4JYT

Crystal Structure of Matriptase in complex with Inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Discovery of Pyridyl Bis(oxy)dibenzimidamide Derivatives as Selective Matriptase Inhibitors

Goswami, R.Mukherjee, S.Wohlfahrt, G.Ghadiyaram, C.Nagaraj, J.Chandra, B.R.Sistla, R.K.Satyam, L.K.Samiulla, D.S.Moilanen, A.Subramanya, H.S.Ramachandra, M.

(2013) ACS MED.CHEM.LETT. 4: 1152-1157

  • DOI: 10.1021/ml400213v
  • Primary Citation of Related Structures:  4JZ1, 4JZI

  • PubMed Abstract: 
  • Matriptase belongs to trypsin-like serine proteases involved in matrix remodeling/degradation, growth regulation, survival, motility, and cell morphogenesis. Herein, we report a structure-based approach, which led to the discovery of sulfonamide and ...

    Matriptase belongs to trypsin-like serine proteases involved in matrix remodeling/degradation, growth regulation, survival, motility, and cell morphogenesis. Herein, we report a structure-based approach, which led to the discovery of sulfonamide and amide derivatives of pyridyl bis(oxy)benzamidine as potent and selective matriptase inhibitors. Co-crystal structures of selected compounds in complex with matriptase supported compound designing. Additionally, WaterMap analyses indicated the possibility of occupying a distinct pocket within the catalytic domain, exploration of which resulted in >100-fold improvement in potency. Co-crystal structure of 10 with matriptase revealed critical interactions leading to potent target inhibition and selectivity against other serine proteases.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Suppressor of tumorigenicity 14 protein
A
241Homo sapiensGene Names: ST14 (PRSS14, SNC19, TADG15)
EC: 3.4.21.109
Find proteins for Q9Y5Y6 (Homo sapiens)
Go to Gene View: ST14
Go to UniProtKB:  Q9Y5Y6
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
N4A
Query on N4A

Download SDF File 
Download CCD File 
A
4,4'-[{3-[(naphthalen-2-ylsulfonyl)amino]pyridine-2,6-diyl}bis(oxy)]dibenzenecarboximidamide
C29 H24 N6 O4 S
YVYNZHGMLLXWDD-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
N4AKi: 40 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.216 
  • Space Group: C 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 66.423α = 90.00
b = 140.658β = 90.00
c = 51.325γ = 90.00
Software Package:
Software NamePurpose
CrystalCleardata collection
SCALEPACKdata scaling
DENZOdata reduction
AMoREphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-03-19
    Type: Initial release
  • Version 1.1: 2015-02-25
    Type: Database references