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 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

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

  • 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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tumor necrosis factor
A, B, C, D
157Homo sapiensMutation(s): 0 
Gene Names: TNF (TNFA, TNFSF2)
Find proteins for P01375 (Homo sapiens)
Go to Gene View: TNF
Go to UniProtKB:  P01375
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ALA-CYS-PRO-PRO-CYS-LEU-TRP-GLN-VAL-LEU-CYS-GLY
E, F
12N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
B, C, D, E
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
38A
Query on 38A

Download SDF File 
Download CCD File 
E, F
(2,4,6-trimethylbenzene-1,3,5-triyl)trimethanol
C12 H18 O3
RZPWWYFQBDXLBQ-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 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 78.444α = 90.00
b = 78.444β = 90.00
c = 230.375γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing
Aimlessdata scaling
Cootmodel building
iMOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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