Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 23.52 kDa 
• Atom Count: 1,917 
• Modelled Residue Count: 215 
• Deposited Residue Count: 215 
• Unique protein chains: 1

 1VSN

Crystal structure of a potent small molecule inhibitor bound to cathepsin K

• PDB DOI:  https://doi.org/10.2210/pdb1VSN/pdb
• Entry: 1VSN supersedes: 2FDZ

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2007-03-19 Released: 2007-04-24 
• Deposition Author(s): McGrath, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.209 
• R-Value Work: 0.171 
• R-Value Observed: 0.212 

Literature

Identification of a potent and selective non-basic cathepsin K inhibitor.

Li, C.S., Deschenes, D., Desmarais, S., Falgueyret, J.P., Gauthier, J.Y., Kimmel, D.B., McGrath, M.E., McKay, D.J., Percival, M.D., Riendeau, D., Rodan, S.B., Truong, V.L., Wesolowski, G., Zamboni, R., Black, W.C.

(2006) Bioorg Med Chem Lett 16: 1985-1989

• PubMed: 16413777 
• DOI: https://doi.org/10.1016/j.bmcl.2005.12.071
• Primary Citation of Related Structures:  
  1VSN


• PubMed Abstract: 
  

Based on our previous study with trifluoroethylamine as a P2-P3 amide isostere of cathepsin K inhibitor, further optimization led to identification of compound 22 (L-873724) as a potent and selective non-basic cathepsin K inhibitor. This compound showed excellent pharmacokinetics and efficacy in an ovariectomized (OVX) rhesus monkey model. The volumes of distribution close to unity were consistent with this compound not being lysosomotropic, which is a characteristic of basic cathepsin K inhibitors.

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Organizational Affiliation: 

Merck Frosst Centre for Therapeutic Research, PO Box 1005, Pointe-Claire-Dorval, Que., Canada H9R 4P8. [e-mail]

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NFT	B [auth A]	N-(2-AMINOETHYL)-N~2~-{(1S)-1-[4'-(AMINOSULFONYL)BIPHENYL-4-YL]-2,2,2-TRIFLUOROETHYL}-L-LEUCINAMIDE C22 H29 F3 N4 O3 S QPXXBNKMAHUXBB-PMACEKPBSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
NFT	PDBBind:  1VSN	IC50: 0.2 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.209 
• R-Value Work: 0.171 
• R-Value Observed: 0.212 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.42	α = 90
b = 51	β = 90
c = 104.2	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
REFMAC	refinement
PDB_EXTRACT	data extraction
bioteX	data reduction
XTALVIEW	refinement
d*TREK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-04-24 
Deposition Author(s): McGrath, M.
• This entry supersedes: 2FDZ

Revision History  

• Version 1.0: 2007-04-24
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-04
  Changes: Refinement description
• Version 1.4: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description