1FT4

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


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

  • 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 ...

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SOLUBLE TUMOR NECROSIS FACTOR RECEPTOR 1 AB162Homo sapiensMutation(s): 0 
Gene Names: TNFRSF1ATNFARTNFR1
Find proteins for P19438 (Homo sapiens)
Explore P19438 
Go to UniProtKB:  P19438
NIH Common Fund Data Resources
PHAROS:  P19438
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
703
Query on 703

Download Ideal Coordinates CCD File 
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
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
703IC50 :  270   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Work: 0.274 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.8α = 90
b = 67.8β = 90
c = 190γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
X-PLORrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-10-12
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description