1KYN

Cathepsin-G


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.328 
  • R-Value Work: 0.258 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Nonpeptide inhibitors of cathepsin G: optimization of a novel beta-ketophosphonic acid lead by structure-based drug design.

Greco, M.N.Hawkins, M.J.Powell, E.T.Almond Jr., H.R.Corcoran, T.W.de Garavilla, L.Kauffman, J.A.Recacha, R.Chattopadhyay, D.Andrade-Gordon, P.Maryanoff, B.E.

(2002) J.Am.Chem.Soc. 124: 3810-3811


  • PubMed Abstract: 
  • The serine protease cathepsin G (EC 3.4.21.20; Cat G), which is stored in the azurophilic granules of neutrophils (polymorphonuclear leukocytes) and released on degranulation, has been implicated in various pathological conditions associated with inf ...

    The serine protease cathepsin G (EC 3.4.21.20; Cat G), which is stored in the azurophilic granules of neutrophils (polymorphonuclear leukocytes) and released on degranulation, has been implicated in various pathological conditions associated with inflammation. By employing high-throughput screening, we identified beta-ketophosphonic acid 1 as a moderate inhibitor of Cat G (IC(50) = 4.1 microM). We were fortunate to obtain a cocrystal of 1 with Cat G and solve its structure by X-ray crystallography (3.5 A). Structural details from the X-ray analysis of 1.Cat G served as a platform for optimization of this lead compound by structure-based drug design. With the aid of molecular modeling, substituents were attached to the 3-position of the 2-naphthyl ring of 1, which occupies the S1 pocket of Cat G, to provide an extension into the hydrophobic S3 region. Thus, we arrived at analogue 7 with an 80-fold potency improvement over 1 (IC(50) = 53 nM). From these results, it is evident that the beta-ketophosphonic acid unit can form the basis for a novel class of serine protease inhibitors.


    Organizational Affiliation

    Johnson & Johnson Pharmaceutical Research & Development, Spring House, Pennsylvania 19477-0776, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
cathepsin G
A, B
235Homo sapiensGene Names: CTSG
EC: 3.4.21.20
Find proteins for P08311 (Homo sapiens)
Go to Gene View: CTSG
Go to UniProtKB:  P08311
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KTP
Query on KTP

Download SDF File 
Download CCD File 
A, B
(2-NAPHTHALEN-2-YL-1-NAPHTHALEN-1-YL-2-OXO-ETHYL)-PHOSPHONIC ACID
BIS-NAPTHYL BETA-KETOPHOSPHONIC ACID
C22 H17 O4 P
OFHMUASCSJJNNA-JOCHJYFZSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
KTPIC50: 4100 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.328 
  • R-Value Work: 0.258 
  • Space Group: P 41
Unit Cell:
Length (Å)Angle (°)
a = 59.440α = 90.00
b = 59.440β = 90.00
c = 130.620γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
AMoREphasing
DENZOdata reduction
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-05-01
    Type: Initial release
  • Version 1.1: 2008-03-26
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance