Macromolecule Content

Total Structure Weight: 47.86 kDa
Atom Count: 3931
Residue Count: 425
Unique protein chains: 1

3KWB

Structure of CatK covalently bound to a dioxo-triazine inhibitor

DOI: 10.2210/pdb3KWB/pdb

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

Deposited: 2009-12-01 Released: 2010-04-07
Deposition Author(s): Uitdehaag, J.C.M., van Zeeland, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.02 Å
R-Value Free: 0.263
R-Value Work: 0.194
R-Value Observed: 0.202

wwPDB Validation 3D Report Full Report

This is version 1.1 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

PubMed: 20153187 Search on PubMed
DOI: 10.1016/j.bmcl.2010.01.116
Primary Citation of Related Structures:
3KWB

PubMed Abstract:

Macromolecules

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cathepsin K	X, Y	215	Homo sapiens	Mutation(s): 0 Gene Names: CTSK, CTSO, CTSO2 EC: 3.4.22.38
Find proteins for P43235 (Homo sapiens) Explore P43235 Go to UniProtKB: P43235
NIH Common Fund Data Resources
PHAROS P43235 GTEx ENSG00000143387
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ORH Query on ORH Download CCD File	X, 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		Ligand Interaction

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
ORH	IC50 : 17 nM PDBBind
ORH	IC50: 17 nM BindingDB

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.02 Å
R-Value Free: 0.263
R-Value Work: 0.194
R-Value Observed: 0.202
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.452	α = 90
b = 69.338	β = 98.83
c = 90.85	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
AMoRE	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Deposited Date: 2009-12-01
Released Date: 2010-04-07

Deposition Author(s):

Uitdehaag, J.C.M.

van Zeeland, M.

Revision History

Version 1.0: 2010-04-07
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance

RCSB PDB is funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.