem Lett 20: 1821-1824

• PubMed: 20185308 
• DOI: https://doi.org/10.1016/j.bmcl.2010.02.009
• Primary Citation of Related Structures:  
  3L5P, 3L5R, 3L5S, 3L5T, 3L5U, 3L5V


• PubMed Abstract: 
  

  In the course of a fragment screening campaign by in silico docking followed by X-ray crystallography, a novel binding site for migration inhibitory factor (MIF) inhibitors was demonstrated. The site is formed by rotation of the side-chain of Tyr-36 to reveal a surface binding site in MIF that is hydrophobic and surrounded by aromatic side-chain residues. The crystal structures of two small inhibitors that bind to this site and of a quinolinone inhibitor, that spans the canonical deep pocket near Pro-1 and the new surface binding site, have been solved. These results suggest new opportunities for structure-based design of MIF inhibitors.

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Organizational Affiliation: 

Discovery Research, Sanofi-aventis, Bridgewater, NJ 08807, USA. [e-mail]

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)

Macromolecule Content

• Total Structure Weight: 41.21 kDa 
• Atom Count: 2,963 
• Modelled Residue Count: 350 
• Deposited Residue Count: 366 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Macrophage migration inhibitory factor	A, B, C	122	Homo sapiens	Mutation(s): 0  Gene Names: GLIF, MIF, 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
47X	D [auth A]	3-(3,4-dihydroxyphenyl)-7-hydroxy-4H-chromen-4-one C15 H10 O5 DDKGKOOLFLYZDL-UHFFFAOYSA-N
SO4	E [auth B], F [auth B], G [auth B], I [auth B], K [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	H [auth B], J [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
47X	BindingDB:  3L5R	Ki: min: 38, max: 1.50e+4 (nM) from 2 assay(s)
		IC50: 38 (nM) from 1 assay(s)
	PDBBind:  3L5R	IC50: 38 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 0.233 
• R-Value Work: 0.196 
• R-Value Observed: 0.197 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.602	α = 90
b = 67.694	β = 90
c = 89.269	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
CNS	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
CNX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-09 
Deposition Author(s): McLean, L., Zhang, Y.

Revision History  

• Version 1.0: 2010-03-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description