1YT7 | pdb_00001yt7

Cathepsin K complexed with a constrained ketoamide inhibitor

• PDB DOI: https://doi.org/10.2210/pdb1YT7/pdb

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


• Deposited: 2005-02-10 Released: 2005-07-19 
• Deposition Author(s): Barrett, D.G., Boncek, V.M., Catalano, J.G., Deaton, D.N., Hassell, A.M., Jurgensen, C.H., Long, S.T., McFadyen, R.B., Miller, A.B., Miller, L.R., Payne, J.A., Ray, J.A., Samano, V., Shewchuk, L.M., Tavares, F.X., Wells-Knecht, K.J., Willard, D.H., Wright, L.L., Zhou, H.Q.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.251 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.186 (DCC) 

Starting Model: experimental

Literature

P(2)-P(3) conformationally constrained ketoamide-based inhibitors of cathepsin K.

Barrett, D.G., Boncek, V.M., Catalano, J.G., Deaton, D.N., Hassell, A.M., Jurgensen, C.H., Long, S.T., McFadyen, R.B., Miller, A.B., Miller, L.R., Payne, J.A., Ray, J.A., Samano, V., Shewchuk, L.M., Tavares, F.X., Wells-Knecht, K.J., Willard, D.H., Wright, L.L., Zhou, H.Q.

(2005) Bioorg Med Chem Lett 15: 3540-3546

• PubMed: 15982880 
• DOI: https://doi.org/10.1016/j.bmcl.2005.05.062
• Primary Citation Related Structures: 
  1YT7


• PubMed Abstract: 
  

  An orally bioavailable series of ketoamide-based cathepsin K inhibitors with good pharmacokinetic properties has been identified. Starting from a potent inhibitor endowed with poor drug properties, conformational constraint of the P(2)-P(3) linker and modifications to P(1') elements led to an enhancement in potency, solubility, clearance, and bioavailability. These optimized inhibitors attenuated bone resorption in a rat TPTX hypocalcemic bone resorption model.

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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: 24.3 kDa 
• Atom Count: 1,790 
• Modeled Residue Count: 214 
• 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3FC	D [auth A]	(1R)-2,2-DIMETHYL-1-({5-[4-(TRIFLUOROMETHYL)PHENYL]-1,3,4-OXADIAZOL-2-YL}METHYL)PROPYL (1S)-1-{OXO[(2-OXO-1,3-OXAZOLIDIN-3-YL)AMINO]ACETYL}PENTYLCARBAMATE C26 H32 F3 N5 O7 IXXKXSFSQVTOKQ-ZWKOTPCHSA-N
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.251 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.186 (DCC) 

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.645	α = 90
b = 65.645	β = 90
c = 34.467	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-07-19 
Deposition Author(s): Barrett, D.G., Boncek, V.M., Catalano, J.G., Deaton, D.N., Hassell, A.M., Jurgensen, C.H., Long, S.T., McFadyen, R.B., Miller, A.B., Miller, L.R., Payne, J.A., Ray, J.A., Samano, V., Shewchuk, L.M., Tavares, F.X., Wells-Knecht, K.J., Willard, D.H., Wright, L.L., Zhou, H.Q.

Revision History  

• Version 1.0: 2005-07-19
  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: 2024-11-13
  Changes: Structure summary