Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 23991.22 
• Atom Count: 1698 
• Residue Count: 213 
• Unique protein chains: 1

3OVZ

Cathepsin K in complex with a covalent inhibitor with a ketoamide warhead

• DOI: 10.2210/pdb3OVZ/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens


• Deposited: 2010-09-17 Released: 2010-12-22 
• Deposition Author(s): Fradera, X., van Zeeland, M., Uitdehaag, J.C.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free: 0.308 
• R-Value Work: 0.244 

Literature

Trifluoromethylphenyl as P2 for ketoamide-based cathepsin S inhibitors.

Cai, J., Robinson, J., Belshaw, S., Everett, K., Fradera, X., van Zeeland, M., van Berkom, L., van Rijnsbergen, P., Popplestone, L., Baugh, M., Dempster, M., Bruin, J., Hamilton, W., Kinghorn, E., Westwood, P., Kerr, J., Rankovic, Z., Arbuckle, W., Bennett, D.J., Jones, P.S., Long, C., Martin, I., Uitdehaag, J.C., Meulemans, T.

(2010) Bioorg.Med.Chem.Lett. 20: 6890-6894

• PubMed: 21030256 
• DOI: 10.1016/j.bmcl.2010.10.012
• Primary Citation of Related Structures:  
  3OVX


• PubMed Abstract: 
  

The trifluoromethylphenyl P2 motif from previously reported heteroarylnitrile series has been successfully applied for the design and synthesis of highly potent novel ketoamide-based cathepsin S inhibitors. The key in this process is the change of the torsion angle between the P2 phenyl ring and the attached secondary amide by adding a small Cl, F, or Me group at the 2-position.

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Organizational Affiliation: 

Merck Research Laboratories, MSD, Newhouse, Lanarkshire, United Kingdom. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Cathepsin K	A	213	Homo sapiens	Mutation(s): 0  Gene Names: CTSK (CTSO, CTSO2) EC: 3.4.22.38
Find proteins for P43235 (Homo sapiens) Go to Gene View: CTSK Go to UniProtKB:  P43235

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
O96	A	N-[(1S)-3-amino-1-ethyl-2,3-dioxopropyl]-2-chloro-4-(pyridin-2-ylmethoxy)-3-(trifluoromethyl)benzamide C19 H17 Cl F3 N3 O4 VMSZYKRQEOLBRN-LBPRGKRZSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
O96	IC50: 8.7 nM (100) BINDINGDB
O96	IC50: 8.7 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free: 0.308 
• R-Value Work: 0.244 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 55.741	α = 90.00
b = 55.741	β = 90.00
c = 128.916	γ = 90.00

Software Package:

Software Name	Purpose
MOLREP	phasing
d*TREK	data reduction
CrystalClear	data collection
REFMAC	refinement
d*TREK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-09-17 
• Released Date: 2010-12-22 
• Deposition Author(s): Fradera, X., van Zeeland, M., Uitdehaag, J.C.M.

Revision History 

• Version 1.0: 2010-12-22
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Version format compliance
• Version 1.2: 2011-10-12
  Type: Derived calculations
• Version 1.3: 2012-05-09
  Type: Data collection
• Version 1.4: 2018-01-31
  Type: Experimental preparation