7KP9 | pdb_00007kp9

asymmetric hTNF-alpha


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 
    0.241 (Depositor), 0.251 (DCC) 
  • R-Value Work: 
    0.188 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 
    0.190 (Depositor) 

Starting Model: other
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Structural insights into the disruption of TNF-TNFR1 signalling by small molecules stabilising a distorted TNF.

McMillan, D.Martinez-Fleites, C.Porter, J.Fox 3rd, D.Davis, R.Mori, P.Ceska, T.Carrington, B.Lawson, A.Bourne, T.O'Connell, J.

(2021) Nat Commun 12: 582-582

  • DOI: https://doi.org/10.1038/s41467-020-20828-3
  • Primary Citation Related Structures: 
    7KP7, 7KP8, 7KP9

  • PubMed Abstract: 

    Tumour necrosis factor (TNF) is a trimeric protein which signals through two membrane receptors, TNFR1 and TNFR2. Previously, we identified small molecules that inhibit human TNF by stabilising a distorted trimer and reduce the number of receptors bound to TNF from three to two. Here we present a biochemical and structural characterisation of the small molecule-stabilised TNF-TNFR1 complex, providing insights into how a distorted TNF trimer can alter signalling function. We demonstrate that the inhibitors reduce the binding affinity of TNF to the third TNFR1 molecule. In support of this, we show by X-ray crystallography that the inhibitor-bound, distorted, TNF trimer forms a complex with a dimer of TNFR1 molecules. This observation, along with data from a solution-based network assembly assay, leads us to suggest a model for TNF signalling based on TNF-TNFR1 clusters, which are disrupted by small molecule inhibitors.


  • Organizational Affiliation
    • UCB Pharma, Slough, SL1 3WE, UK. david.mcmillan@ucb.com.

Macromolecule Content 

  • Total Structure Weight: 52.82 kDa 
  • Atom Count: 3,373 
  • Modeled Residue Count: 418 
  • Deposited Residue Count: 474 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Tumor necrosis factor
A, B, C
158Homo 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 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A7G
(Subject of Investigation/LOI)

Query on A7G



Download:Ideal Coordinates CCD File
D [auth C]1-{[2-(difluoromethoxy)phenyl]methyl}-2-methyl-6-[6-(piperazin-1-yl)pyridin-3-yl]-1H-benzimidazole
C25 H25 F2 N5 O
LRHACCJNWLLTDS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free:  0.241 (Depositor), 0.251 (DCC) 
  • R-Value Work:  0.188 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 0.190 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.52α = 90
b = 81.96β = 90
c = 93.24γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-13
    Type: Initial release
  • Version 1.1: 2021-02-03
    Changes: Database references
  • Version 1.2: 2024-04-03
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-10-16
    Changes: Structure summary