1FT4

PHOTOCHEMICALLY-ENHANCED BINDING OF SMALL MOLECULES TO THE TUMOR NECROSIS FACTOR RECEPTOR-1

PDB DOI: 10.2210/pdb1FT4/pdb

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

Deposited: 2000-09-11 Released: 2001-10-12
Deposition Author(s): Muckelbauer, J.K., Chang, C.-H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Work: 0.274

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Photochemically enhanced binding of small molecules to the tumor necrosis factor receptor-1 inhibits the binding of TNF-alpha.

Carter, P.H., Scherle, P.A., Muckelbauer, J.K., Voss, M.E., Liu, R.Q., Thompson, L.A., Tebben, A.J., Solomon, K.A., Lo, Y.C., Li, Z., Strzemienski, P., Yang, G., Falahatpisheh, N., Xu, M., Wu, Z., Farrow, N.A., Ramnarayan, K., Wang, J., Rideout, D., Yalamoori, V., Domaille, P., Underwood, D.J., Trzaskos, J.M., Friedman, S.M., Newton, R.C., Decicco, C.P., Muckelbauer, J.A.

(2001) Proc Natl Acad Sci U S A 98: 11879-11884

PubMed: 11592999 Search on PubMedSearch on PubMed Central
DOI: 10.1073/pnas.211178398
Primary Citation of Related Structures:
1FT4

PubMed Abstract:

The binding of tumor necrosis factor alpha (TNF-alpha) to the type-1 TNF receptor (TNFRc1) plays an important role in inflammation. Despite the clinical success of biologics (antibodies, soluble receptors) for treating TNF-based autoimmune conditions, no potent small molecule antagonists have been developed. Our screening of chemical libraries revealed that N-alkyl 5-arylidene-2-thioxo-1,3-thiazolidin-4-ones were antagonists of this protein-protein interaction. After chemical optimization, we discovered IW927, which potently disrupted the binding of TNF-alpha to TNFRc1 (IC(50) = 50 nM) and also blocked TNF-stimulated phosphorylation of Ikappa-B in Ramos cells (IC(50) = 600 nM). This compound did not bind detectably to the related cytokine receptors TNFRc2 or CD40, and did not display any cytotoxicity at concentrations as high as 100 microM. Detailed evaluation of this and related molecules revealed that compounds in this class are "photochemically enhanced" inhibitors, in that they bind reversibly to the TNFRc1 with weak affinity (ca. 40-100 microM) and then covalently modify the receptor via a photochemical reaction. We obtained a crystal structure of IV703 (a close analog of IW927) bound to the TNFRc1. This structure clearly revealed that one of the aromatic rings of the inhibitor was covalently linked to the receptor through the main-chain nitrogen of Ala-62, a residue that has already been implicated in the binding of TNF-alpha to the TNFRc1. When combined with the fact that our inhibitors are reversible binders in light-excluded conditions, the results of the crystallography provide the basis for the rational design of nonphotoreactive inhibitors of the TNF-alpha-TNFRc1 interaction.

Related Citations:

Crystallographic Evidence for Dimerization of Unliganded Tumor Necrosis Factor Receptor
Naismith, J.H., Devine, T.Q., Brandhuber, B.J., Sprang, S.R.
(1995) J Biol Chem 270: 13303

Crystal Structure of the Soluble Human 55 Kd Tnf Receptor-Human Tnfb Complex: Implication for Tnf Receptor Activation
Banner, D.W., D'Arcy, A., Janes, W., Gentz, W., Schoenfeld, H.-J., Broger, C., Loetscher, H., Lesslauer, W.
(1993) Cell 73: 431

Organizational Affiliation:

DuPont Pharmaceuticals Company, Experimental Station, Wilmington, DE 19880-0500, USA. percy.h.carter@dupontpharma.com

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SOLUBLE TUMOR NECROSIS FACTOR RECEPTOR 1	A, B	162	Homo sapiens	Mutation(s): 0 Gene Names: TNFRSF1A, TNFAR, TNFR1
UniProt & NIH Common Fund Data Resources
Find proteins for P19438 (Homo sapiens) Explore P19438 Go to UniProtKB: P19438
PHAROS: P19438
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P19438
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
703 Query on 703 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	5-(3-MORPHOLIN-4-YL-PROPYL)-2-(3-NITRO-PHENYL)-4-THIOXO-4,5-DIHYDRO-1-THIA-3B,5-DIAZA-CYCLOPENTA[A]PENTALEN-6-ONE C₂₁ H₂₀ N₄ O₄ S₂ UXGUZFZBZPPZGL-UHFFFAOYSA-N		Ligand Interaction