4OYQ | pdb_00004oyq

(6-isothiocyanatohexyl)benzene inhibitor complexed with Macrophage Migration Inhibitory Factor

• PDB DOI: https://doi.org/10.2210/pdb4OYQ/pdb

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


• Deposited: 2014-02-12 Released: 2014-03-05 
• Deposition Author(s): Spencer, E.S., Dale, E.J., Gommans, A.L., Vo, C.T., Rutledge, M.T., Nakatani, Y., Gamble, A.B., Smith, R.A.J., Wilbanks, S.M., Hampton, M.B., Tyndall, J.D.A.
• Funding Organization(s): University of Otago

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.195 (Depositor), 0.195 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.174 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: experimental

Literature

(6-isothiocyanatohexyl)benzene inhibitor complexed with Macrophage Migration Inhibitory Factor

Spencer, E.S., Dale, E.J., Gommans, A.L., Vo, C.T., Rutledge, M.T., Nakatani, Y., Gamble, A.B., Smith, R.A.J., Wilbanks, S.M., Hampton, M.B., Tyndall, J.D.A.

To be published.

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: 38.29 kDa 
• Atom Count: 2,907 
• Modeled 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 (UniProt)
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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1X2	D [auth A], G [auth B], K [auth C]	6-isothiocyanatohexylbenzene C13 H17 N S VJNWEQGIPZMBMA-UHFFFAOYSA-N
SO4	E [auth A], H [auth B], I [auth B], L [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	F [auth A], J [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
1X2	BindingDB:  4OYQ	IC50: 4200 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.195 (Depositor), 0.195 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.174 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.69	α = 90
b = 67.69	β = 90
c = 88.77	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
PDB_EXTRACT	data extraction
PHENIX	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2014-03-05 
Deposition Author(s): Spencer, E.S., Dale, E.J., Gommans, A.L., Vo, C.T., Rutledge, M.T., Nakatani, Y., Gamble, A.B., Smith, R.A.J., Wilbanks, S.M., Hampton, M.B., Tyndall, J.D.A.

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Funding Organization	Location	Grant Number
University of Otago	New Zealand	--

Revision History  

• Version 1.0: 2014-03-05
  Type: Initial release
  
• Version 1.1: 2014-03-12
  Changes: Data collection, Other
• Version 1.2: 2014-08-06
  Changes: Database references, Structure summary
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy
• Version 2.0: 2024-12-25
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary