2HH5

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


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
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wwPDB Validation   3D Report Full Report


This is version 1.3 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 SA [auth B],
B [auth A]
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 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GNQ
Query on GNQ

Download Ideal Coordinates CCD File 
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
Query on ZN

Download Ideal Coordinates CCD File 
C [auth B]
D [auth B]
E [auth B]
H [auth A]
I [auth A]
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
Query on CL

Download Ideal Coordinates CCD File 
F [auth B],
K [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Binding Affinity Annotations 
IDSourceBinding 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 = 109.542α = 90
b = 109.542β = 90
c = 98.529γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PROCESSdata reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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