3JSG

Crystal structure of macrophage migration inhibitory factor (mif) with hydroxyquinoline inhibitor 707 at 1.58a resolution

• PDB DOI: https://doi.org/10.2210/pdb3JSG/pdb

• Classification: ISOMERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-09-10 Released: 2009-11-10 
• Deposition Author(s): Mclean, L., Zhang, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 0.201 
• R-Value Work: 0.188 
• R-Value Observed: 0.188 

Starting Model: experimental

Literature

Discovery of covalent inhibitors for MIF tautomerase via cocrystal structures with phantom hits from virtual screening.

McLean, L.R., Zhang, Y., Li, H., Li, Z., Lukasczyk, U., Choi, Y.M., Han, Z., Prisco, J., Fordham, J., Tsay, J.T., Reiling, S., Vaz, R.J., Li, Y.

(2009) Bioorg Med Chem Lett 19: 6717-6720

• PubMed: 19836948 
• DOI: https://doi.org/10.1016/j.bmcl.2009.09.106
• Primary Citation of Related Structures:  
  3JSF, 3JSG, 3JTU


• PubMed Abstract: 
  

  Biochemical and X-ray crystallographic studies confirmed that hydroxyquinoline derivatives identified by virtual screening were actually covalent inhibitors of the MIF tautomerase. Adducts were formed by N-alkylation of the Pro-1 at the catalytic site with a loss of an amino group of the inhibitor.

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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 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 41.28 kDa 
• Atom Count: 3,003 
• Modelled Residue Count: 349 
• 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) Explore P14174  Go to UniProtKB:  P14174
PHAROS:  P14174 GTEx:  ENSG00000240972

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0IN	D [auth A], F [auth B], G [auth C]	7-(pyridin-3-ylmethyl)quinolin-8-ol C15 H12 N2 O DNRIDZXSDROVMC-UHFFFAOYSA-N
SO4	E [auth A], H [auth C], I [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 0.201 
• R-Value Work: 0.188 
• R-Value Observed: 0.188 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.493	α = 90
b = 67.616	β = 90
c = 88.886	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-11-10 
Deposition Author(s): Mclean, L., Zhang, Y.

Revision History  

• Version 1.0: 2009-11-10
  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