2GV7

Structure of Matriptase in Complex with Inhibitor CJ-672


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.197 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

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


Macromolecules
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 (PDB Primary Data), 3.4.21.109 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y5Y6 (Homo sapiens)
Explore Q9Y5Y6 
Go to UniProtKB:  Q9Y5Y6
PHAROS:  Q9Y5Y6
GTEx:  ENSG00000149418 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y5Y6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
672
Query on 672

Download Ideal Coordinates CCD File 
B [auth A](S)-4-(4-(3-(3-CARBAMIMIDOYLPHENYL)-2-(2,4,6-TRIISOPROPYLPHENYLSULFONAMIDO)PROPANOYL)PIPERAZINE-1-CARBONYL)PIPERIDINE-1-CARBOXIMIDAMIDE
C36 H54 N8 O4 S
KSEVHDWJTMMENT-HKBQPEDESA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
672 BindingDB:  2GV7 Ki: min: 4.3, max: 14 (nM) from 2 assay(s)
PDBBind:  2GV7 Ki: 14 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.197 
  • Space Group: C 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.07α = 90
b = 140.15β = 90
c = 51.73γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
CNSrefinement

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: 2024-10-30
    Changes: Data collection, Database references, Derived calculations, Structure summary