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

Experimental Data Snapshot

  • Resolution: 2.80 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.246 

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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

  • DOI: https://doi.org/10.1021/jm000481x
  • Primary Citation of Related Structures:  
    1NL6, 1NLJ

  • PubMed Abstract: 

    The synthesis, in vitro activities, and pharmacokinetics of a series of azepanone-based inhibitors of the cysteine protease cathepsin K (EC 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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cathepsin K
A, B
215Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P43235 (Homo sapiens)
Explore P43235 
Go to UniProtKB:  P43235
PHAROS:  P43235
GTEx:  ENSG00000143387 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43235
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 750

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C40 H47 N5 O7
Binding Affinity Annotations 
IDSourceBinding Affinity
750 PDBBind:  1NL6 Ki: 4.80e-3 (nM) from 1 assay(s)
BindingDB:  1NL6 Ki: min: 4.80e-3, max: 4.8 (nM) from 2 assay(s)
IC50: 30 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.80 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.246 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.816α = 90
b = 75.888β = 90
c = 114.841γ = 90
Software Package:
Software NamePurpose
MAR345data collection
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.4: 2023-08-16
    Changes: Data collection, Database references, Derived calculations, Refinement description