7E45

Crystal structure of compound 7 bound to MIF

PDB DOI: https://doi.org/10.2210/pdb7E45/pdb

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

Deposited: 2021-02-10 Released: 2023-02-15
Deposition Author(s): Fan, C.P., Yang, L.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.43 Å
R-Value Free: 0.186
R-Value Work: 0.161
R-Value Observed: 0.162

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Identification and Structure-Activity Relationships of Dietary Flavonoids as Human Macrophage Migration Inhibitory Factor (MIF) Inhibitors.

Yang, L., Guo, D., Fan, C.

(2021) J Agric Food Chem 69: 10138-10150

PubMed: 34459191 Search on PubMed
DOI: https://doi.org/10.1021/acs.jafc.1c03367
Primary Citation of Related Structures:
7E45, 7E47, 7E49, 7E4A, 7E4B, 7E4C

PubMed Abstract:
Dietary flavonoids are known to have anti-inflammatory and anticancer effects, but their influences on human macrophage migration inhibitory factor (MIF), a vital proinflammatory cytokine recognized as a therapeutic target for infectious diseases and cancers, have been rarely reported. Here, we identified 24 dietary flavonoids that could inhibit the tautomerase activity of MIF, five of which exerted IC ₅₀ values lower than the positive control ISO-1 in the micromolar range: morin (IC ₅₀ = 11.01 ± 0.45 μM) and amentoflavone (IC ₅₀ = 13.32 ± 0.64 μM) exhibited the most potent efficacy followed by apigenin (IC ₅₀ = 42.74 ± 4.20 μM), naringin (IC ₅₀ = 51.38 ± 2.12 μM), and fisetin (IC ₅₀ = 51.99 ± 0.63 μM). X-ray crystallography, molecular docking, and cellular experiments were utilized to illustrate the molecular binding details and structure-activity relationships. Scaffold modifications of flavonoids significantly influenced the potency. What stands out for morin is the unique 2'-OH substitution. In addition, amentoflavone situated at the MIF trimer pore may impact MIF-CD74 signaling. The results also showed that flavonoids could suppress cell chemotaxis and nitric oxide production in RAW264.7 cells. Our results elucidate the molecular mechanism of flavonoids acting on MIF and shed light on developing lead compounds against MIF-involved diseases.

Organizational Affiliation

School of Basic Medical Sciences, Wuhan University, Wuhan 430072, P. R. China.

Macromolecule Content

Total Structure Weight: 38.14 kDa
Atom Count: 3,060
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) 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HWO Query on HWO Download Ideal Coordinates CCD File SDF format, chain N [auth B] MOL2 format, chain N [auth B] mmCIF format, chain N [auth B]	N [auth B]	(2R)-7-[(2R,3R,4R,5S,6S)-6-(hydroxymethyl)-3-[(2R,3R,4R,5R,6S)-6-methyl-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-4,5-bis(oxidanyl)oxan-2-yl]oxy-2-(4-methoxy-3-oxidanyl-phenyl)-5-oxidanyl-2,3-dihydrochromen-4-one C₂₈ H₃₄ O₁₅ ARGKVCXINMKCAZ-LIVPLLNOSA-N		Interactions Focus chain N [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain Q [auth C] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth B] D [auth A], E [auth A], F [auth A], G [auth A], H [auth B], I [auth B], J [auth B], K [auth B], L [auth B], M [auth B], O [auth C], P [auth C], Q [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C]