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⇱ RCSB PDB - 3O1G: Cathepsin K covalently bound to a 2-cyano pyrimidine inhibitor with a benzyl P3 group.

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Structures from the PDB archive		1,062,058
Computed Structure Models (CSM)

 3O1G | pdb_00003o1g

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 
    0.198 (Depositor), 0.208 (DCC) 
  • R-Value Work: 
    0.168 (Depositor), 0.175 (DCC) 
  • R-Value Observed: 
    0.170 (Depositor) 

Starting Model: other
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wwPDB Validation3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history. 

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

  • DOI: https://doi.org/10.1016/j.bmcl.2010.08.101
  • Primary Citation 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.

    • Organizational Affiliation: 
    • Merck Research Laboratories, MSD, Newhouse, Lanarkshire, ML1 5SH Scotland, United Kingdom. zoran.rankovic@merck.com

Macromolecule Content 

  • Total Structure Weight: 24.21 kDa 
  • Atom Count: 1,953 
  • Modeled Residue Count: 215 
  • Deposited Residue Count: 215 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cathepsin K215Homo sapiensMutation(s): 0 
Gene Names: CTSK, CTSO, CTSO2
EC: 3.4.22.38
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UniProt & NIH Common Fund Data Resources
Find proteins for P43235 (Homo sapiens)
Explore P43235 
Go to UniProtKB:  P43235
PHAROS:  P43235
GTEx:  ENSG00000143387 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43235
Sequence Annotations
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Reference Sequence

Small Molecules

Binding Affinity Annotations 
IDSourceBinding Affinity
O75 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 (Depositor), 0.208 (DCC) 
  • R-Value Work:  0.168 (Depositor), 0.175 (DCC) 
  • R-Value Observed: 0.170 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.504α = 90
b = 62.504β = 90
c = 113.478γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
MOLREPphasing
REFMACrefinement
CrystalCleardata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.