Asymmetric hTNF-alpha

Experimental Data Snapshot

  • Resolution: 2.80 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.192 

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Small molecules that inhibit TNF signalling by stabilising an asymmetric form of the trimer.

O'Connell, J.Porter, J.Kroeplien, B.Norman, T.Rapecki, S.Davis, R.McMillan, D.Arakaki, T.Burgin, A.Fox Iii, D.Ceska, T.Lecomte, F.Maloney, A.Vugler, A.Carrington, B.Cossins, B.P.Bourne, T.Lawson, A.

(2019) Nat Commun 10: 5795-5795

  • DOI: https://doi.org/10.1038/s41467-019-13616-1
  • Primary Citation of Related Structures:  
    6OOY, 6OOZ, 6OP0

  • PubMed Abstract: 

    Tumour necrosis factor (TNF) is a cytokine belonging to a family of trimeric proteins; it has been shown to be a key mediator in autoimmune diseases such as rheumatoid arthritis and Crohn's disease. While TNF is the target of several successful biologic drugs, attempts to design small molecule therapies directed to this cytokine have not led to approved products. Here we report the discovery of potent small molecule inhibitors of TNF that stabilise an asymmetrical form of the soluble TNF trimer, compromising signalling and inhibiting the functions of TNF in vitro and in vivo. This discovery paves the way for a class of small molecule drugs capable of modulating TNF function by stabilising a naturally sampled, receptor-incompetent conformation of TNF. Furthermore, this approach may prove to be a more general mechanism for inhibiting protein-protein interactions.

  • Organizational Affiliation

    UCB Pharma, Slough, SL1 3WE, UK. james.oconnell@ucb.com.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tumor necrosis factor
A, B, C
157Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P01375 (Homo sapiens)
Explore P01375 
Go to UniProtKB:  P01375
PHAROS:  P01375
GTEx:  ENSG00000232810 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01375
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A6Y (Subject of Investigation/LOI)
Query on A6Y

Download Ideal Coordinates CCD File 
E [auth C](S)-{1-[(2,5-dimethylphenyl)methyl]-1H-benzimidazol-2-yl}(pyridin-4-yl)methanol
C22 H21 N3 O
Query on CL

Download Ideal Coordinates CCD File 
Experimental Data & Validation

Experimental Data

  • Resolution: 2.80 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.192 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.52α = 90
b = 81.17β = 90
c = 93.35γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-25
    Type: Initial release
  • Version 1.1: 2020-01-01
    Changes: Database references
  • Version 1.2: 2024-04-03
    Changes: Data collection, Database references, Refinement description