6HGY

CRYSTAL STRUCTURE OF CATHEPSIN K WITH N-DESMETHYL THALASSOSPIRAMIDE C

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.256 

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Literature

Total Synthesis of Covalent Cysteine Protease Inhibitor N-Desmethyl Thalassospiramide C and Crystallographic Evidence for Its Mode of Action.

Fournier, J., Chen, K., Mailyan, A.K., Jackson, J.J., Buckman, B.O., Emayan, K., Yuan, S., Rajagopalan, R., Misialek, S., Adler, M., Blaesse, M., Griessner, A., Zakarian, A.

(2019) Org Lett 21: 508-512

  • DOI: https://doi.org/10.1021/acs.orglett.8b03821
  • Primary Citation of Related Structures:  
    6HGY

  • PubMed Abstract: 

    • A total synthesis of N-desmethyl thalassospiramide C, a unique strained macrocyclic proteobacterial depsipeptide, enabled a detailed crystallographic study of its covalent complex with cathepsin K, a member of a medicinally important family of cysteine proteases ...

    A total synthesis of N-desmethyl thalassospiramide C, a unique strained macrocyclic proteobacterial depsipeptide, enabled a detailed crystallographic study of its covalent complex with cathepsin K, a member of a medicinally important family of cysteine proteases. The study provides support for the mechanism of action, and the insight gained can be used for structure-based drug design targeting these calpain proteases.

    Organizational Affiliation: 

    Department of Chemistry and Biochemistry , University of California , Santa Barbara , California 93111 , United States.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cathepsin KA215Homo sapiensMutation(s): 0 
Gene Names: CTSK, CTSO, CTSO2
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43235
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
G4B (Subject of Investigation/LOI)
Query on G4B
Download Ideal Coordinates CCD File 
B [auth A]THALASSOSPIRAMIDE C
C43 H61 N5 O9
VEICWPPPDFDHMQ-GMWCJVCTSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.256 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.56α = 90
b = 44.884β = 115.91
c = 49.99γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-26
    Type: Initial release