2AZ5 | pdb_00002az5

Crystal Structure of TNF-alpha with a small molecule inhibitor

• PDB DOI: https://doi.org/10.2210/pdb2AZ5/pdb

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


• Deposited: 2005-09-09 Released: 2005-11-29 
• Deposition Author(s): He, M.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.278 (Depositor), 0.278 (DCC) 
• R-Value Work: 
  0.220 (Depositor), 0.217 (DCC) 
• R-Value Observed: 
  0.227 (Depositor) 

Starting Model: experimental

Literature

Small-molecule inhibition of TNF-alpha.

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.

(2005) Science 310: 1022-1025

• PubMed: 16284179 
• DOI: https://doi.org/10.1126/science.1116304
• Primary Citation Related Structures: 
  2AZ5


• 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.

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Organizational Affiliation: 
• Sunesis Pharmaceuticals, Incorporated, 341 Oyster Point Boulevard, South San Francisco, CA 94080, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 66.74 kDa 
• Atom Count: 4,500 
• Modeled Residue Count: 542 
• Deposited Residue Count: 592 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
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]	A, B, C, D	148	Homo sapiens	Mutation(s): 0  Gene Names: TNF, TNFA, TNFSF2
UniProt & NIH Common Fund Data Resources
Find proteins for P01375 (Homo sapiens) Explore P01375  Go to UniProtKB:  P01375
PHAROS:  P01375 GTEx:  ENSG00000232810

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
307	E [auth A], F [auth C]	6,7-DIMETHYL-3-[(METHYL{2-[METHYL({1-[3-(TRIFLUOROMETHYL)PHENYL]-1H-INDOL-3-YL}METHYL)AMINO]ETHYL}AMINO)METHYL]-4H-CHROMEN-4-ONE C32 H32 F3 N3 O2 JZNXLPPJRFFECJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.278 (Depositor), 0.278 (DCC) 
• R-Value Work:  0.220 (Depositor), 0.217 (DCC) 
• R-Value Observed: 0.227 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 165.254	α = 90
b = 165.254	β = 90
c = 63.728	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-11-29 
Deposition Author(s): He, M.M.

Revision History  

• Version 1.0: 2005-11-29
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-02-07
  Changes: Experimental preparation
• Version 1.4: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.5: 2024-10-09
  Changes: Structure summary