2F7D | pdb_00002f7d

A mutant rabbit cathepsin K with a nitrile inhibitor

• PDB DOI: https://doi.org/10.2210/pdb2F7D/pdb

• Classification: HYDROLASE
• Organism(s): Oryctolagus cuniculus
• Expression System: Komagataella pastoris
• Mutation(s): Yes 


• Deposited: 2005-11-30 Released: 2006-03-07 
• Deposition Author(s): Somoza, J.R.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.205 (Depositor), 0.205 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.174 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Literature

Beta-substituted cyclohexanecarboxamide: a nonpeptidic framework for the design of potent inhibitors of cathepsin K.

Crane, S.N., Black, W.C., Palmer, J.T., Davis, D.E., Setti, E., Robichaud, J., Paquet, J., Oballa, R.M., Bayly, C.I., McKay, D.J., Somoza, J.R., Chauret, N., Seto, C., Scheigetz, J., Wesolowski, G., Masse, F., Desmarais, S., Ouellet, M.

(2006) J Med Chem 49: 1066-1079

• PubMed: 16451072 
• DOI: https://doi.org/10.1021/jm051059p
• Primary Citation Related Structures: 
  2F7D


• PubMed Abstract: 
  

  A new series of nonpeptidic cathepsin K inhibitors that are based on a beta-substituted cyclohexanecarboxamide motif has been developed. Lead optimization yielded compounds with sub-nanomolar potency and exceptional selectivity profiles against cathepsins B, L, and S. Use of fluorine atoms to block metabolism on the cyclohexyl ring led to compounds with excellent pharmacokinetic properties. Considering the well-established role of cathepsin K in osteoclast-mediated bone turnover, compounds such as (-)-34a (hrab Cat K IC(50) 0.28 nM; >800-fold selectivity vs Cat B, L, and S; PK data in dogs: F 55%, t(1/2) = 15 h) exhibit great potential for development as an orally bioavailable therapeutic for treatment of diseases that involve bone loss.

---

Organizational Affiliation: 
• Merck Frosst Centre for Therapeutic Research, 16711 TransCanada Highway, Kirkland, Quebec, Canada, H9H 3L1. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 23.91 kDa 
• Atom Count: 1,772 
• 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	Oryctolagus cuniculus	Mutation(s): 2  Gene Names: CTSK EC: 3.4.22.38
UniProt
Find proteins for P43236 (Oryctolagus cuniculus) Explore P43236  Go to UniProtKB:  P43236

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NOQ	B [auth A]	(1R,2R)-N-(2-AMINOETHYL)-2-{[(4-METHOXYPHENYL)SULFONYL]METHYL}CYCLOHEXANECARBOXAMIDE C17 H26 N2 O4 S QTGNVZPFJQOWFL-XJKSGUPXSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.205 (Depositor), 0.205 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.174 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.125	α = 90
b = 51.15	β = 90
c = 104.245	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-03-07 
Deposition Author(s): Somoza, J.R.

Revision History  

• Version 1.0: 2006-03-07
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-18
  Changes: Advisory, Refinement description
• Version 1.4: 2021-10-20
  Changes: Advisory, Database references, Derived calculations
• Version 1.5: 2024-11-06
  Changes: Data collection, Structure summary