2R9N | pdb_00002r9n

Cathepsin S complexed with Compound 26

• PDB DOI: https://doi.org/10.2210/pdb2R9N/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-09-13 Released: 2007-12-18 
• Deposition Author(s): Ward, Y.D., Emmanuel, M.J., Thomson, D.S., Liu, W., Bekkali, Y., Frye, L.L., Girardot, M., Morwick, T., Young, E.R.R., Zindell, R., Hrapchak, M., DeTuri, M., White, A., Crane, K.M., White, D.M., Wang, Y., Hao, M.-H., Grygon, C.A., Labadia, M.E., Wildeson, J., Freeman, D., Nelson, R., Capolino, A., Peterson, J.D., Raymond, E.L., Brown, M.L., Spero, D.M.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.220 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.180 (DCC) 

Starting Model: experimental

Literature

Design and Synthesis of Reversible Inhibitors of Cathepsin S: alpha,alpha-Disubstitution at the P1 Residue Provides Potent Inhibitors in Cellular Assays and In Vivo Models of Antigen Presentation

Ward, Y.D., Emmanuel, M.J., Thomson, D.S., Liu, W., Bekkali, Y., Frye, L.L., Girardot, M., Morwick, T., Young, E.R.R., Zindell, R., Hrapchak, M., DeTuri, M., White, A., Crane, K.M., White, D.M., Wang, Y., Hao, M.-H., Grygon, C.A., Labadia, M.E., Wildeson, J., Freeman, D., Nelson, R., Capolino, A., Peterson, J.D., Raymond, E.L., Brown, M.L., Spero, D.M.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 50.33 kDa 
• Atom Count: 3,744 
• Modeled Residue Count: 434 
• Deposited Residue Count: 444 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cathepsin S	A, B	222	Homo sapiens	Mutation(s): 0  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
Y14	C [auth A], D [auth B]	N-[(1S)-2-{[(3S)-1-benzyl-3-cyanopyrrolidin-3-yl]amino}-1-(cyclohexylmethyl)-2-oxoethyl]morpholine-4-carboxamide C26 H37 N5 O3 OHVQFYYBGNOGJV-JYFHCDHNSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.220 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.180 (DCC) 

Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.296	α = 90
b = 85.296	β = 90
c = 149.961	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-12-18 
Deposition Author(s): Ward, Y.D., Emmanuel, M.J., Thomson, D.S., Liu, W., Bekkali, Y., Frye, L.L., Girardot, M., Morwick, T., Young, E.R.R., Zindell, R., Hrapchak, M., DeTuri, M., White, A., Crane, K.M., White, D.M., Wang, Y., Hao, M.-H., Grygon, C.A., Labadia, M.E., Wildeson, J., Freeman, D., Nelson, R., Capolino, A., Peterson, J.D., Raymond, E.L., Brown, M.L., Spero, D.M.

Revision History  

• Version 1.0: 2007-12-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2019-07-24
  Changes: Data collection, Refinement description
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-10-30
  Changes: Structure summary