Crystal structure of cathepsin K bound to the covalent inhibitor lichostatinal

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 

wwPDB Validation   3D Report Full Report

This is version 2.3 of the entry. See complete history


Affinity Crystallography: A New Approach to Extracting High-Affinity Enzyme Inhibitors from Natural Extracts.

Aguda, A.H.Lavallee, V.Cheng, P.Bott, T.M.Meimetis, L.G.Law, S.Nguyen, N.T.Williams, D.E.Kaleta, J.Villanueva, I.Davies, J.Andersen, R.J.Brayer, G.D.Bromme, D.

(2016) J Nat Prod 79: 1962-1970

  • DOI: https://doi.org/10.1021/acs.jnatprod.6b00215
  • Primary Citation of Related Structures:  
    4YV8, 4YVA

  • PubMed Abstract: 

    Natural products are an important source of novel drug scaffolds. The highly variable and unpredictable timelines associated with isolating novel compounds and elucidating their structures have led to the demise of exploring natural product extract libraries in drug discovery programs. Here we introduce affinity crystallography as a new methodology that significantly shortens the time of the hit to active structure cycle in bioactive natural product discovery research. This affinity crystallography approach is illustrated by using semipure fractions of an actinomycetes culture extract to isolate and identify a cathepsin K inhibitor and to compare the outcome with the traditional assay-guided purification/structural analysis approach. The traditional approach resulted in the identification of the known inhibitor antipain (1) and its new but lower potency dehydration product 2, while the affinity crystallography approach led to the identification of a new high-affinity inhibitor named lichostatinal (3). The structure and potency of lichostatinal (3) was verified by total synthesis and kinetic characterization. To the best of our knowledge, this is the first example of isolating and characterizing a potent enzyme inhibitor from a partially purified crude natural product extract using a protein crystallographic approach.

  • Organizational Affiliation

    Department of Oral Biological and Medical Sciences, Faculty of Dentistry, ‡Department of Biochemistry and Molecular Biology, Faculty of Medicine, §Department of Chemistry and Earth, Ocean & Atmospheric Sciences, Faculty of Science, ⊥Department of Microbiology, Faculty of Science, and ∥Centre for Blood Research, University of British Columbia , Vancouver, BC Canada , V6T 1Z3.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cathepsin K215Homo 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

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Lichostatinal5actinomycete 095-35Mutation(s): 0 
Sequence Annotations
  • Reference Sequence
Small Molecules
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.717α = 90
b = 56.717β = 90
c = 130.365γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)CanadaFRN 111082

Revision History  (Full details and data files)

  • Version 1.0: 2016-05-04
    Type: Initial release
  • Version 1.1: 2016-08-24
    Changes: Database references
  • Version 1.2: 2016-09-07
    Changes: Database references
  • Version 1.3: 2017-09-27
    Changes: Data collection, Derived calculations
  • Version 2.0: 2019-05-15
    Changes: Data collection, Polymer sequence
  • Version 2.1: 2020-01-08
    Changes: Author supporting evidence
  • Version 2.2: 2023-09-27
    Changes: Data collection, Database references, Refinement description
  • Version 2.3: 2023-11-15
    Changes: Data collection