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URL: https://www.rcsb.org/structure/3KW9

⇱ RCSB PDB - 3KW9: X-ray structure of Cathepsin K covalently bound to a triazine ligand

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

 3KW9 | pdb_00003kw9

X-ray structure of Cathepsin K covalently bound to a triazine ligand

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.259 (Depositor), 0.247 (DCC) 
  • R-Value Work: 
    0.230 (Depositor) 
  • R-Value Observed: 
    0.233 (Depositor) 

wwPDB Validation3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history. 

Literature

Design and optimization of a series of novel 2-cyano-pyrimidines as cathepsin K inhibitors.

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

(2010) Bioorg Med Chem Lett 20: 1524-1527

  • DOI: https://doi.org/10.1016/j.bmcl.2010.01.100
  • Primary Citation Related Structures: 
    3KW9, 3KWZ, 3KX1

  • PubMed Abstract: 

    Morphing structural features of HTS-derived chemotypes led to the discovery of novel 2-cyano-pyrimidine inhibitors of cathepsin K with good pharmacokinetic profiles, for example, compound 20 showed high catK potency (IC(50)=4nM), >580-fold selectivity over catL and catB, and oral bioavailability in the rat of 52%.

    • Organizational Affiliation: 
    • Schering-Plough Corporation, Newhouse, Lanarkshire, ML1 5SH Scotland, United Kingdom. zoran.rankovic@spcorp.com

Macromolecule Content 

  • Total Structure Weight: 23.92 kDa 
  • Atom Count: 1,771 
  • 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
👁 Image
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
Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ORG

Query on ORG


Download:Ideal Coordinates CCD File
B [auth A]4-(cyclohexylamino)-6-piperazin-1-yl-1,3,5-triazine-2-carbonitrile
C14 H21 N7
ZBLLHXCRPWKVCY-UHFFFAOYSA-N		👁 Image
TFA

Query on TFA


Download:Ideal Coordinates CCD File
C [auth A]trifluoroacetic acid
C2 H F3 O2
DTQVDTLACAAQTR-UHFFFAOYSA-N		👁 Image
Binding Affinity Annotations 
IDSourceBinding Affinity
ORG BindingDB:  3KW9 IC50: 1 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.259 (Depositor), 0.247 (DCC) 
  • R-Value Work:  0.230 (Depositor) 
  • R-Value Observed: 0.233 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.391α = 90
b = 55.391β = 90
c = 128.719γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
CNSphasing

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: 2010-03-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2013-06-19
    Changes: Database references
  • Version 1.3: 2017-11-01
    Changes: Refinement description
  • Version 1.4: 2024-11-06
    Changes: Data collection, Database references, Derived calculations, 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.