Crystal Structure of Matriptase with Inhibitor CJ-730

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.182 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


Secondary Amides of Sulfonylated 3-Amidinophenylalanine. New Potent and Selective Inhibitors of Matriptase.

Steinmetzer, T.Schweinitz, A.Sturzebecher, A.Donnecke, D.Uhland, K.Schuster, O.Steinmetzer, P.Muller, F.Friedrich, R.Than, M.E.Bode, W.Sturzebecher, J.

(2006) J Med Chem 49: 4116-4126

  • DOI: https://doi.org/10.1021/jm051272l
  • Primary Citation of Related Structures:  
    2GV6, 2GV7

  • PubMed Abstract: 

    Matriptase is an epithelium-derived type II transmembrane serine protease and has been implicated in the activation of substrates such as pro-HGF/SF and pro-uPA, which are likely involved in tumor progression and metastasis. Through screening, we have identified bis-basic secondary amides of sulfonylated 3-amidinophenylalanine as matriptase inhibitors. X-ray analyses of analogues 8 and 31 in complex with matriptase revealed that these inhibitors occupy, in addition to part of the previously described S4-binding site, the cleft formed by the molecular surface and the unique 60 loop of matriptase. Therefore, optimization of the inhibitors included the incorporation of appropriate sulfonyl substituents that could improve binding of these inhibitors into both characteristic matriptase subsites. The most potent derivatives inhibit matriptase highly selective with K(i) values below 5 nM. Molecular modeling revealed that their improved affinity results from interaction with the S4 site of matriptase. Analogues 8 and 59 were studied in an orthotopic xenograft mouse model of prostate cancer. Compared to control, both inhibitors reduced tumor growth, as well as tumor dissemination.

  • Organizational Affiliation

    Curacyte Chemistry GmbH, Winzerlaer Strasse 2, D-07745 Jena, Germany. torsten.steinmetzer@curacyte.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Suppressor of tumorigenicity 14241Homo sapiensMutation(s): 0 
Gene Names: ST14
EC: 3.4.21
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y5Y6 (Homo sapiens)
Explore Q9Y5Y6 
Go to UniProtKB:  Q9Y5Y6
GTEx:  ENSG00000149418 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y5Y6
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 730

Download Ideal Coordinates CCD File 
C28 H35 N7 O3 S
Binding Affinity Annotations 
IDSourceBinding Affinity
730 PDBBind:  2GV6 Ki: 46 (nM) from 1 assay(s)
Binding MOAD:  2GV6 Ki: 46 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.10 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.182 
  • Space Group: C 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.84α = 90
b = 141.02β = 90
c = 51.02γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

  • Released Date: 2006-06-06 
  • Deposition Author(s): Bode, W.

Revision History  (Full details and data files)

  • Version 1.0: 2006-06-06
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-06-23
    Changes: Advisory, Data collection, Derived calculations