5J7Q

Macrophage Migration Inhibitory Factor bound to Inhibitor K664 Derivative

PDB DOI: https://doi.org/10.2210/pdb5J7Q/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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.233
R-Value Work: 0.195
R-Value Observed: 0.199

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 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

PubMed: 27156768 Search on PubMed
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.

Macromolecule Content

Total Structure Weight: 38.21 kDa
Atom Count: 2,836
Modelled Residue Count: 342
Deposited Residue Count: 342
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

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
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
6H2 Query on 6H2 Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	4-(imidazo[1,2-a]pyridin-2-yl)benzene-1,2-diol C₁₃ H₁₀ N₂ O₂ JFYGSKNPLRBMMG-UHFFFAOYSA-N		Interactions Focus chain D [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain K [auth C] SDF format, chain L [auth C] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain K [auth C] MOL2 format, chain L [auth C] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain K [auth C] mmCIF format, chain L [auth C]	E [auth A] F [auth A] G [auth B] H [auth B] J [auth C] E [auth A], F [auth A], G [auth B], H [auth B], J [auth C], K [auth C], L [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain N [auth C] MOL2 format, chain I [auth B] MOL2 format, chain N [auth C] mmCIF format, chain I [auth B] mmCIF format, chain N [auth C]	I [auth B], N [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain N [auth C]
IPA Query on IPA Download Ideal Coordinates CCD File SDF format, chain M [auth C] MOL2 format, chain M [auth C] mmCIF format, chain M [auth C]	M [auth C]	ISOPROPYL ALCOHOL C₃ H₈ O KFZMGEQAYNKOFK-UHFFFAOYSA-N		Interactions Focus chain M [auth C]

Binding Affinity Annotations
ID	Source	Binding Affinity
6H2	BindingDB: 5J7Q	Ki: 2.66e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.233
R-Value Work: 0.195
R-Value Observed: 0.199
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.699	α = 90
b = 67.732	β = 90
c = 88.152	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-05-04

Deposition Author(s):

Robertson, M.J.

Jorgensen, W.L.

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