1AYU

CRYSTAL STRUCTURE OF CYSTEINE PROTEASE HUMAN CATHEPSIN K IN COMPLEX WITH A COVALENT SYMMETRIC BISCARBOHYDRAZIDE INHIBITOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Design of potent and selective human cathepsin K inhibitors that span the active site.

Thompson, S.K.Halbert, S.M.Bossard, M.J.Tomaszek, T.A.Levy, M.A.Zhao, B.Smith, W.W.Abdel-Meguid, S.S.Janson, C.A.D'Alessio, K.J.McQueney, M.S.Amegadzie, B.Y.Hanning, C.R.DesJarlais, R.L.Briand, J.Sarkar, S.K.Huddleston, M.J.Ijames, C.F.Carr, S.A.Garnes, K.T.Shu, A.Heys, J.R.Bradbeer, J.Zembryki, D.Lee-Rykaczewski, L.James, I.E.Lark, M.W.Drake, F.H.Gowen, M.Gleason, J.G.Veber, D.F.

(1997) Proc.Natl.Acad.Sci.USA 94: 14249-14254

  • Primary Citation of Related Structures:  1AYV, 1AYW

  • PubMed Abstract: 
  • Potent and selective active-site-spanning inhibitors have been designed for cathepsin K, a cysteine protease unique to osteoclasts. They act by mechanisms that involve tight binding intermediates, potentially on a hydrolytic pathway. X-ray crystallog ...

    Potent and selective active-site-spanning inhibitors have been designed for cathepsin K, a cysteine protease unique to osteoclasts. They act by mechanisms that involve tight binding intermediates, potentially on a hydrolytic pathway. X-ray crystallographic, MS, NMR spectroscopic, and kinetic studies of the mechanisms of inhibition indicate that different intermediates or transition states are being represented that are dependent on the conditions of measurement and the specific groups flanking the carbonyl in the inhibitor. The species observed crystallographically are most consistent with tetrahedral intermediates that may be close approximations of those that occur during substrate hydrolysis. Initial kinetic studies suggest the possibility of irreversible and reversible active-site modification. Representative inhibitors have demonstrated antiresorptive activity both in vitro and in vivo and therefore are promising leads for therapeutic agents for the treatment of osteoporosis. Expansion of these inhibitor concepts can be envisioned for the many other cysteine proteases implicated for therapeutic intervention.


    Organizational Affiliation

    Department of Medicinal Chemistry, SmithKline Beecham Pharmaceuticals, King of Prussia, PA 19406, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CATHEPSIN K
A
215Homo sapiensGene Names: CTSK (CTSO, CTSO2)
EC: 3.4.22.38
Find proteins for P43235 (Homo sapiens)
Go to Gene View: CTSK
Go to UniProtKB:  P43235
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
INA
Query on INA

Download SDF File 
Download CCD File 
A
1,5-BIS(N-BENZYLOXYCARBONYL-L-LEUCINYL)CARBOHYDRAZIDE
C29 H40 N6 O7
HGDUWJVGIGLVOH-ZEQRLZLVSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
INAKi: 0.7 nM (100) BINDINGDB
INAKi: 0.7 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.208 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 38.330α = 90.00
b = 51.300β = 90.00
c = 103.860γ = 90.00
Software Package:
Software NamePurpose
XENGENdata scaling
XENGENdata reduction
X-PLORmodel building
XENGENdata collection
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-11-25
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2012-02-29
    Type: Database references