4R0I

CRYSTAL STRUCTURE of MATRIPTASE in COMPLEX WITH INHIBITOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.223 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Discovery of O-(3-carbamimidoylphenyl)-l-serine amides as matriptase inhibitors using a fragment-linking approach

Goswami, R.Wohlfahrt, G.Mukherjee, S.Ghadiyaram, C.Nagaraj, J.Satyam, L.K.Subbarao, K.Gopinath, S.Krishnamurthy, N.R.Subramanya, H.S.Ramachandra, M.

(2015) Bioorg Med Chem Lett 25: 616-620

  • DOI: https://doi.org/10.1016/j.bmcl.2014.12.008
  • Primary Citation of Related Structures:  
    4R0I

  • PubMed Abstract: 

    Matriptase is a cell-surface trypsin-like serine protease of epithelial origin, which cleaves and activates proteins including hepatocyte growth factor/scatter factor and proteases such as uPA, which are involved in the progression of various cancers. Here we report a fragment-linking approach, which led to the discovery of O-(3-carbamimidoylphenyl)-l-serine amides as potent matriptase inhibitors. The co-crystal structure of one of the potent inhibitors, 6 in complex with matriptase catalytic domain validated the working hypothesis guiding the development of this congeneric series and revealed the structural basis for matriptase inhibition. Replacement of a naphthyl group in 6 with 2,4,6-tri-isopropyl phenyl resulted in 10 with improved matriptase inhibition, which exhibited significant primary tumor growth inhibition in a mouse model of prostate cancer. Compounds such as 10, identified using a fragment-linking approach, can be explored further to understand the role of matriptase as a drug target in cancer and inflammation.


  • Organizational Affiliation

    Aurigene Discovery Technologies Limited, 39-40 KIADB Industrial Area, Electronic City Phase II, Bangalore 560 100, India.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Suppressor of tumorigenicity 14 protein241Homo sapiensMutation(s): 0 
Gene Names: ST14PRSS14SNC19TADG15
EC: 3.4.21.109
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
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
SERINE PROTEASE, MATRIPTASE, MEMBRANE-TYPE SERINE PROTEASE 1, MT-SP14Homo sapiensMutation(s): 0 
Gene Names: ST14PRSS14SNC19TADG15
EC: 3.4.21.109
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y5Y6 (Homo sapiens)
Explore Q9Y5Y6 
Go to UniProtKB:  Q9Y5Y6
PHAROS:  Q9Y5Y6
GTEx:  ENSG00000149418 
Entity Groups  
UniProt GroupQ9Y5Y6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3KM
Query on 3KM

Download Ideal Coordinates CCD File 
C [auth A]3-({(2S)-3-[4-(2-aminoethyl)piperidin-1-yl]-2-[(naphthalen-2-ylsulfonyl)amino]-3-oxopropyl}oxy)benzenecarboximidamide
C27 H33 N5 O4 S
LNOODAVJDWKXFO-VWLOTQADSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
3KM Binding MOAD:  4R0I Ki: 300 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.223 
  • Space Group: C 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.842α = 90
b = 140.448β = 90
c = 51.899γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-02-11
    Type: Initial release
  • Version 1.1: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description