5QBY

Crystal structure of human Cathepsin-S with bound ligand

• PDB DOI: https://doi.org/10.2210/pdb5QBY/pdb
• Deposition Group: G_1002040 ExploreG_1002040
• Entry: 5QBY supersedes: 3MPE

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2017-08-04 Released: 2017-12-20 
• Deposition Author(s): Bembenek, S.D., Ameriks, M.K., Mirzadegan, T., Yang, H., Shao, C., Burley, S.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.204 
• R-Value Work: 0.171 
• R-Value Observed: 0.172 

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

• PubMed: 20541404 
• DOI: https://doi.org/10.1016/j.bmcl.2010.05.086
• Primary Citation of Related Structures:  
  5QBV, 5QBY


• 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 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).

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Organizational Affiliation: 

Johnson & Johnson Pharmaceutical Research & Development, L.L.C., 3210 Merryfield Row, San Diego, CA 92121, USA. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 50.36 kDa 
• Atom Count: 3,872 
• Modelled Residue Count: 438 
• Deposited Residue Count: 446 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cathepsin S	A, B	223	Homo sapiens	Mutation(s): 1  Gene Names: CTSS EC: 3.4.22.27
UniProt & NIH Common Fund Data Resources
Find proteins for P25774 (Homo sapiens) Explore P25774  Go to UniProtKB:  P25774
PHAROS:  P25774 GTEx:  ENSG00000163131

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
N2A	C [auth A], D [auth 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

Binding Affinity Annotations
ID	Source	Binding Affinity
N2A	BindingDB:  5QBY	IC50: min: 40, max: 6700 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.204 
• R-Value Work: 0.171 
• R-Value Observed: 0.172 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 171.238	α = 90
b = 34.376	β = 125.1
c = 103.815	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-12-20 
Deposition Author(s): Bembenek, S.D., Ameriks, M.K., Mirzadegan, T., Yang, H., Shao, C., Burley, S.K.
• This entry supersedes: 3MPE

Revision History  

• Version 1.0: 2017-12-20
  Type: Initial release
  
• Version 1.1: 2018-02-21
  Changes: Structure summary
• Version 1.2: 2021-02-10
  Changes: Structure summary
• Version 1.3: 2021-11-17
  Changes: Database references, Structure summary
• Version 1.4: 2024-11-06
  Changes: Data collection, Refinement description, Structure summary