1U9V

Crystal Structure of the Cysteine Protease Human Cathepsin K in Complex with the Covalent Inhibitor NVP-ABE854

• PDB DOI:  https://doi.org/10.2210/pdb1U9V/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2004-08-11 Released: 2005-08-11 
• Deposition Author(s): Cowan-Jacob, S.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.231 
• R-Value Work: 0.170 
• R-Value Observed: 0.170 

Literature

Novel purine nitrile derived inhibitors of the cysteine protease cathepsin K

Altmann, E., Cowan-Jacob, S.W., Missbach, M.

(2004) J Med Chem 47: 5833-5836

• PubMed: 15537340 
• DOI: https://doi.org/10.1021/jm0493111
• Primary Citation of Related Structures:  
  1U9V, 1U9W, 1U9X


• PubMed Abstract: 
  

  Starting from the high-throughput screening hit 1a, novel cathepsin K inhibitors have been developed based on a purine scaffold. High-resolution X-ray structures of several derivatives have revealed the binding mode of these unique cysteine protease inhibitors.

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Organizational Affiliation: 

Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 24.11 kDa 
• Atom Count: 1,739 
• Modelled Residue Count: 215 
• Deposited Residue Count: 217 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cathepsin K	A	217	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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IHE	B [auth A]	6-(CYCLOHEXYLAMINO)-9-[2-(4-METHYLPIPERAZIN-1-YL)-ETHYL]-9H-PURINE-2-CARBONITRILE C19 H28 N8 OGODDSLNRULSMM-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
IHE	PDBBind:  1U9V	IC50: 6 (nM) from 1 assay(s)
	BindingDB:  1U9V	IC50: 6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.231 
• R-Value Work: 0.170 
• R-Value Observed: 0.170 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.2	α = 90
b = 63.2	β = 90
c = 113.8	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
AUTOMAR	data reduction
AMoRE	phasing
X-PLOR	refinement
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-08-11 
Deposition Author(s): Cowan-Jacob, S.W.

Revision History  

• Version 1.0: 2005-08-11
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description