6HGY | pdb_00006hgy

CRYSTAL STRUCTURE OF CATHEPSIN K WITH N-DESMETHYL THALASSOSPIRAMIDE C

• PDB DOI: https://doi.org/10.2210/pdb6HGY/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-08-23 Released: 2019-06-26 
• Deposition Author(s): Zakarian, A., Buckman, B.O., Adler, M., Griessner, A., Blaesse, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.310 (Depositor), 0.318 (DCC) 
• R-Value Work: 
  0.250 (Depositor), 0.254 (DCC) 
• R-Value Observed: 
  0.256 (Depositor) 

Starting Model: experimental

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

• PubMed: 30628449 
• DOI: https://doi.org/10.1021/acs.orglett.8b03821
• Primary Citation 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. 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.

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Organizational Affiliation: 
• Department of Chemistry and Biochemistry , University of California , Santa Barbara , California 93111 , United States.
Blade Therapeutics , 442 Littlefield Avenue , South San Francisco , California 94080 , United States.
Bayside Pharma , 2600 Hilltop Drive , Richmond , California 94806 , United States.
ChemPartner , 280 Utah Avenue Suite 100 , South San Francisco , California 94080 , United States.
Proteros Biostructures GmbH , Bunsenstraße 7 a , 82152 Planegg-Martinsried , Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 24.32 kDa 
• Atom Count: 1,733 
• Modeled Residue Count: 215 
• Deposited Residue Count: 215 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cathepsin K	A	215	Homo sapiens	Mutation(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 GTEx:  ENSG00000143387

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
G4B (Subject of Investigation/LOI)	B [auth A]	THALASSOSPIRAMIDE C C43 H61 N5 O9 VEICWPPPDFDHMQ-GMWCJVCTSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.310 (Depositor), 0.318 (DCC) 
• R-Value Work:  0.250 (Depositor), 0.254 (DCC) 
• R-Value Observed: 0.256 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.56	α = 90
b = 44.884	β = 115.91
c = 49.99	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-06-26 
Deposition Author(s): Zakarian, A., Buckman, B.O., Adler, M., Griessner, A., Blaesse, M.

Revision History  

• Version 1.0: 2019-06-26
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Advisory, Data collection, Database references, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary