2HHN

Cathepsin S in complex with non covalent arylaminoethyl amide.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.157 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history. 


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

  • 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.

    • Organizational Affiliation: 

    Genomics Institute of the Novartis Research Foundation, 10675 John J. Hopkins Dr., San Diego, CA 92121, USA. dtully@gnf.org


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cathepsin S
A, B
220Homo sapiensMutation(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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25774
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GNQ
Query on GNQ
Download Ideal Coordinates CCD File 
G [auth B]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
SO4
Query on SO4
Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A],
F [auth A]		SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Binding Affinity Annotations 
IDSourceBinding Affinity
GNQ PDBBind:  2HHN Ki: 32 (nM) from 1 assay(s)
Binding MOAD:  2HHN Ki: 32 (nM) from 1 assay(s)
BindingDB:  2HHN Ki: 32 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.157 
  • Space Group: P 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.532α = 90
b = 85.532β = 90
c = 150.403γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-05-08
    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: 2017-10-18
    Changes: Advisory, Refinement description
  • Version 1.4: 2023-08-30
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description