2AZ5

Crystal Structure of TNF-alpha with a small molecule inhibitor

Summary for 2AZ5

• Entry DOI: 10.2210/pdb2az5/pdb
• Descriptor: Tumor necrosis factor (TNF-alpha) (Tumor necrosis factor ligand superfamily member 2) (TNF-a) (Cachectin) [Contains: Tumor necrosis factor, membrane form; Tumor necrosis factor, soluble form], 6,7-DIMETHYL-3-[(METHYL{2-[METHYL({1-[3-(TRIFLUOROMETHYL)PHENYL]-1H-INDOL-3-YL}METHYL)AMINO]ETHYL}AMINO)METHYL]-4H-CHROMEN-4-ONE (3 entities in total)
• Functional Keywords: tnf-alpha trimer disruption by binding of a small molecule inhibitor, cytokine
• Biological source: Homo sapiens (human)
• Cellular location: Cell membrane ; Single-pass type II membrane protein . Tumor necrosis factor, membrane form: Membrane; Single-pass type II membrane protein. Tumor necrosis factor, soluble form: Secreted. C-domain 1: Secreted. C-domain 2: Secreted: P01375
• Total number of polymer chains: 4
• Total formula weight: 66737.64

Authors

He, M.M. (deposition date: 2005-09-09, release date: 2005-11-29, Last modification date: 2024-10-09)

Primary citation

He, M.M.,Smith, A.S.,Oslob, J.D.,Flanagan, W.M.,Braisted, A.C.,Whitty, A.,Cancilla, M.T.,Wang, J.,Lugovskoy, A.A.,Yoburn, J.C.,Fung, A.D.,Farrington, G.,Eldredge, J.K.,Day, E.S.,Cruz, L.A.,Cachero, T.G.,Miller, S.K.,Friedman, J.E.,Choong, I.C.,Cunningham, B.C.
Small-molecule inhibition of TNF-alpha.
Science, 310:1022-1025, 2005

PubMed Abstract: We have identified a small-molecule inhibitor of tumor necrosis factor alpha (TNF-alpha) that promotes subunit disassembly of this trimeric cytokine family member. The compound inhibits TNF-alpha activity in biochemical and cell-based assays with median inhibitory concentrations of 22 and 4.6 micromolar, respectively. Formation of an intermediate complex between the compound and the intact trimer results in a 600-fold accelerated subunit dissociation rate that leads to trimer dissociation. A structure solved by x-ray crystallography reveals that a single compound molecule displaces a subunit of the trimer to form a complex with a dimer of TNF-alpha subunits.

PubMed: 16284179
DOI: 10.1126/science.1116304

Experimental method

X-RAY DIFFRACTION (2.1 Å)