2F1G

Cathepsin S in complex with non-covalent 2-(Benzoxazol-2-ylamino)-acetamide

• PDB DOI: https://doi.org/10.2210/pdb2F1G/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2005-11-14 Released: 2006-04-04 
• Deposition Author(s): Spraggon, G., Hornsby, M., Lesley, S.A., Tully, D.C., Harris, J.L., Karenewsky, D.S., Kulathila, R., Clark, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.230 (Depositor) 
• R-Value Work: 
  0.189 (Depositor) 
• R-Value Observed: 
  0.191 (Depositor) 

Literature

Synthesis and evaluation of arylaminoethyl amides as noncovalent inhibitors of cathepsin S. Part 3: Heterocyclic P3.

Tully, D.C., Liu, H., Alper, P.B., Chatterjee, A.K., Epple, R., Roberts, M.J., Williams, J.A., Nguyen, K.T., Woodmansee, D.H., Tumanut, C., Li, J., Spraggon, G., Chang, J., Tuntland, T., Harris, J.L., Karanewsky, D.S.

(2006) Bioorg Med Chem Lett 16: 1975-1980

• PubMed: 16446091 
• DOI: https://doi.org/10.1016/j.bmcl.2005.12.095
• Primary Citation of Related Structures:  
  2F1G


• PubMed Abstract: 
  

  A series of N(alpha)-2-benzoxazolyl-alpha-amino acid-(arylaminoethyl)amides were identified as potent, selective, and noncovalent inhibitors of cathepsin S. Structure-activity relationships including strategies for modulating the selectivities among cathepsins S, K, and L, and in vivo pharmacokinetics are discussed. A X-ray structure of compound 3 bound to the active site of cathepsin S is also reported.

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Organizational Affiliation: 

Genomics Institute of the Novartis Research Foundation, 10675 John J. Hopkins Dr., 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: 49.75 kDa 
• Atom Count: 3,820 
• Modelled Residue Count: 437 
• Deposited Residue Count: 440 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cathepsin S	A, B	220	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GNF	C [auth A], D [auth B]	N~2~-1,3-BENZOXAZOL-2-YL-3-CYCLOHEXYL-N-{2-[(4-METHOXYPHENYL)AMINO]ETHYL}-L-ALANINAMIDE C25 H32 N4 O3 VFNWTXUFNNOQHD-QFIPXVFZSA-N
GOL	E [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
GNF	BindingDB:  2F1G	Ki: 29 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.230 (Depositor) 
• R-Value Work:  0.189 (Depositor) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.25	α = 90
b = 85.25	β = 90
c = 151.613	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-04-04 
Deposition Author(s): Spraggon, G., Hornsby, M., Lesley, S.A., Tully, D.C., Harris, J.L., Karenewsky, D.S., Kulathila, R., Clark, K.

Revision History  

• Version 1.0: 2006-04-04
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2024-10-09
  Changes: Data collection, Database references, Derived calculations, Structure summary