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⇱ RCSB PDB - 3KWB: Structure of CatK covalently bound to a dioxo-triazine inhibitor

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

 3KWB | pdb_00003kwb

Structure of CatK covalently bound to a dioxo-triazine inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 
    0.263 (Depositor), 0.196 (DCC) 
  • R-Value Work: 
    0.194 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 
    0.202 (Depositor) 

wwPDB Validation3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 

Literature

Dioxo-triazines as a novel series of cathepsin K inhibitors

Rankovic, Z., Cai, J., Fradera, X., Dempster, M., Mistry, A., Mitchell, A., Long, C., Hamilton, E., King, A., Boucharens, S., Jamieson, C., Gillespie, J., Cumming, I., Uitdehaag, J., van Zeeland, M.

(2010) Bioorg Med Chem Lett 20: 1488-1490

  • DOI: https://doi.org/10.1016/j.bmcl.2010.01.116
  • Primary Citation Related Structures: 
    3KWB

  • PubMed Abstract: 

    A novel dioxo-triazine series of cathepsin K inhibitors was identified from HTS. A rapid exploratory programme led to the discovery of potent and selective cathepsin K inhibitors, typified by compound 24 which displayed IC(50) values of 17nM against catK and >10,000nM in catL, catB and catS assays.

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

Macromolecule Content 

  • Total Structure Weight: 47.86 kDa 
  • Atom Count: 3,931 
  • Modeled Residue Count: 425 
  • Deposited Residue Count: 430 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cathepsin KA [auth X],
B [auth Y]		215Homo 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 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ORH

Query on ORH


Download:Ideal Coordinates CCD File
C [auth X],
D [auth Y]		3,5-dioxo-4-(3-piperidin-1-ylpropyl)-2-[3-(trifluoromethyl)phenyl]-2,3,4,5-tetrahydro-1,2,4-triazine-6-carbonitrile
C19 H20 F3 N5 O2
HKAVWQNLXOMWLR-UHFFFAOYSA-N		👁 Image
Binding Affinity Annotations 
IDSourceBinding Affinity
ORH BindingDB:  3KWB IC50: 17 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free:  0.263 (Depositor), 0.196 (DCC) 
  • R-Value Work:  0.194 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 0.202 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 31.452α = 90
b = 69.338β = 98.83
c = 90.85γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
AMoREphasing

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: 2010-04-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 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.