2HH5

Crystal Structure of Cathepsin S in complex with a Zinc mediated non-covalent arylaminoethyl amide

• PDB DOI: https://doi.org/10.2210/pdb2HH5/pdb

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


• Deposited: 2006-06-27 Released: 2006-08-15 
• Deposition Author(s): Spraggon, G., Hornsby, M., Lesley, S.A., Tully, D.C., Harris, J.L., Karenewsky, D.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.220 
• R-Value Work: 0.173 
• R-Value Observed: 0.176 

Starting Model: experimental

Literature

Synthesis and SAR of arylaminoethyl amides as noncovalent inhibitors of cathepsin S: P3 cyclic ethers.

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

(2006) Bioorg Med Chem Lett 16: 5112-5117

• PubMed: 16876402 
• DOI: https://doi.org/10.1016/j.bmcl.2006.07.033
• Primary Citation of Related Structures:  
  2HH5, 2HHN


• PubMed Abstract: 
  

  The synthesis and structure-activity relationship of a series of arylaminoethyl amide cathepsin S inhibitors are reported. Optimization of P3 and P2 groups to improve overall physicochemical properties resulted in significant improvements in oral bioavailability over early lead compounds. An X-ray structure of compound 37 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: 50.39 kDa 
• Atom Count: 3,757 
• Modelled Residue Count: 434 
• Deposited Residue Count: 440 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cathepsin S	A [auth B], B [auth A]	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GNQ	G [auth B], L [auth A]	N-[(1R)-1-[(BENZYLSULFONYL)METHYL]-2-{[(1S)-1-METHYL-2-{[4-(TRIFLUOROMETHOXY)PHENYL]AMINO}ETHYL]AMINO}-2-OXOETHYL]MORPHOLINE-4-CARBOXAMIDE C25 H31 F3 N4 O6 S LIOLGHUQUQDMDF-AVRDEDQJSA-N
ZN	C [auth B], D [auth B], E [auth B], H [auth A], I [auth A], J [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	F [auth B], K [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
GNQ	BindingDB:  2HH5	Ki: 32 (nM) from 1 assay(s)
	PDBBind:  2HH5	Ki: 32 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.220 
• R-Value Work: 0.173 
• R-Value Observed: 0.176 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.542	α = 90
b = 109.542	β = 90
c = 98.529	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PROCESS	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-08-15 
Deposition Author(s): Spraggon, G., Hornsby, M., Lesley, S.A., Tully, D.C., Harris, J.L., Karenewsky, D.S.

Revision History  

• Version 1.0: 2006-08-15
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description