5J7P

Macrophage Migration Inhibitory Factor bound to Covalent Inhibitor RDR03785

• PDB DOI: https://doi.org/10.2210/pdb5J7P/pdb

• Classification: Isomerase/Isomerase Inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-04-06 Released: 2016-05-04 
• Deposition Author(s): Robertson, M.J., Jorgensen, W.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.201 
• R-Value Work: 0.178 
• R-Value Observed: 0.180 

Starting Model: experimental

Literature

Irregularities in enzyme assays: The case of macrophage migration inhibitory factor.

Cisneros, J.A., Robertson, M.J., Valhondo, M., Jorgensen, W.L.

(2016) Bioorg Med Chem Lett 26: 2764-2767

• PubMed: 27156768 
• DOI: https://doi.org/10.1016/j.bmcl.2016.04.074
• Primary Citation of Related Structures:  
  5J7P, 5J7Q


• PubMed Abstract: 
  

  Inhibitors of human macrophage migration inhibitory factor (MIF) previously reported in the literature have been reexamined by synthesis, assaying for tautomerase activity, and protein crystallography. Substantial inconsistencies between prior and current assay results are noted. They appear to arise from difficulties with the tautomerase substrates, solubility issues, and especially covalent inhibition. Incubation time variation shows that 3, 4, 6, and 9 are covalent or slow-binding inhibitors. Two protein crystal structures are provided; one confirms that the twice-discovered 3 is a covalent inhibitor.

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Organizational Affiliation: 

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

Macromolecule Content

• Total Structure Weight: 39.02 kDa 
• Atom Count: 3,133 
• 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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6H1	D [auth A], K [auth B], P [auth C]	6-{[4-(trifluoromethyl)phenyl]methyl}-2H-1,3-benzodioxol-5-ol C15 H11 F3 O3 CZTARKWMYGFNTE-UHFFFAOYSA-N
SO4	E [auth A], F [auth A], G [auth A], H [auth A], L [auth B], M [auth B], Q [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	N [auth B], O [auth B], R [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
IPA	I [auth A], J [auth A]	ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.201 
• R-Value Work: 0.178 
• R-Value Observed: 0.180 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.629	α = 90
b = 95.629	β = 90
c = 103.497	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-05-04 
Deposition Author(s): Robertson, M.J., Jorgensen, W.L.

Revision History  

• Version 1.0: 2016-05-04
  Type: Initial release
  
• Version 1.1: 2016-05-25
  Changes: Database references
• Version 1.2: 2016-06-08
  Changes: Database references
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description