6AK2

Crystal structure of the syntenin PDZ1 domain in complex with the peptide inhibitor KSL-128018


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.212 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

A High-Affinity Peptide Ligand Targeting Syntenin Inhibits Glioblastoma.

Haugaard-Kedstrom, L.M.Clemmensen, L.S.Sereikaite, V.Jin, Z.Fernandes, E.F.A.Wind, B.Abalde-Gil, F.Daberger, J.Vistrup-Parry, M.Aguilar-Morante, D.Leblanc, R.Egea-Jimenez, A.L.Albrigtsen, M.Jensen, K.E.Jensen, T.M.T.Ivarsson, Y.Vincentelli, R.Hamerlik, P.Andersen, J.H.Zimmermann, P.Lee, W.Stromgaard, K.

(2021) J Med Chem 64: 1423-1434

  • DOI: 10.1021/acs.jmedchem.0c00382
  • Primary Citation of Related Structures:  
    6AK2

  • PubMed Abstract: 
  • Despite the recent advances in cancer therapeutics, highly aggressive cancer forms, such as glioblastoma (GBM), still have very low survival rates. The intracellular scaffold protein syntenin, comprising two postsynaptic density protein-95/discs-large/zona occludens-1 (PDZ) domains, has emerged as a novel therapeutic target in highly malignant phenotypes including GBM ...

    Despite the recent advances in cancer therapeutics, highly aggressive cancer forms, such as glioblastoma (GBM), still have very low survival rates. The intracellular scaffold protein syntenin, comprising two postsynaptic density protein-95/discs-large/zona occludens-1 (PDZ) domains, has emerged as a novel therapeutic target in highly malignant phenotypes including GBM. Here, we report the development of a novel, highly potent, and metabolically stable peptide inhibitor of syntenin, KSL-128114, which binds the PDZ1 domain of syntenin with nanomolar affinity. KSL-128114 is resistant toward degradation in human plasma and mouse hepatic microsomes and displays a global PDZ domain selectivity for syntenin. An X-ray crystal structure reveals that KSL-128114 interacts with syntenin PDZ1 in an extended noncanonical binding mode. Treatment with KSL-128114 shows an inhibitory effect on primary GBM cell viability and significantly extends survival time in a patient-derived xenograft mouse model. Thus, KSL-128114 is a novel promising candidate with therapeutic potential for highly aggressive tumors, such as GBM.


    Organizational Affiliation

    Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Syntenin-1A, B81Rattus norvegicusMutation(s): 0 
Gene Names: Sdcbp
UniProt
Find proteins for Q9JI92 (Rattus norvegicus)
Explore Q9JI92 
Go to UniProtKB:  Q9JI92
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
peptide inhibitor KSL-128018C [auth D], D [auth E]7synthetic constructMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TBG
Query on TBG
C [auth D], D [auth E]L-PEPTIDE LINKINGC6 H13 N O2VAL
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.212 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.58α = 90
b = 38.396β = 92.52
c = 56.777γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-04
    Type: Initial release
  • Version 1.1: 2021-03-17
    Changes: Database references