Crystal Structure of Human Cathepsin S Bound to a Non-covalent Inhibitor.

Experimental Data Snapshot

  • Resolution: 1.58 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.198 

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Discovery of Cathepsin S Inhibitor LY3000328 for the Treatment of Abdominal Aortic Aneurysm.

Jadhav, P.K.Schiffler, M.A.Gavardinas, K.Kim, E.J.Matthews, D.P.Staszak, M.A.Coffey, D.S.Shaw, B.W.Cassidy, K.C.Brier, R.A.Zhang, Y.Christie, R.M.Matter, W.F.Qing, K.Durbin, J.D.Wang, Y.Deng, G.G.

(2014) ACS Med Chem Lett 5: 1138-1142

  • DOI: https://doi.org/10.1021/ml500283g
  • Primary Citation of Related Structures:  
    4P6E, 4P6G

  • PubMed Abstract: 

    Cathepsin S (Cat S) plays an important role in many pathological conditions, including abdominal aortic aneurysm (AAA). Inhibition of Cat S may provide a new treatment for AAA. To date, several classes of Cat S inhibitors have been reported, many of which form covalent interactions with the active site Cys25. Herein, we report the discovery of a novel series of noncovalent inhibitors of Cat S through a medium-throughput focused cassette screen and the optimization of the resulting hits. Structure-based optimization efforts led to Cat S inhibitors such as 5 and 9 with greatly improved potency and drug disposition properties. This series of compounds binds to the S2 and S3 subsites without interacting with the active site Cys25. On the basis of in vitro potency, selectivity, and efficacy in a CaCl2-induced AAA in vivo model, 5 (LY3000328) was selected for clinical development.

  • Organizational Affiliation

    Lilly Research Laboratories, A Division of Eli Lilly and Company, Lilly Corporate Center , Indianapolis, Indiana 46285, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cathepsin S
A, B, C, D
226Homo sapiensMutation(s): 0 
Gene Names: CTSS
UniProt & NIH Common Fund Data Resources
Find proteins for P25774 (Homo sapiens)
Explore P25774 
Go to UniProtKB:  P25774
PHAROS:  P25774
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25774
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
2FZ BindingDB:  4P6G IC50: 7.7 (nM) from 1 assay(s)
Binding MOAD:  4P6G IC50: 7.7 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.58 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.198 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.253α = 100.9
b = 67.311β = 94.86
c = 67.778γ = 117.99
Software Package:
Software NamePurpose

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-29
    Type: Initial release