2BDL

Cathepsin K complexed with a pyrrolidine ketoamide-based inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.196 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Novel, potent P2-P3 pyrrolidine derivatives of ketoamide-based cathepsin K inhibitors.

Barrett, D.G.Catalano, J.G.Deaton, D.N.Hassell, A.M.Long, S.T.Miller, A.B.Miller, L.R.Ray, J.A.Samano, V.Shewchuk, L.M.Wells-Knecht, K.J.Willard Jr., D.H.Wright, L.L.

(2006) Bioorg Med Chem Lett 16: 1735-1739

  • DOI: https://doi.org/10.1016/j.bmcl.2005.11.101
  • Primary Citation of Related Structures:  
    2BDL

  • PubMed Abstract: 

    Starting from a potent pantolactone ketoamide cathepsin K inhibitor discovered from structural screening, conversion of the lactone scaffold to a pyrrolidine scaffold allowed exploration of the S(3) subsite of cathepsin K. Manipulation of P3 and P1' groups afforded potent inhibitors with drug-like properties.


  • Organizational Affiliation

    Department of Medicinal Chemistry, GlaxoSmithKline, Research Triangle Park, NC 27709, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cathepsin K215Homo sapiensMutation(s): 0 
Gene Names: CTSKCTSOCTSO2
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 
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
4PR
Query on 4PR

Download Ideal Coordinates CCD File 
B [auth A](3S)-1-{[(3,5-DIMETHYLISOXAZOL-4-YL)AMINO]CARBONYL}-4,4-DIMETHYLPYRROLIDIN-3-YL{(1S)-1-[1-HYDROXY-2-OXO-2-{[(1R)-1-PHENYLETHYL]AMINO}ETHYL]PENTYL}CARBAMATE
C28 H41 N5 O6
VVZICJQTDYOKIN-TYVKFHQSSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
4PR PDBBind:  2BDL IC50: 15 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.196 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.06α = 90
b = 50.338β = 90
c = 105.891γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-03-21
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-07-24
    Changes: Data collection, Derived calculations, Refinement description
  • Version 1.4: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description