2FTD

Crystal structure of Cathepsin K complexed with 7-Methyl-Substituted Azepan-3-one compound

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.237 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 


Literature

Structure activity relationships of 5-, 6-, and 7-methyl-substituted azepan-3-one cathepsin K inhibitors.

Yamashita, D.S., Marquis, R.W., Xie, R., Nidamarthy, S.D., Oh, H.J., Jeong, J.U., Erhard, K.F., Ward, K.W., Roethke, T.J., Smith, B.R., Cheng, H.Y., Geng, X., Lin, F., Offen, P.H., Wang, B., Nevins, N., Head, M.S., Haltiwanger, R.C., Narducci Sarjeant, A.A., Liable-Sands, L.M., Zhao, B., Smith, W.W., Janson, C.A., Gao, E., Tomaszek, T., McQueney, M., James, I.E., Gress, C.J., Zembryki, D.L., Lark, M.W., Veber, D.F.

(2006) J Med Chem 49: 1597-1612

  • DOI: https://doi.org/10.1021/jm050915u
  • Primary Citation of Related Structures:  
    2FTD

  • PubMed Abstract: 

    • The syntheses, in vitro characterizations, and rat and monkey in vivo pharmacokinetic profiles of a series of 5-, 6-, and 7-methyl-substituted azepanone-based cathepsin K inhibitors are described. Depending on the particular regiochemical substitution and stereochemical configuration, methyl-substituted azepanones were identified that had widely varied cathepsin K inhibitory potency as well as pharmacokinetic properties compared to the 4S-parent azepanone analogue, 1 (human cathepsin K, K(i,app) = 0 ...

    The syntheses, in vitro characterizations, and rat and monkey in vivo pharmacokinetic profiles of a series of 5-, 6-, and 7-methyl-substituted azepanone-based cathepsin K inhibitors are described. Depending on the particular regiochemical substitution and stereochemical configuration, methyl-substituted azepanones were identified that had widely varied cathepsin K inhibitory potency as well as pharmacokinetic properties compared to the 4S-parent azepanone analogue, 1 (human cathepsin K, K(i,app) = 0.16 nM, rat oral bioavailability = 42%, rat in vivo clearance = 49.2 mL/min/kg). Of particular note, the 4S-7-cis-methylazepanone analogue, 10, had a K(i,app) = 0.041 nM vs human cathepsin K and 89% oral bioavailability and an in vivo clearance rate of 19.5 mL/min/kg in the rat. Hypotheses that rationalize some of the observed characteristics of these closely related analogues have been made using X-ray crystallography and conformational analysis. These examples demonstrate the potential for modulation of pharmacological properties of cathepsin inhibitors by substituting the azepanone core. The high potency for inhibition of cathepsin K coupled with the favorable rat and monkey pharmacokinetic characteristics of compound 10, also known as SB-462795 or relacatib, has made it the subject of considerable in vivo evaluation for safety and efficacy as an inhibitor of excessive bone resorption in rat, monkey, and human studies, which will be reported elsewhere.

    Organizational Affiliation: 

    Department of Medicinal Chemistry, GlaxoSmithKline, 1250 S. Collegeville Rd, Collegeville, Pennsylvania 19426, USA. Dennis.S.Yamashita@gsk.com



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cathepsin KA, B215Macaca mulattaMutation(s): 0 
Gene Names: CTSK
EC: 3.4.22.38
UniProt
Find proteins for P61277 (Macaca mulatta)
Explore P61277 
Go to UniProtKB:  P61277
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61277
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ILI
Query on ILI
Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]		N-[(1S)-1-({[(3S,4S,7R)-3-HYDROXY-7-METHYL-1-(PYRIDIN-2-YLSULFONYL)-2,3,4,7-TETRAHYDRO-1H-AZEPIN-4-YL]AMINO}CARBONYL)-3-METHYLBUTYL]-1-BENZOFURAN-2-CARBOXAMIDE
C27 H32 N4 O6 S
IJRITYSDIWFZKF-GBAJDQEWSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
ILI PDBBind:  2FTD Ki: 0.04 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.237 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.874α = 90
b = 74.874β = 90
c = 339.555γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-01-30
    Type: Initial release
  • Version 1.1: 2008-02-06
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance