1SNK

Cathepsin K complexed with carbamate derivatized norleucine aldehyde

• PDB DOI: https://doi.org/10.2210/pdb1SNK/pdb

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


• Deposited: 2004-03-11 Released: 2004-06-22 
• Deposition Author(s): Boros, E.E., Deaton, D.N., Hassell, A.M., McFadyen, R.B., Miller, A.B., Miller, L.R., Shewchuk, L.M., Thompson, J.B., Willard Jr., D.H., Wright, L.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.286 
• R-Value Work: 0.208 
• R-Value Observed: 0.208 

Literature

Exploration of the P(2)-P(3) SAR of aldehyde cathepsin K inhibitors

Boros, E.E., Deaton, D.N., Hassell, A.M., McFadyen, R.B., Miller, A.B., Miller, L.R., Paulick, M.G., Shewchuk, L.M., Thompson, J.B., Willard Jr., D.H., Wright, L.L.

(2004) Bioorg Med Chem Lett 14: 3425-3429

• PubMed: 15177446 
• DOI: https://doi.org/10.1016/j.bmcl.2004.04.084
• Primary Citation of Related Structures:  
  1SNK


• PubMed Abstract: 
  

  The synthesis and biological activity of a series of aldehyde inhibitors of cathepsin K are reported. Exploration of the properties of the S2 and S3 subsites with a series of carbamate derivatized norleucine aldehydes substituted at the P2 and P3 positions afforded analogs with cathepsin K IC50s between 600 nM and 130 pM.

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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: 24.18 kDa 
• Atom Count: 1,789 
• Modelled Residue Count: 214 
• Deposited Residue Count: 214 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cathepsin K	A	214	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
MYE	E [auth A]	N2-({[(4-BROMOPHENYL)METHYL]OXY}CARBONYL)-N1-[(1S)-1-FORMYLPENTYL]-L-LEUCINAMIDE C20 H29 Br N2 O4 UEDKSAKLZBMNMA-ROUUACIJSA-N
SO4	B [auth A], C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
MYE	PDBBind:  1SNK	IC50: 0.25 (nM) from 1 assay(s)
	BindingDB:  1SNK	IC50: 0.25 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.286 
• R-Value Work: 0.208 
• R-Value Observed: 0.208 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.073	α = 90
b = 62.073	β = 90
c = 113.378	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-06-22 
Deposition Author(s): Boros, E.E., Deaton, D.N., Hassell, A.M., McFadyen, R.B., Miller, A.B., Miller, L.R., Shewchuk, L.M., Thompson, J.B., Willard Jr., D.H., Wright, L.L.

Revision History  

• Version 1.0: 2004-06-22
  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: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description