1U9X | pdb_00001u9x

Crystal Structure of the Cysteine Protease Human Cathepsin K in Complex with the Covalent Inhibitor NVP-ABJ688

• PDB DOI: https://doi.org/10.2210/pdb1U9X/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: 2.10 Å
• R-Value Free: 
  0.217 (Depositor), 0.217 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.174 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

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 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: 24.2 kDa 
• Atom Count: 1,784 
• Modeled Residue Count: 216 
• 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  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 GTEx:  ENSG00000143387

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IHJ	B [auth A]	9-CYCLOPENTYL-6-{2-[3-(4-METHYL-PIPERAZIN-1-YL)-PROPOXY]-PHENYLAMINO}-9H-PURINE-2-CARBONITRILE C25 H32 N8 O VWGLHPDSAYQVRM-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
IHJ	BindingDB:  1U9X	IC50: 7 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.217 (Depositor), 0.217 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.174 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.5	α = 90
b = 63.5	β = 90
c = 116.2	γ = 90

Software Package:

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

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: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary