1NL6

Crystal Structure Of The Cysteine Protease Human Cathepsin K In Complex With A Covalent Azepanone Inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.246 

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.A Dodds, R.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

  • Primary Citation of Related Structures:  1NLJ

  • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cathepsin K
A, B
215Homo sapiensGene Names: CTSK (CTSO, CTSO2)
EC: 3.4.22.38
Find proteins for P43235 (Homo sapiens)
Go to Gene View: CTSK
Go to UniProtKB:  P43235
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
750
Query on 750

Download SDF File 
Download CCD File 
A, B
5-(2-MORPHOLIN-4-YLETHOXY)BENZOFURAN-2-CARBOXYLIC ACID ((S)-3-METHYL-1-{(S)-3-OXO-1-[2-(3-PYRIDIN-2-YLPHENYL)ACETYL]AZEPAN-4-YLCARBAMOYL}BUTYL)AMIDE
C40 H47 N5 O7
KRMYDWCAHQJBOD-HEVIKAOCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
750IC50: 30 nM (100) BINDINGDB
750Ki: 0 - 4.8 nM (100) BINDINGDB
750Ki: 0.0048 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.246 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 71.816α = 90.00
b = 75.888β = 90.00
c = 114.841γ = 90.00
Software Package:
Software NamePurpose
MAR345data collection
CNSrefinement
CNSphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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