4WR8

Macrophage Migration Inhibitory Factor in complex with a biaryltriazole inhibitor (3b-180)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.225 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Design, synthesis, and protein crystallography of biaryltriazoles as potent tautomerase inhibitors of macrophage migration inhibitory factor.

Dziedzic, P.Cisneros, J.A.Robertson, M.J.Hare, A.A.Danford, N.E.Baxter, R.H.Jorgensen, W.L.

(2015) J Am Chem Soc 137: 2996-3003

  • DOI: https://doi.org/10.1021/ja512112j
  • Primary Citation of Related Structures:  
    4WR8, 4WRB

  • PubMed Abstract: 

    Optimization is reported for biaryltriazoles as inhibitors of the tautomerase activity of human macrophage migration inhibitory factor (MIF), a proinflammatory cytokine associated with numerous inflammatory diseases and cancer. A combined approach was taken featuring organic synthesis, enzymatic assaying, crystallography, and modeling including free-energy perturbation (FEP) calculations. X-ray crystal structures for 3a and 3b bound to MIF are reported and provided a basis for the modeling efforts. The accommodation of the inhibitors in the binding site is striking with multiple hydrogen bonds and aryl-aryl interactions. Additional modeling encouraged pursuit of 5-phenoxyquinolinyl analogues, which led to the very potent compound 3s. Activity was further enhanced by addition of a fluorine atom adjacent to the phenolic hydroxyl group as in 3w, 3z, 3aa, and 3bb to strengthen a key hydrogen bond. It is also shown that physical properties of the compounds can be modulated by variation of solvent-exposed substituents. Several of the compounds are likely the most potent known MIF tautomerase inhibitors; the most active ones are more than 1000-fold more active than the well-studied (R)-ISO-1 and more than 200-fold more active than the chromen-4-one Orita-13.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Macrophage migration inhibitory factor
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R
114Homo sapiensMutation(s): 0 
Gene Names: MIFGLIFMMIF
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
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3TX
Query on 3TX

Download Ideal Coordinates CCD File 
EB [auth L]
IA [auth F]
OB [auth O]
TA [auth I]
Y [auth C]
EB [auth L],
IA [auth F],
OB [auth O],
TA [auth I],
Y [auth C],
YB [auth R]
4-[4-(quinolin-2-yl)-1H-1,2,3-triazol-1-yl]phenol
C17 H12 N4 O
QSDNOMVFORBNKO-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth C]
AB [auth J]
AC [auth R]
BA [auth C]
BB [auth K]
AA [auth C],
AB [auth J],
AC [auth R],
BA [auth C],
BB [auth K],
BC [auth R],
CA [auth D],
CB [auth K],
DA [auth D],
DB [auth K],
EA [auth D],
FA [auth E],
FB [auth L],
GA [auth E],
GB [auth L],
HA [auth E],
HB [auth L],
JA [auth F],
JB [auth M],
KA [auth F],
KB [auth M],
LA [auth F],
LB [auth N],
MB [auth N],
NA [auth G],
NB [auth N],
OA [auth G],
PA [auth G],
PB [auth O],
QA [auth H],
QB [auth O],
RA [auth H],
RB [auth O],
S [auth A],
SA [auth H],
SB [auth P],
T [auth A],
TB [auth P],
U [auth A],
UA [auth I],
UB [auth P],
V [auth B],
VA [auth I],
VB [auth Q],
W [auth B],
WA [auth I],
WB [auth Q],
X [auth B],
XB [auth Q],
YA [auth J],
Z [auth C],
ZA [auth J],
ZB [auth R]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
NA
Query on NA

Download Ideal Coordinates CCD File 
IB [auth L],
MA [auth F],
XA [auth I]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
3TX BindingDB:  4WR8 Ki: min: 230, max: 590 (nM) from 3 assay(s)
Kd: 260 (nM) from 1 assay(s)
IC50: 640 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.225 
  • Space Group: P 4 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 138.644α = 90
b = 138.644β = 90
c = 266.586γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM32136

Revision History  (Full details and data files)

  • Version 1.0: 2015-03-11
    Type: Initial release
  • Version 1.1: 2015-03-18
    Changes: Structure summary
  • Version 1.2: 2017-09-27
    Changes: Author supporting evidence, Derived calculations, Other, Refinement description, Source and taxonomy
  • Version 1.3: 2019-12-25
    Changes: Author supporting evidence
  • Version 1.4: 2023-12-27
    Changes: Data collection, Database references