2BDL

Cathepsin K complexed with a pyrrolidine ketoamide-based inhibitor

• PDB DOI: https://doi.org/10.2210/pdb2BDL/pdb

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


• Deposited: 2005-10-20 Released: 2006-03-21 
• Deposition Author(s): Shewchuk, L.M.

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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 

Starting Model: experimental

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

• PubMed: 16376075 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 24.07 kDa 
• Atom Count: 1,876 
• Modelled Residue Count: 215 
• Deposited Residue Count: 215 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cathepsin K	A	215	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 GTEx:  ENSG00000143387

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4PR	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
ID	Source	Binding 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 = 38.06	α = 90
b = 50.338	β = 90
c = 105.891	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
CNS	refinement
HKL-2000	data collection
HKL-2000	data reduction
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-03-21 
Deposition Author(s): Shewchuk, L.M.

Revision History  

• 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
• Version 1.5: 2024-11-20
  Changes: Structure summary