4O9V

Crystal structure of matriptase in complex with inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.174 

wwPDB Validation 3D Report Full Report



Literature

Structure-guided discovery of 1,3,5 tri-substituted benzenes as potent and selective matriptase inhibitors exhibiting in vivo antitumor efficacy.

Goswami, R.Mukherjee, S.Ghadiyaram, C.Wohlfahrt, G.Sistla, R.K.Nagaraj, J.Satyam, L.K.Subbarao, K.Palakurthy, R.K.Gopinath, S.Krishnamurthy, N.R.Ikonen, T.Moilanen, A.Subramanya, H.S.Kallio, P.Ramachandra, M.

(2014) Bioorg Med Chem 22: 3187-3203

  • DOI: 10.1016/j.bmc.2014.04.013
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Matriptase is a serine protease implicated in cancer invasion and metastasis. Expression of matriptase is frequently dysregulated in human cancers and matriptase has been reported to activate latent growth factors such as hepatocyte growth factor/sca ...

    Matriptase is a serine protease implicated in cancer invasion and metastasis. Expression of matriptase is frequently dysregulated in human cancers and matriptase has been reported to activate latent growth factors such as hepatocyte growth factor/scatter factor, and proteases such as urokinase plasminogen activator suggesting that matriptase inhibitors could have therapeutic potential in treatment of cancer. Here we report a structure-based approach which led to the discovery of selective and potent matriptase inhibitors with benzene as central core having 1,3,5 tri-substitution pattern. X-ray crystallography of one of the potent analogs in complex with matriptase revealed strong hydrogen bonding and salt-bridge interactions in the S1 pocket, as well as strong CH-π contacts between the P2/P4 cyclohexyl and Trp215 side-chain. An additional interaction of the pendant amine at cyclohexyl with Gln175 side-chain results in substantial improvement in matriptase inhibition and selectivity against other related serine proteases. Compounds 15 and 26 showed tumor growth inhibition in a subcutaneous DU-145 prostate cancer mouse model. These compounds could be useful as tools to further explore the biology of matriptase as a drug target.


    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Suppressor of tumorigenicity 14 protein
A
241Homo sapiensMutation(s): 0 
Gene Names: ST14PRSS14SNC19TADG15
EC: 3.4.21.109
Find proteins for Q9Y5Y6 (Homo sapiens)
Go to UniProtKB:  Q9Y5Y6
NIH Common Fund Data Resources
PHAROS  Q9Y5Y6
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Peptide CGLR
B
4Homo sapiensMutation(s): 0 
Gene Names: ST14PRSS14SNC19TADG15
EC: 3.4.21.109
Find proteins for Q9Y5Y6 (Homo sapiens)
Go to UniProtKB:  Q9Y5Y6
NIH Common Fund Data Resources
PHAROS  Q9Y5Y6
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NT4
Query on NT4

Download CCD File 
A
N-(trans-4-aminocyclohexyl)-3,5-bis(4-carbamimidoylphenoxy)benzamide
C27 H30 N6 O3
PCTUHSSCHRLPLB-MXVIHJGJSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
NT4Ki:  10   nM  BindingDB
NT4Ki:  10   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.174 
  • Space Group: C 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.645α = 90
b = 140.683β = 90
c = 51.859γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-05-28
    Type: Initial release