1AYV

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.312 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.209 

wwPDB Validation   3D Report Full Report


This is version 1.4 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 U S A 94: 14249-14254

  • DOI: 10.1073/pnas.94.26.14249
  • Primary Citation of Related Structures:  
    1AYW, 1AYV, 1AYU

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CATHEPSIN KA215Homo sapiensMutation(s): 0 
Gene Names: CTSKCTSOCTSO2
EC: 3.4.22.38
Find proteins for P43235 (Homo sapiens)
Explore P43235 
Go to UniProtKB:  P43235
NIH Common Fund Data Resources
PHAROS  P43235
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IN6
Query on IN6

Download CCD File 
A
N-[2-[1-(N-BENZYLOXYCARBONYLAMINO)-3-METHYLBUTYL]THIAZOL-4-YLCARBONYL]-N'-(BENZYLOXYCARBONYL-L-LEUCINYL)HYDRAZIDE
C31 H39 N5 O6 S
FNMSKYFYFLZDOO-DQEYMECFSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
IN6Ki :  10   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.312 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.209 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.31α = 90
b = 51.27β = 90
c = 103.87γ = 90
Software Package:
Software NamePurpose
XENGENdata collection
XENGENdata reduction
X-PLORmodel building
X-PLORrefinement
XENGENdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-11-25
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2012-02-29
    Changes: Database references
  • Version 1.4: 2018-03-07
    Changes: Data collection, Other