9BNQ | pdb_00009bnq

N-(4-(isothiocyanatomethyl)phenyl)methanesulfonamide complexed with Macrophage Migration Inhibitory Factor

PDB DOI: https://doi.org/10.2210/pdb9BNQ/pdb

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

Deposited: 2024-05-02 Released: 2024-07-24
Deposition Author(s): Fellner, M., Rutledge, M.T., Putha, L., Kok, L.K., Gamble, A.B., Wilbanks, S.M., Vernall, A.J., Tyndall, J.D.A.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.09 Å
R-Value Free:
0.154 (Depositor), 0.158 (DCC)
R-Value Work:
0.137 (Depositor), 0.143 (DCC)
R-Value Observed:
0.138 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Covalent Isothiocyanate Inhibitors of Macrophage Migration Inhibitory Factor as Potential Colorectal Cancer Treatments.

Putha, L., Kok, L.K., Fellner, M., Rutledge, M.T., Gamble, A.B., Wilbanks, S.M., Vernall, A.J., Tyndall, J.D.A.

(2024) ChemMedChem 19: e202400394-e202400394

PubMed: 38977403 Search on PubMed
DOI: https://doi.org/10.1002/cmdc.202400394
Primary Citation Related Structures:
9BNQ, 9BNR

PubMed Abstract:
Macrophage migration inhibitory factor (MIF) is a proinflammatory cytokine with roles in innate and adaptive human immune responses, as well as inflammation. MIF exerts its biological activity by binding to the cell surface receptor CD74 as well as intracellular signalling proteins. MIF also possesses keto-enol tautomerase activity. Inhibition of the tautomerase activity has been associated with loss of biological activity of MIF and a potential anticancer target. Isothiocyanates (ITCs) are a class of compounds present in cruciferous vegetables that inhibit the MIF tautomerase activity via covalent modification of the N-terminal proline. A range of substituted ITCs featuring benzyl, phenethyl and phenyl propyl isothiocyanates were designed, synthesised and tested to determine any structure activity relationship for inhibiting MIF. Crystal structures of covalent compounds 8 and 9 in complex with rhMIF revealed key hydrogen bonding and edge-to-face π stacking interactions. Compound 9 and 11 with sub micromolar activity were tested in the NCI60 cancer cell lines panel. Both compounds showed tissue-specific reduced growth in colon and renal cancer cell lines, while one of these showed potent, dose-dependent inhibition of growth against all seven colon cancer cell lines (GI50 < 2.5 µM) and all eight renal cancer cell lines (GI50 < 2.2 µM).

Organizational Affiliation

University of Otago, School of Pharmacy, NEW ZEALAND.

Macromolecule Content

Total Structure Weight: 38.4 kDa
Atom Count: 3,188
Modeled Residue Count: 342
Deposited Residue Count: 342
Unique protein chains: 1

Macromolecules

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P14174
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1AQU (Subject of Investigation/LOI) Query on A1AQU Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain H [auth B] SDF format, chain K [auth C] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B] MOL2 format, chain K [auth C] mmCIF format, chain D [auth A] mmCIF format, chain H [auth B] mmCIF format, chain K [auth C]	D [auth A], H [auth B], K [auth C]	N-{[4-(methanesulfonamido)phenyl]methyl}methanethioamide C₉ H₁₂ N₂ O₂ S₂ UYZBHSQAOCSARR-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain H [auth B] Focus chain K [auth C] Interactions & Density Focus chain D [auth A] Focus chain H [auth B] Focus chain K [auth C]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain L [auth C] SDF format, chain M [auth C] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain L [auth C] MOL2 format, chain M [auth C] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain L [auth C] mmCIF format, chain M [auth C]	E [auth A], F [auth A], I [auth B], L [auth C], M [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain M [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain M [auth C]
IPA Query on IPA Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain J [auth C] MOL2 format, chain G [auth B] MOL2 format, chain J [auth C] mmCIF format, chain G [auth B] mmCIF format, chain J [auth C]	G [auth B], J [auth C]	ISOPROPYL ALCOHOL C₃ H₈ O KFZMGEQAYNKOFK-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Focus chain J [auth C] Interactions & Density Focus chain G [auth B] Focus chain J [auth C]