3OVZ | pdb_00003ovz

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

• PDB DOI: https://doi.org/10.2210/pdb3OVZ/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens
• Mutation(s): No 


• 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 (Depositor), 0.300 (DCC) 
• R-Value Work: 
  0.244 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.247 (Depositor) 

Starting Model: other

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: https://doi.org/10.1016/j.bmcl.2010.10.012
• Primary Citation of Related Structures:  
  3OVX, 3OVZ


• 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]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 23.99 kDa 
• Atom Count: 1,777 
• Modeled Residue Count: 213 
• Deposited Residue Count: 213 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cathepsin K	A	213	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
O96	B [auth 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
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
O96	BindingDB:  3OVZ	IC50: 8.7 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free:  0.308 (Depositor), 0.300 (DCC) 
• R-Value Work:  0.244 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.247 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.741	α = 90
b = 55.741	β = 90
c = 128.916	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• 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
  Changes: Version format compliance
• Version 1.2: 2011-10-12
  Changes: Derived calculations
• Version 1.3: 2012-05-09
  Changes: Data collection
• Version 1.4: 2018-01-31
  Changes: Experimental preparation
• Version 1.5: 2024-04-03
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.6: 2024-10-16
  Changes: Structure summary