5J7P

Macrophage Migration Inhibitory Factor bound to Covalent Inhibitor RDR03785

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
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history. 


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

  • 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.

    • Organizational Affiliation: 

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


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Macrophage migration inhibitory factor
A, B, C
114Homo sapiensMutation(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)
Explore P14174 
Go to UniProtKB:  P14174
PHAROS:  P14174
GTEx:  ENSG00000240972 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14174
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6H1
Query on 6H1
Download Ideal Coordinates CCD File 
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
Query on SO4
Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
L [auth B]
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
Query on GOL
Download Ideal Coordinates CCD File 
N [auth B],
O [auth B],
R [auth C]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
IPA
Query on IPA
Download Ideal Coordinates CCD File 
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 = 95.629α = 90
b = 95.629β = 90
c = 103.497γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.4: 2024-11-13
    Changes: Structure summary