1YK7

Cathepsin K complexed with a cyanopyrrolidine inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.190 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Novel and potent cyclic cyanamide-based cathepsin K inhibitors.

Deaton, D.N.Hassell, A.M.McFadyen, R.B.Miller, A.B.Miller, L.R.Shewchuk, L.M.Tavares, F.X.Willard, D.H.Wright, L.L.

(2005) Bioorg Med Chem Lett 15: 1815-1819

  • DOI: 10.1016/j.bmcl.2005.02.033
  • Primary Citation of Related Structures:  
    1YK7

  • PubMed Abstract: 
  • Starting from a PDE IV inhibitor hit derived from high throughput screening of the compound collection, a key pyrrolidine cyanamide pharmacophore was identified. Modifications of the pyrrolidine ring produced enhancements in cathepsin K inhibition. A ...

    Starting from a PDE IV inhibitor hit derived from high throughput screening of the compound collection, a key pyrrolidine cyanamide pharmacophore was identified. Modifications of the pyrrolidine ring produced enhancements in cathepsin K inhibition. An X-ray co-crystal structure of a cyanamide with cathepsin K confirmed the mode of inhibition.


    Organizational Affiliation

    Department of Medicinal Chemistry, GlaxoSmithKline, Research Triangle Park, NC 27709, USA. david.n.deaton@gsk.com



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
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NBL
Query on NBL

Download CCD File 
A
N2-[(BENZYLOXY)CARBONYL]-N1-[(3S)-1-CYANOPYRROLIDIN-3-YL]-L-LEUCINAMIDE
C19 H26 N4 O3
IMTUSTXBVIALBC-SJORKVTESA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
NBLIC50 :  19   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.190 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 32.241α = 90
b = 66.653β = 90
c = 93.187γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-03-22
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance