4YV8

Crystal structure of cathepsin K bound to the covalent inhibitor lichostatinal


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • 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 2.1 of the entry. See complete history


Literature

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: 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 ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cathepsin KA215Homo sapiensMutation(s): 0 
Gene Names: CTSKCTSOCTSO2
EC: 3.4.22.38
UniProt & NIH Common Fund Data Resources
Find proteins for P43235 (Homo sapiens)
Explore P43235 
Go to UniProtKB:  P43235
PHAROS:  P43235
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
LichostatinalB5actinomycete 095-35Mutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A], D [auth A], E [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
RGL
Query on RGL
BL-PEPTIDE LINKINGC6 H15 N4 OARG
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_002162
Query on PRD_002162
BLichostatinalOligopeptide / Enzyme inhibitor Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report




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