6OOY

Asymmetric hTNF-alpha


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.205 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

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.


Macromolecules
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 
Gene Names: TNFTNFATNFSF2
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
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A7M (Subject of Investigation/LOI)
Query on A7M

Download Ideal Coordinates CCD File 
E [auth C]{1-[(2,5-dimethylphenyl)methyl]-1H-benzimidazol-2-yl}methanol
C17 H18 N2 O
RZRPPZWEPMDGEI-UHFFFAOYSA-N
MRD
Query on MRD

Download Ideal Coordinates CCD File 
D [auth A](4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
A7M Binding MOAD:  6OOY Kd: 2.20e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.205 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.53α = 90
b = 81.6β = 90
c = 92.26γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
REFMACrefinement

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