5QC4 | pdb_00005qc4

Crystal structure of human Cathepsin-S with bound ligand

• PDB DOI: https://doi.org/10.2210/pdb5QC4/pdb
• Deposition Group: G_1002040 | Explore  G_1002040  
• Entry: 5QC4 supersedes: 3KWN

• 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: 2.00 Å
• R-Value Free: 
  0.210 (Depositor), 0.212 (DCC) 
• R-Value Work: 
  0.152 (Depositor), 0.154 (DCC) 
• R-Value Observed: 
  0.155 (Depositor) 

Literature

Thioether acetamides as P3 binding elements for tetrahydropyrido-pyrazole cathepsin S inhibitors.

Wiener, D.K., Lee-Dutra, A., Bembenek, S., Nguyen, S., Thurmond, R.L., Sun, S., Karlsson, L., Grice, C.A., Jones, T.K., Edwards, J.P.

(2010) Bioorg Med Chem Lett 20: 2379-2382

• PubMed: 20188543 
• DOI: https://doi.org/10.1016/j.bmcl.2010.01.103
• Primary Citation Related Structures: 
  5QC4


• PubMed Abstract: 
  

  A series of tetrahydropyrido-pyrazole cathepsin S (CatS) inhibitors with thioether acetamide functional groups were prepared with the goal of improving upon the cellular activity of amidoethylthioethers. This Letter describes altered amide connectivity, in conjunction with changes to other binding elements, resulting in improved potency, as well as increased knowledge of the relationship between this chemotype and human CatS activity.

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Organizational Affiliation: 
• Johnson & Johnson Pharmaceutical Research & Development, L.L.C., 3210 Merryfield Row, San Diego, CA 92121, United States. [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: 50.34 kDa 
• Atom Count: 4,037 
• Modeled Residue Count: 441 
• 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
BC7	C [auth A], D [auth B]	2-[5-[5-ethanoyl-1-[(2~{R})-2-oxidanyl-3-[4-(2-oxidanylpropan-2-yl)piperidin-1-yl]propyl]-6,7-dihydro-4~{H}-pyrazolo[4,3-c]pyridin-3-yl]-2-(trifluoromethyl)phenyl]sulfanyl-1-pyrrolidin-1-yl-ethanone C32 H44 F3 N5 O4 S QMRXULKWYQUBRF-XMMPIXPASA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.210 (Depositor), 0.212 (DCC) 
• R-Value Work:  0.152 (Depositor), 0.154 (DCC) 
• R-Value Observed: 0.155 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.02	α = 70.75
b = 52.97	β = 71.79
c = 58.58	γ = 73.21

Software Package:

Software Name	Purpose
PHENIX	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: 3KWN

Revision History  

• Version 1.0: 2017-12-20
  Type: Initial release
  
• Version 1.1: 2018-02-21
  Changes: Structure summary
• Version 2.0: 2018-06-06
  Changes: Atomic model, Data collection, Refinement description, Structure summary
• Version 2.1: 2021-02-10
  Changes: Structure summary
• Version 2.2: 2021-11-17
  Changes: Database references, Structure summary
• Version 2.3: 2024-11-13
  Changes: Data collection, Structure summary