4X6H

Development of N-(Functionalized benzoyl)-homocycloleucyl-glycinonitriles as Potent Cathepsin K Inhibitors.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.155 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Development of N-(Functionalized benzoyl)-homocycloleucyl-glycinonitriles as Potent Cathepsin K Inhibitors.

Borisek, J.Vizovisek, M.Sosnowski, P.Turk, B.Turk, D.Mohar, B.Novic, M.

(2015) J.Med.Chem. 58: 6928-6937

  • DOI: 10.1021/acs.jmedchem.5b00746
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Cathepsin K is a major drug target for osteoporosis and related-bone disorders. Using a combination of virtual combinatorial chemistry, QSAR modeling, and molecular docking studies, a series of cathepsin K inhibitors based on N-(functionalized benzoy ...

    Cathepsin K is a major drug target for osteoporosis and related-bone disorders. Using a combination of virtual combinatorial chemistry, QSAR modeling, and molecular docking studies, a series of cathepsin K inhibitors based on N-(functionalized benzoyl)-homocycloleucyl-glycinonitrile scaffold was developed. In order to avoid previous problems of cathepsin K inhibitors associated with lysosomotropism of compounds with basic character that resulted in off-target effects, a weakly- to nonbasic moiety was incorporated into the P3 position. Compounds 5, 6, and 9 were highly selective for cathepsin K when compared with cathepsins L and S, with the Ki values in the 10-30 nM range. The kinetic studies revealed that the new compounds exhibited reversible tight binding to cathepsin K, while the X-ray structural studies showed covalent and noncovalent binding between the nitrile group and the catalytic cysteine (Cys25) site.


    Organizational Affiliation

    Department of Biochemistry, Molecular and Structural Biology, Jozef Stefan Institute , Jamova cesta 39, SI-1000 Ljubljana, Slovenia.,National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia.,Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Jamova cesta 39, SI-1000 Ljubljana, Slovenia.,Faculty of Chemistry and Chemical Technology, University of Ljubljana , Ve─Źna pot 113, SI-1000 Ljubljana, Slovenia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cathepsin K
A
215Homo sapiensMutation(s): 0 
Gene Names: CTSK (CTSO, CTSO2)
EC: 3.4.22.38
Find proteins for P43235 (Homo sapiens)
Go to Gene View: CTSK
Go to UniProtKB:  P43235
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
3XT
Query on 3XT

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Download CCD File 
A
4-amino-3-fluoro-N-(1-{[(2Z)-2-iminoethyl]carbamoyl}cyclohexyl)benzamide
C16 H21 F N4 O2
ULJOBOHEOALILQ-LSCVHKIXSA-N
 Ligand Interaction
I37
Query on I37

Download SDF File 
Download CCD File 
A
4-amino-N-{1-[(cyanomethyl)carbamoyl]cyclohexyl}-3-fluorobenzamide
C16 H19 F N4 O2
NEJGUCSKQVFSJQ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
I37Ki: 22 nM (100) BINDINGDB
I37Ki: 22 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.155 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 36.439α = 90.00
b = 54.551β = 90.00
c = 88.015γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
PROTEUM PLUSdata reduction
PROTEUM PLUSdata reduction
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-09-23
    Type: Initial release