1TU6

Cathepsin K complexed with a ketoamide inhibitor

• PDB DOI: https://doi.org/10.2210/pdb1TU6/pdb

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


• Deposited: 2004-06-24 Released: 2004-09-21 
• Deposition Author(s): Barrett, D.G., Catalano, J.G., Deaton, D.N., Hassell, A.M., Long, S.T., Miller, A.B., Miller, L.R., Shewchuk, L.M., Wells-Knecht, K.J., Wright, L.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.214 
• R-Value Work: 0.190 
• R-Value Observed: 0.190 

Starting Model: experimental

Literature

Potent and selective P2-P3 ketoamide inhibitors of cathepsin K with improved pharmacokinetic properties via favorable P1', P1, and/or P3 substitutions

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

(2004) Bioorg Med Chem Lett 14: 4897-4902

• PubMed: 15341947 
• DOI: https://doi.org/10.1016/j.bmcl.2004.07.031
• Primary Citation of Related Structures:  
  1TU6


• PubMed Abstract: 
  

  A series of ketoamides were synthesized and evaluated for inhibitory activity against cathepsin K. Exploration of the interactions between achiral P(2) substituents and the cysteine protease based on molecular modelling suggestions resulted in potent cathepsin K inhibitors that demonstrated high selectivity versus cathepsins B, H, and L. Subsequent modifications of the P(3), P(1), and P(1') moieties afforded orally bioavailable inhibitors.

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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: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 48.22 kDa 
• Atom Count: 3,751 
• Modelled Residue Count: 430 
• Deposited Residue Count: 430 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cathepsin K	A, B	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FSP	E [auth A], G [auth B]	[1-(4-FLUOROBENZYL)CYCLOBUTYL]METHYL (1S)-1-[OXO(1H-PYRAZOL-5-YLAMINO)ACETYL]PENTYLCARBAMATE C23 H29 F N4 O4 QTPYRNAKLBXKNP-SFHVURJKSA-N
SO4	C [auth A], D [auth A], F [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
FSP	PDBBind:  1TU6	IC50: 0.83 (nM) from 1 assay(s)
	BindingDB:  1TU6	IC50: min: 0.83, max: 0.83 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.214 
• R-Value Work: 0.190 
• R-Value Observed: 0.190 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.179	α = 90
b = 66.776	β = 90
c = 107.708	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-09-21 
Deposition Author(s): Barrett, D.G., Catalano, J.G., Deaton, D.N., Hassell, A.M., Long, S.T., Miller, A.B., Miller, L.R., Shewchuk, L.M., Wells-Knecht, K.J., Wright, L.L.

Revision History  

• Version 1.0: 2004-09-21
  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: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description