Biological Assembly 1  

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 37128.20 
• Atom Count: 2232 
• Residue Count: 324 
• Unique protein chains: 1

1FT4

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

• DOI: 10.2210/pdb1FT4/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.9 Å
• R-Value Work: 0.274 

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.USA 98: 11879-11884

• PubMed: 11592999 
• DOI: 10.1073/pnas.211178398


• 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.

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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




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Organizational Affiliation: 

DuPont Pharmaceuticals Company, Experimental Station, Wilmington, DE 19880-0500, USA. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
SOLUBLE TUMOR NECROSIS FACTOR RECEPTOR 1	A, B	162	Homo sapiens	Gene Names: TNFRSF1A (TNFAR, TNFR1)
Find proteins for P19438 (Homo sapiens) Go to Gene View: TNFRSF1A Go to UniProtKB:  P19438

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
703	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 6-[3-(4-MORPHOLINYL)PROPYL]-2-(3-NITROPHENYL)-5-THIOXO-5,6,-DIHYDRO-7H-THIENOL[2',3':4,5]PYRROLO[1,2-C] IMIDAZOL-7-ONE C21 H20 N4 O4 S2 UXGUZFZBZPPZGL-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
703	IC50: 270 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.9 Å
• R-Value Work: 0.274 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 67.800	α = 90.00
b = 67.800	β = 90.00
c = 190.000	γ = 90.00

Software Package:

Software Name	Purpose
EPMR	phasing
DENZO	data reduction
X-PLOR	refinement
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

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

Revision History 

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