4DMY

Cathepsin K inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.128 
  • R-Value Observed: 0.131 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

(1R,2R)-N-(1-cyanocyclopropyl)-2-(6-methoxy-1,3,4,5-tetrahydropyrido[4,3-b]indole-2-carbonyl)cyclohexanecarboxamide (AZD4996): a potent and highly selective cathepsin K inhibitor for the treatment of osteoarthritis.

Dossetter, A.G.Beeley, H.Bowyer, J.Cook, C.R.Crawford, J.J.Finlayson, J.E.Heron, N.M.Heyes, C.Highton, A.J.Hudson, J.A.Jestel, A.Kenny, P.W.Krapp, S.Martin, S.MacFaul, P.A.McGuire, T.M.Gutierrez, P.M.Morley, A.D.Morris, J.J.Page, K.M.Ribeiro, L.R.Sawney, H.Steinbacher, S.Smith, C.Vickers, M.

(2012) J Med Chem 55: 6363-6374

  • DOI: 10.1021/jm3007257
  • Primary Citation of Related Structures:  
    4DMX, 4DMY

  • PubMed Abstract: 
  • Directed screening of nitrile compounds revealed 3 as a highly potent cathepsin K inhibitor but with cathepsin S activity and very poor stability to microsomes. Synthesis of compounds with reduced molecular complexity, such as 7, revealed key SAR and ...

    Directed screening of nitrile compounds revealed 3 as a highly potent cathepsin K inhibitor but with cathepsin S activity and very poor stability to microsomes. Synthesis of compounds with reduced molecular complexity, such as 7, revealed key SAR and demonstrated that baseline physical properties and in vitro stability were in fact excellent for this series. The tricycle carboline P3 unit was discovered by hypothesis-based design using existing structural information. Optimization using small substituents, knowledge from matched molecular pairs, and control of lipophilicity yielded compounds very close to the desired profile, of which 34 (AZD4996) was selected on the basis of pharmacokinetic profile.


    Organizational Affiliation

    AstraZeneca R&D, Mereside, Alderley Park, Macclesfield, Cheshire, SK10 4TG, UK. al.dossetter@astrazeneca.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cathepsin KAB215Homo sapiensMutation(s): 0 
Gene Names: CTSKCTSOCTSO2
EC: 3.4.22.38
Find proteins for P43235 (Homo sapiens)
Explore P43235 
Go to UniProtKB:  P43235
NIH Common Fund Data Resources
PHAROS  P43235
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0LC
Query on 0LC

Download CCD File 
A, B
(1R,2R)-N-(1-cyanocyclopropyl)-2-[(8-fluoro-1,3,4,5-tetrahydro-2H-pyrido[4,3-b]indol-2-yl)carbonyl]cyclohexanecarboxamide
C23 H25 F N4 O2
HGJTURTZFKNELD-HZPDHXFCSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
B
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0LCIC50 :  1   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.128 
  • R-Value Observed: 0.131 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 31.927α = 90
b = 69.554β = 99.83
c = 90.645γ = 90
Software Package:
Software NamePurpose
MAR345data collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report



Entry History 

Revision History 

  • Version 1.0: 2012-07-11
    Type: Initial release
  • Version 1.1: 2013-01-02
    Changes: Database references
  • Version 1.2: 2014-11-26
    Changes: Structure summary
  • Version 1.3: 2017-11-15
    Changes: Refinement description
  • Version 1.4: 2018-01-24
    Changes: Structure summary