1KYN

Cathepsin-G


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 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

  • DOI: 10.1021/ja017506h
  • Primary Citation of Related Structures:  
    1KYN

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
cathepsin GAB235Homo sapiensMutation(s): 0 
Gene Names: CTSG
EC: 3.4.21.20
Find proteins for P08311 (Homo sapiens)
Explore P08311 
Go to UniProtKB:  P08311
NIH Common Fund Data Resources
PHAROS  P08311
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KTP
Query on KTP

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.328 
  • R-Value Work: 0.258 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.44α = 90
b = 59.44β = 90
c = 130.62γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLORrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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