3L5R

Crystal structure of macrophage migration inhibitory factor (MIF) with phenylchromenone inhibitor at 1.94A resolution

PDB DOI: https://doi.org/10.2210/pdb3L5R/pdb

Classification: ISOMERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-12-22 Released: 2010-03-09
Deposition Author(s): McLean, L., Zhang, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free: 0.233
R-Value Work: 0.196
R-Value Observed: 0.197

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

Fragment screening of inhibitors for MIF tautomerase reveals a cryptic surface binding site.

McLean, L.R., Zhang, Y., Li, H., Choi, Y.M., Han, Z., Vaz, R.J., Li, Y.

(2010) Bioorg Med Chem Lett 20: 1821-1824

PubMed: 20185308 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2010.02.009
Primary Citation of Related Structures:
3L5P, 3L5R, 3L5S, 3L5T, 3L5U, 3L5V

PubMed Abstract:
In the course of a fragment screening campaign by in silico docking followed by X-ray crystallography, a novel binding site for migration inhibitory factor (MIF) inhibitors was demonstrated. The site is formed by rotation of the side-chain of Tyr-36 to reveal a surface binding site in MIF that is hydrophobic and surrounded by aromatic side-chain residues. The crystal structures of two small inhibitors that bind to this site and of a quinolinone inhibitor, that spans the canonical deep pocket near Pro-1 and the new surface binding site, have been solved. These results suggest new opportunities for structure-based design of MIF inhibitors.

Organizational Affiliation

Discovery Research, Sanofi-aventis, Bridgewater, NJ 08807, USA. Larry.Mclean@sanofi-aventis.com

Macromolecule Content

Total Structure Weight: 41.21 kDa
Atom Count: 2,963
Modelled Residue Count: 350
Deposited Residue Count: 366
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Macrophage migration inhibitory factor	A, B, C	122	Homo sapiens	Mutation(s): 0 Gene Names: GLIF, MIF, 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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P14174
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
47X Query on 47X 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]	3-(3,4-dihydroxyphenyl)-7-hydroxy-4H-chromen-4-one C₁₅ H₁₀ O₅ DDKGKOOLFLYZDL-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain F [auth B] SDF format, chain G [auth B] SDF format, chain I [auth B] SDF format, chain K [auth C] MOL2 format, chain E [auth B] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] MOL2 format, chain I [auth B] MOL2 format, chain K [auth C] mmCIF format, chain E [auth B] mmCIF format, chain F [auth B] mmCIF format, chain G [auth B] mmCIF format, chain I [auth B] mmCIF format, chain K [auth C]	E [auth B], F [auth B], G [auth B], I [auth B], K [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain I [auth B] Focus chain K [auth C] Interactions & Density Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain I [auth B] Focus chain K [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain J [auth C] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C]	H [auth B], J [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Focus chain J [auth C] Interactions & Density Focus chain H [auth B] Focus chain J [auth C]

Binding Affinity Annotations
ID	Source	Binding Affinity
47X	BindingDB: 3L5R	Ki: min: 38, max: 1.50e+4 (nM) from 2 assay(s)
	BindingDB: 3L5R	IC50: 38 (nM) from 1 assay(s)
	PDBBind: 3L5R	IC50: 38 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free: 0.233
R-Value Work: 0.196
R-Value Observed: 0.197
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.602	α = 90
b = 67.694	β = 90
c = 89.269	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
CNS	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
CNX	refinement

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-03-09

Deposition Author(s):

McLean, L.

Zhang, Y.

Revision History (Full details and data files)

Version 1.0: 2010-03-09
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description