5JM4

Crystal structure of 14-3-3zeta in complex with a cyclic peptide involving an adamantyl and a dicarboxy side chain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure-Based Design of Non-natural Macrocyclic Peptides That Inhibit Protein-Protein Interactions.

Kruger, D.M.Glas, A.Bier, D.Pospiech, N.Wallraven, K.Dietrich, L.Ottmann, C.Koch, O.Hennig, S.Grossmann, T.N.

(2017) J. Med. Chem. 60: 8982-8988

  • DOI: 10.1021/acs.jmedchem.7b01221

  • PubMed Abstract: 
  • Macrocyclic peptides can interfere with challenging biomolecular targets including protein-protein interactions. Whereas there are various approaches that facilitate the identification of peptide-derived ligands, their evolution into higher affinity ...

    Macrocyclic peptides can interfere with challenging biomolecular targets including protein-protein interactions. Whereas there are various approaches that facilitate the identification of peptide-derived ligands, their evolution into higher affinity binders remains a major hurdle. We report a virtual screen based on molecular docking that allows the affinity maturation of macrocyclic peptides taking non-natural amino acids into consideration. These macrocycles bear large and flexible substituents that usually complicate the use of docking approaches. A virtual library containing more than 1400 structures was screened against the target focusing on docking poses with the core structure resembling a known bioactive conformation. Based on this screen, a macrocyclic peptide 22 involving two non-natural amino acids was evolved showing increased target affinity and biological activity. Predicted binding modes were verified by X-ray crystallography. The presented workflow allows the screening of large macrocyclic peptides with diverse modifications thereby expanding the accessible chemical space and reducing synthetic efforts.


    Organizational Affiliation

    Department of Chemistry & Pharmaceutical Sciences, VU University Amsterdam , De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands.,Chemical Genomics Centre of the Max Planck Society , Otto-Hahn-Str. 15, 44227 Dortmund, Germany.,Faculty of Chemistry and Chemical Biology, TU Dortmund University , Otto-Hahn-Str. 6, 44227 Dortmund, Germany.,Department of Biomedical Engineering, Institute of Complex Molecular Systems, Eindhoven University of Technology , Den Dolech 2, 5612 AZ Eindhoven, The Netherlands.,Department of Chemistry, University of Duisburg-Essen , Universit├Ątstr. 7, 45141 Essen, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
14-3-3 protein zeta/delta
A, B
230Homo sapiensMutation(s): 0 
Gene Names: YWHAZ
Find proteins for P63104 (Homo sapiens)
Go to Gene View: YWHAZ
Go to UniProtKB:  P63104
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
GLN-GLY-MKD-ANG-ASP-MKD-LEU-ASP-LEU-ALA-CLU
D, E
11N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BEZ
Query on BEZ

Download SDF File 
Download CCD File 
A, B
BENZOIC ACID
C7 H6 O2
WPYMKLBDIGXBTP-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
6L9
Query on 6L9
D, E
NON-POLYMERC6 H10 N2 O5

--

A1G
Query on A1G
D, E
NON-POLYMERC12 H19 N O2

--

MKD
Query on MKD
D, E
L-PEPTIDE LINKINGC9 H19 N O2

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.198 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 84.920α = 90.00
b = 105.740β = 90.00
c = 113.930γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
XSCALEdata scaling
PDB_EXTRACTdata extraction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Emmy Noether programGermanyGR3592/2-1
German Research FoundationGermanySFB1093

Revision History 

  • Version 1.0: 2017-05-10
    Type: Initial release
  • Version 1.1: 2018-10-24
    Type: Author supporting evidence, Data collection, Database references
  • Version 1.2: 2018-12-19
    Type: Data collection, Derived calculations