1RGR

Cyclic Peptides Targeting PDZ Domains of PSD-95: Structural Basis for Enhanced Affinity and Enzymatic Stability


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 22 
  • Selection Criteria: structures with acceptable covalent geometry,structures with the least restraint violations 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Targeting Specific PDZ Domains of PSD-95; Structural Basis for Enhanced Affinity and Enzymatic Stability of a Cyclic Peptide.

Piserchio, A.Salinas, G.D.Li, T.Marshall, J.Spaller, M.R.Mierke, D.F.

(2004) Chem Biol 11: 469-473

  • DOI: 10.1016/j.chembiol.2004.03.013
  • Primary Citation of Related Structures:  
    1RGR

  • PubMed Abstract: 
  • A cyclic peptide, Tyr-Lys-c[-Lys-Thr-Glu(betaAla)-]-Val, incorporating a beta-Ala lactam side chain linker and designed to target the PDZ domains of the postsynaptic density protein 95 (PSD-95), has been synthesized and structurally characterized by NMR while free and bound to the PDZ1 domain of PSD-95 ...

    A cyclic peptide, Tyr-Lys-c[-Lys-Thr-Glu(betaAla)-]-Val, incorporating a beta-Ala lactam side chain linker and designed to target the PDZ domains of the postsynaptic density protein 95 (PSD-95), has been synthesized and structurally characterized by NMR while free and bound to the PDZ1 domain of PSD-95. While bound, the lactam linker of the peptide makes a number of unique contacts outside the canonical PDZ binding motif, providing a novel target for PDZ-domain specificity as well as producing a 10-fold enhancement in binding affinity. Additionally, the cyclization greatly enhances the enzymatic stability, increasing the duration that the peptide inhibits the association between PSD-95 and glutamate receptors, effectively inhibiting the clustering of kainate receptors for over 14 hr after application. Highly specific regulation of kainate receptor action may provide a novel route for treatment of drug addiction and epilepsy.


    Organizational Affiliation

    Department of Chemistry, Division of Biology & Medicine, Brown University, Providence, RI 02912 USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Presynaptic density protein 95A99Rattus norvegicusMutation(s): 0 
Gene Names: Dlg4Psd95Dlgh4
Find proteins for P31016 (Rattus norvegicus)
Explore P31016 
Go to UniProtKB:  P31016
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
postsynaptic protein CRIPT peptideB6N/AMutation(s): 2 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BAL
Query on BAL

Download Ideal Coordinates CCD File 
C [auth B]BETA-ALANINE
C3 H7 N O2
UCMIRNVEIXFBKS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 22 
  • Selection Criteria: structures with acceptable covalent geometry,structures with the least restraint violations 
  • OLDERADO: 1RGR Olderado

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-05-18
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance