1KYN | pdb_00001kyn

Cathepsin-G


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 
    0.328 (Depositor), 0.301 (DCC) 
  • R-Value Work: 
    0.258 (Depositor), 0.222 (DCC) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1KYN

Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.1021/ja017506h
  • Primary Citation 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 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.

Macromolecule Content 

  • Total Structure Weight: 54.36 kDa 
  • Atom Count: 3,607 
  • Modeled Residue Count: 448 
  • Deposited Residue Count: 470 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
cathepsin G
A, B
235Homo sapiensMutation(s): 0 
EC: 3.4.21.20
UniProt & NIH Common Fund Data Resources
Find proteins for P08311 (Homo sapiens)
Explore P08311 
Go to UniProtKB:  P08311
PHAROS:  P08311
GTEx:  ENSG00000100448 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08311
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
KTP

Query on KTP



Download:Ideal Coordinates CCD File
C [auth A],
D [auth B]
(2-NAPHTHALEN-2-YL-1-NAPHTHALEN-1-YL-2-OXO-ETHYL)-PHOSPHONIC ACID
C22 H17 O4 P
OFHMUASCSJJNNA-JOCHJYFZSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
KTP BindingDB:  1KYN IC50: 4100 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free:  0.328 (Depositor), 0.301 (DCC) 
  • R-Value Work:  0.258 (Depositor), 0.222 (DCC) 
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



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2024-10-30
    Changes: Data collection, Database references, Derived calculations, Structure summary