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URL: https://www.rcsb.org/structure/1U9X

⇱ RCSB PDB - 1U9X: Crystal Structure of the Cysteine Protease Human Cathepsin K in Complex with the Covalent Inhibitor NVP-ABJ688

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

 1U9X | pdb_00001u9x

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

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) 

wwPDB Validation3D Report Full Report


Ligand Structure Quality Assessment 


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

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

  • 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.

    • Organizational Affiliation: 
    • Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland. eva.altmann@pharma.novartis.com

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

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cathepsin K217Homo sapiensMutation(s): 0 
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
IHJ

Query on IHJ


Download:Ideal Coordinates CCD File
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		👁 Image
Binding Affinity Annotations 
IDSourceBinding 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 = 63.5α = 90
b = 63.5β = 90
c = 116.2γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
AUTOMARdata reduction
X-PLORmodel building
X-PLORrefinement
XDSdata reduction
X-PLORphasing

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: 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

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.