3O1G

Cathepsin K covalently bound to a 2-cyano pyrimidine inhibitor with a benzyl P3 group.

• PDB DOI: https://doi.org/10.2210/pdb3O1G/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus
• Mutation(s): No 


• Deposited: 2010-07-21 Released: 2010-10-06 
• Deposition Author(s): Fradera, X., van Zeeland, M., Uitdehaag, J.C.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.198 
• R-Value Work: 0.168 
• R-Value Observed: 0.170 

Starting Model: other

Literature

Optimisation of 2-cyano-pyrimidine inhibitors of cathepsin K: improving selectivity over hERG.

Rankovic, Z., Cai, J., Kerr, J., Fradera, X., Robinson, J., Mistry, A., Finlay, W., McGarry, G., Andrews, F., Caulfield, W., Cumming, I., Dempster, M., Waller, J., Arbuckle, W., Anderson, M., Martin, I., Mitchell, A., Long, C., Baugh, M., Westwood, P., Kinghorn, E., Jones, P., Uitdehaag, J.C., van Zeeland, M., Potin, D., Saniere, L., Fouquet, A., Chevallier, F., Deronzier, H., Dorleans, C., Nicolai, E.

(2010) Bioorg Med Chem Lett 20: 6237-6241

• PubMed: 20843687 
• DOI: https://doi.org/10.1016/j.bmcl.2010.08.101
• Primary Citation of Related Structures:  
  3O0U, 3O1G


• PubMed Abstract: 
  

  Several structure-guided optimisation strategies were explored in order to improve the hERG selectivity profile of cathepsin K inhibitor 1, whilst maintaining its otherwise excellent in vitro and in vivo profile. Ultimately, attenuation of clogP and pK(a) properties proved a successful approach and led to the discovery of a potent analogue 23, which, in addition to the desired selectivity over hERG (>1000-fold), displayed a highly attractive overall profile.

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Organizational Affiliation: 

Merck Research Laboratories, MSD, Newhouse, Lanarkshire, ML1 5SH Scotland, United Kingdom. [e-mail]

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: 24.21 kDa 
• Atom Count: 1,953 
• Modelled 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
O75	D [auth A]	N-benzyl-3-(2-cyano-6-propylpyrimidin-4-yl)-N-[2-(dimethylamino)ethyl]-5-(trifluoromethyl)benzamide C27 H28 F3 N5 O AGGVJWZHDDIPAU-UHFFFAOYSA-N
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
O75	PDBBind:  3O1G	IC50: 1 (nM) from 1 assay(s)
	BindingDB:  3O1G	IC50: 1 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.198 
• R-Value Work: 0.168 
• R-Value Observed: 0.170 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.504	α = 90
b = 62.504	β = 90
c = 113.478	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
MOLREP	phasing
REFMAC	refinement
CrystalClear	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-10-06 
Deposition Author(s): Fradera, X., van Zeeland, M., Uitdehaag, J.C.M.

Revision History  

• Version 1.0: 2010-10-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-04-03
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-11-06
  Changes: Structure summary