5QBY

Crystal structure of human Cathepsin-S with bound ligand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Diazinones as P2 replacements for pyrazole-based cathepsin S inhibitors

Ameriks, M.K.Bembenek, S.D.Burdett, M.T.Choong, I.C.Edwards, J.P.Gebauer, D.Gu, Y.Karlsson, L.Purkey, H.E.Staker, B.L.Sun, S.Thurmond, R.L.Zhu, J.

(2010) Bioorg.Med.Chem.Lett. 20: 4060-4064

  • DOI: 10.1016/j.bmcl.2010.05.086
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • A pyridazin-4-one fragment 4 (hCatS IC(50)=170 microM) discovered through Tethering was modeled into cathepsin S and predicted to overlap in S2 with the tetrahydropyridinepyrazole core of a previously disclosed series of CatS inhibitors. This fragmen ...

    A pyridazin-4-one fragment 4 (hCatS IC(50)=170 microM) discovered through Tethering was modeled into cathepsin S and predicted to overlap in S2 with the tetrahydropyridinepyrazole core of a previously disclosed series of CatS inhibitors. This fragment served as a template to design pyridazin-3-one 12 (hCatS IC(50)=430 nM), which also incorporates P3 and P5 binding elements. A crystal structure of 12 bound to Cys25Ser CatS led to the synthesis of the potent diazinone isomers 22 (hCatS IC(50)=60 nM) and 27 (hCatS IC(50)=40 nM).


    Organizational Affiliation

    Johnson & Johnson Pharmaceutical Research & Development, L.L.C., 3210 Merryfield Row, San Diego, CA 92121, USA. mameriks@its.jnj.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cathepsin S
A, B
223Homo sapiensMutation(s): 1 
Gene Names: CTSS
EC: 3.4.22.27
Find proteins for P25774 (Homo sapiens)
Go to Gene View: CTSS
Go to UniProtKB:  P25774
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
N2A
Query on N2A

Download SDF File 
Download CCD File 
A, B
N-[2-chloro-5-(1-{3-[4-(6-chloro-3-methyl-2-oxo-2,3-dihydro-1H-benzimidazol-1-yl)piperidin-1-yl]propyl}-6-oxo-1,6-dihydropyrimidin-5-yl)benzyl]-4-fluorobenzamide
C34 H33 Cl2 F N6 O3
UUSUCXDJVSXCBL-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.171 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 171.238α = 90.00
b = 34.376β = 125.10
c = 103.815γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
REFMACrefinement
PDB_EXTRACTdata extraction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-12-20
    Type: Initial release
  • Version 1.1: 2018-02-21
    Type: Structure summary