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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This is version 1.0 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: 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 ...

    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. Electronic address: murali_r@aurigene.com.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Suppressor of tumorigenicity 14 proteinA241Homo 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
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
SERINE PROTEASE, MATRIPTASE, MEMBRANE-TYPE SERINE PROTEASE 1, MT-SP1B4Homo 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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / 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
 Ligand Interaction
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

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-02-11
    Type: Initial release