4TWT

Human TNFa dimer in complex with the semi-synthetic bicyclic peptide M21


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.229 

wwPDB Validation 3D Report Full Report



Literature

Subunit disassembly and inhibition of TNF alpha by a semi-synthetic bicyclic peptide.

Luzi, S.Kondo, Y.Bernard, E.Stadler, L.K.Vaysburd, M.Winter, G.Holliger, P.

(2015) Protein Eng Des Sel 28: 45-52

  • DOI: 10.1093/protein/gzu055
  • Primary Citation of Related Structures:  
    4TWT

  • PubMed Abstract: 
  • Macrocyclic peptides are potentially a source of powerful drugs, but their de novo discovery remains challenging. Here we describe the discovery of a high-affinity (Kd = 10 nM) peptide macrocycle (M21) against human tumor necrosis factor-alpha (hTNFα ...

    Macrocyclic peptides are potentially a source of powerful drugs, but their de novo discovery remains challenging. Here we describe the discovery of a high-affinity (Kd = 10 nM) peptide macrocycle (M21) against human tumor necrosis factor-alpha (hTNFα), a key drug target in the treatment of inflammatory disorders, directly from diverse semi-synthetic phage peptide repertoires. The bicyclic peptide M21 (ACPPCLWQVLC) comprises two loops covalently anchored to a 2,4,6-trimethyl-mesitylene core and upon binding induces disassembly of the trimeric TNFα cytokine into dimers and monomers. A 2.9 Å crystal structure of the M21/hTNFα complex reveals the peptide bound to a hTNFα dimer at a normally buried epitope in the trimer interface overlapping the binding site of a previously discovered small molecule ligand (SPD304), which also induces TNF trimer dissociation and synergizes with M21 in the inhibition of TNFα cytotoxicity. The discovery of M21 underlines the potential of semi-synthetic bicyclic peptides as ligands for the discovery of cryptic epitopes, some of which are poorly accessible to antibodies.


    Organizational Affiliation

    MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK ph1@mrc-lmb.cam.ac.uk.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tumor necrosis factorABCD157Homo sapiensMutation(s): 0 
Gene Names: TNFTNFATNFSF2
Find proteins for P01375 (Homo sapiens)
Explore P01375 
Go to UniProtKB:  P01375
NIH Common Fund Data Resources
PHAROS  P01375
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ALA-CYS-PRO-PRO-CYS-LEU-TRP-GLN-VAL-LEU-CYS-GLYEF12synthetic constructMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
38A
Query on 38A

Download CCD File 
E, F
(2,4,6-trimethylbenzene-1,3,5-triyl)trimethanol
C12 H18 O3
RZPWWYFQBDXLBQ-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
B, C, D, E
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.229 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.444α = 90
b = 78.444β = 90
c = 230.375γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
iMOSFLMdata reduction
PHASERphasing
Cootmodel building

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-02-04
    Type: Initial release