1YT7

Cathepsin K complexed with a constrained ketoamide inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.183 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

P(2)-P(3) conformationally constrained ketoamide-based inhibitors of cathepsin K.

Barrett, D.G.Boncek, V.M.Catalano, J.G.Deaton, D.N.Hassell, A.M.Jurgensen, C.H.Long, S.T.McFadyen, R.B.Miller, A.B.Miller, L.R.Payne, J.A.Ray, J.A.Samano, V.Shewchuk, L.M.Tavares, F.X.Wells-Knecht, K.J.Willard, D.H.Wright, L.L.Zhou, H.Q.

(2005) Bioorg Med Chem Lett 15: 3540-3546

  • DOI: 10.1016/j.bmcl.2005.05.062
  • Primary Citation of Related Structures:  
    1YT7

  • PubMed Abstract: 
  • An orally bioavailable series of ketoamide-based cathepsin K inhibitors with good pharmacokinetic properties has been identified. Starting from a potent inhibitor endowed with poor drug properties, conformational constraint of the P(2)-P(3) linker an ...

    An orally bioavailable series of ketoamide-based cathepsin K inhibitors with good pharmacokinetic properties has been identified. Starting from a potent inhibitor endowed with poor drug properties, conformational constraint of the P(2)-P(3) linker and modifications to P(1') elements led to an enhancement in potency, solubility, clearance, and bioavailability. These optimized inhibitors attenuated bone resorption in a rat TPTX hypocalcemic bone resorption model.


    Organizational Affiliation

    Department of Medicinal Chemistry, GlaxoSmithKline, Research Triangle Park, NC 27709, 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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3FC
Query on 3FC

Download CCD File 
A
(1R)-2,2-DIMETHYL-1-({5-[4-(TRIFLUOROMETHYL)PHENYL]-1,3,4-OXADIAZOL-2-YL}METHYL)PROPYL (1S)-1-{OXO[(2-OXO-1,3-OXAZOLIDIN-3-YL)AMINO]ACETYL}PENTYLCARBAMATE
C26 H32 F3 N5 O7
IXXKXSFSQVTOKQ-ZWKOTPCHSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3FCIC50 :  0.12999999523162842   nM  PDBBind
3FCIC50:  130   nM  BindingDB
3FCIC50:  0.12999999523162842   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.183 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.645α = 90
b = 65.645β = 90
c = 34.467γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History 

  • Version 1.0: 2005-07-19
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance