1YK7 | pdb_00001yk7

Cathepsin K complexed with a cyanopyrrolidine inhibitor

• PDB DOI: https://doi.org/10.2210/pdb1YK7/pdb

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


• Deposited: 2005-01-17 Released: 2005-03-22 
• Deposition Author(s): Barrett, D.G., Deaton, D.N., Hassell, A.M., McFadyen, R.B., Miller, A.B., Miller, L.R., Shewchuk, L.M., Tavares, F.X., Willard, D.H., Wright, L.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.270 (Depositor), 0.176 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.199 (DCC) 

Starting Model: experimental

Literature

Novel and potent cyclic cyanamide-based cathepsin K inhibitors.

Deaton, D.N., Hassell, A.M., McFadyen, R.B., Miller, A.B., Miller, L.R., Shewchuk, L.M., Tavares, F.X., Willard, D.H., Wright, L.L.

(2005) Bioorg Med Chem Lett 15: 1815-1819

• PubMed: 15780613 
• DOI: https://doi.org/10.1016/j.bmcl.2005.02.033
• Primary Citation Related Structures: 
  1YK7


• PubMed Abstract: 
  

  Starting from a PDE IV inhibitor hit derived from high throughput screening of the compound collection, a key pyrrolidine cyanamide pharmacophore was identified. Modifications of the pyrrolidine ring produced enhancements in cathepsin K inhibition. An X-ray co-crystal structure of a cyanamide with cathepsin K confirmed the mode of inhibition.

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Organizational Affiliation: 
• Department of Medicinal Chemistry, GlaxoSmithKline, Research Triangle Park, NC 27709, USA. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 23.88 kDa 
• Atom Count: 1,782 
• Modeled 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
NBL	B [auth A]	N2-[(BENZYLOXY)CARBONYL]-N1-[(3S)-1-CYANOPYRROLIDIN-3-YL]-L-LEUCINAMIDE C19 H26 N4 O3 IMTUSTXBVIALBC-SJORKVTESA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.270 (Depositor), 0.176 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.199 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.241	α = 90
b = 66.653	β = 90
c = 93.187	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-03-22 
Deposition Author(s): Barrett, D.G., Deaton, D.N., Hassell, A.M., McFadyen, R.B., Miller, A.B., Miller, L.R., Shewchuk, L.M., Tavares, F.X., Willard, D.H., Wright, L.L.

Revision History  

• Version 1.0: 2005-03-22
  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
• Version 1.4: 2024-11-20
  Changes: Structure summary