1Q6K

Cathepsin K complexed with t-butyl(1S)-1-cyclohexyl-2-oxoethylcarbamate

• PDB DOI: https://doi.org/10.2210/pdb1Q6K/pdb

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


• Deposited: 2003-08-13 Released: 2004-03-16 
• Deposition Author(s): Catalano, J.G., Deaton, D.N., Furfine, E.S., Hassell, A.M., McFadyen, R.B., Miller, A.B., Miller, L.R., Shewchuk, L.M., Willard, D.H., Wright, L.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Observed: 0.200 

Starting Model: experimental

Literature

Exploration of the P1 SAR of aldehyde cathepsin K inhibitors

Catalano, J.G., Deaton, D.N., Furfine, E.S., Hassell, A.M., McFadyen, R.B., Miller, A.B., Miller, L.R., Shewchuk, L.M., Willard, D.H., Wright, L.L.

(2004) Bioorg Med Chem Lett 14: 275-278

• PubMed: 14684342 
• DOI: https://doi.org/10.1016/j.bmcl.2003.09.088
• Primary Citation of Related Structures:  
  1Q6K


• PubMed Abstract: 
  

  The synthesis and biological activity of a series of aldehyde inhibitors of cathepsin K are reported. Exploration of the properties of the S(1) subsite with a series of alpha-amino aldehyde derivatives substituted at the P(1) position afforded compounds with cathepsin K IC(50)s between 52 microM and 15 nM.

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Organizational Affiliation: 

Department of Medicinal Chemistry, GlaxoSmithKline, Five Moore Drive, Research Triangle Park, NC 27709-3398, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 23.86 kDa 
• Atom Count: 1,813 
• 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 OR CTSO 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
TCO	C [auth A]	TERT-BUTYL(1S)-1-CYCLOHEXYL-2-OXOETHYLCARBAMATE C13 H23 N O3 BDSGOSWEKUGHOV-LLVKDONJSA-N
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
TCO	BindingDB:  1Q6K	IC50: 26 (nM) from 1 assay(s)
	PDBBind:  1Q6K	IC50: 26 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Observed: 0.200 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.443	α = 90
b = 56.443	β = 90
c = 130.212	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-03-16 
Deposition Author(s): Catalano, J.G., Deaton, D.N., Furfine, E.S., Hassell, A.M., McFadyen, R.B., Miller, A.B., Miller, L.R., Shewchuk, L.M., Willard, D.H., Wright, L.L.

Revision History  

• Version 1.0: 2004-03-16
  Type: Initial release
  
• Version 1.1: 2008-04-29
  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: 2018-02-14
  Changes: Experimental preparation
• Version 1.5: 2023-08-16
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.6: 2024-10-30
  Changes: Structure summary