1NLJ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.263 
  • R-Value Observed: 0.263 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Azepanone-Based Inhibitors of Human and Rat Cathepsin K

Marquis, R.W.Ru, Y.LoCastro, S.M.Zeng, J.Yamashita, D.S.Oh, H.J.Erhard, K.F.Davis, L.D.Tomaszek, T.A.Tew, D.Salyers, K.Proksch, J.Ward, K.Smith, B.Levy, M.Cummings, M.D.Haltiwanger, R.C.Trescher, G.Wang, B.Hemling, M.E.Quinn, C.J.Cheng, H.-Y.Lin, F.Smith, W.W.Janson, C.A.Zhao, B.McQueney, M.S.D'Alessio, K.Lee, C.P.Marzulli, A.Dodds, R.A.Blake, S.Hwang, S.M.James, I.E.Gress, C.J.Bradley, B.R.Lark, M.W.Gowen, M.Veber, D.F.

(2001) J Med Chem 44: 1380-1395

  • DOI: 10.1021/jm000481x
  • Primary Citation of Related Structures:  
    1NLJ, 1NL6

  • PubMed Abstract: 
  • The synthesis, in vitro activities, and pharmacokinetics of a series of azepanone-based inhibitors of the cysteine protease cathepsin K (EC 3.4.22.38) are described. These compounds show improved configurational stability of the C-4 diastereomeric ce ...

    The synthesis, in vitro activities, and pharmacokinetics of a series of azepanone-based inhibitors of the cysteine protease cathepsin K (EC 3.4.22.38) are described. These compounds show improved configurational stability of the C-4 diastereomeric center relative to the previously published five- and six-membered ring ketone-based inhibitor series. Studies in this series have led to the identification of 20, a potent, selective inhibitor of human cathepsin K (K(i) = 0.16 nM) as well as 24, a potent inhibitor of both human (K(i) = 0.0048 nM) and rat (K(i,app) = 4.8 nM) cathepsin K. Small-molecule X-ray crystallographic analysis of 20 established the C-4 S stereochemistry as being critical for potent inhibition and that unbound 20 adopted the expected equatorial conformation for the C-4 substituent. Molecular modeling studies predicted the higher energy axial orientation at C-4 of 20 when bound within the active site of cathepsin K, a feature subsequently confirmed by X-ray crystallography. Pharmacokinetic studies in the rat show 20 to be 42% orally bioavailable. Comparison of the transport of the cyclic and acyclic analogues through CaCo-2 cells suggests that oral bioavailability of the acyclic derivatives is limited by a P-glycoprotein-mediated efflux mechanism. It is concluded that the introduction of a conformational constraint has served the dual purpose of increasing inhibitor potency by locking in a bioactive conformation as well as locking out available conformations which may serve as substrates for enzyme systems that limit oral bioavailability.


    Organizational Affiliation

    Department of Medicinal Chemistry, GlaxoSmithKline, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, USA. robert_w_marquis@sbphrd.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CATHEPSIN KAB215Homo 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
2CA
Query on 2CA

Download CCD File 
A, B
BENZOFURAN-2-CARBOXYLIC ACID {(S)-3-METHYL-1-[3-OXO-1-(PYRIDIN-2-YLSULFONYL)AZEPAN-4-YLCARBAMOYL]BUTYL}AMIDE
C26 H30 N4 O6 S
VBPPNJCVXGAZDD-PMACEKPBSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
2CAIC50:  70   nM  BindingDB
2CAIC50:  80   nM  BindingDB
2CAKi :  0.1599999964237213   nM  PDBBind
2CAKi:  60   nM  BindingDB
2CAKi:  0.1599999964237213   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.263 
  • R-Value Observed: 0.263 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.96α = 90
b = 100.96β = 90
c = 53.694γ = 90
Software Package:
Software NamePurpose
MAR345data collection
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-01-14
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description