3IEJ

Pyrazole-based Cathepsin S Inhibitors with Arylalkynes as P1 Binding Elements


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.191 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Pyrazole-based cathepsin S inhibitors with arylalkynes as P1 binding elements.

Ameriks, M.K.Axe, F.U.Bembenek, S.D.Edwards, J.P.Gu, Y.Karlsson, L.Randal, M.Sun, S.Thurmond, R.L.Zhu, J.

(2009) Bioorg Med Chem Lett 19: 6131-6134

  • DOI: 10.1016/j.bmcl.2009.09.014
  • Primary Citation of Related Structures:  
    3IEJ

  • PubMed Abstract: 
  • A crystal structure of 1 bound to a Cys25Ser mutant of cathepsin S helped to elucidate the binding mode of a previously disclosed series of pyrazole-based CatS inhibitors and facilitated the design of a new class of arylalkyne analogs. Optimization of the alkyne and tetrahydropyridine portions of the pharmacophore provided potent CatS inhibitors (IC50=40-300 nM), and an X-ray structure of 32 revealed that the arylalkyne moiety binds in the S1 pocket of the enzyme ...

    A crystal structure of 1 bound to a Cys25Ser mutant of cathepsin S helped to elucidate the binding mode of a previously disclosed series of pyrazole-based CatS inhibitors and facilitated the design of a new class of arylalkyne analogs. Optimization of the alkyne and tetrahydropyridine portions of the pharmacophore provided potent CatS inhibitors (IC50=40-300 nM), and an X-ray structure of 32 revealed that the arylalkyne moiety binds in the S1 pocket of the enzyme.


    Organizational Affiliation

    Johnson & Johnson Pharmaceutical Research & Development, L.L.C., 3210 Merryfield Row, San Diego, CA 92121, USA. mameriks@its.jnj.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cathepsin SA, B222Homo sapiensMutation(s): 1 
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25774
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
599
Query on 599

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
2-[3-{4-chloro-3-[(4-chlorophenyl)ethynyl]phenyl}-1-(3-morpholin-4-ylpropyl)-1,4,6,7-tetrahydro-5H-pyrazolo[4,3-c]pyridin-5-yl]-2-oxoethanol
C29 H30 Cl2 N4 O3
IWTCFPKHJADUJG-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
599 PDBBind:  3IEJ IC50: 220 (nM) from 1 assay(s)
BindingDB:  3IEJ IC50: 220 (nM) from 1 assay(s)
Binding MOAD:  3IEJ IC50: 220 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.191 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.264α = 90
b = 37.192β = 108.59
c = 105.863γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

  • Deposited Date: 2009-07-22 
  • Released Date: 2009-10-06 
  • Deposition Author(s): Bembenek, S.

Revision History  (Full details and data files)

  • Version 1.0: 2009-10-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-10-13
    Changes: Database references, Derived calculations