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URL: https://www.rcsb.org/structure/4DMY

⇱ RCSB PDB - 4DMY: Cathepsin K inhibitor

👁 RCSB PDB
255,630
Structures from the PDB archive		1,062,058
Computed Structure Models (CSM)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 
    0.190 (Depositor), 0.198 (DCC) 
  • R-Value Work: 
    0.128 (Depositor), 0.141 (DCC) 
  • R-Value Observed: 
    0.131 (Depositor) 

wwPDB Validation3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.5 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: https://doi.org/10.1021/jm3007257
  • Primary Citation 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 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

Macromolecule Content 

  • Total Structure Weight: 48.34 kDa 
  • Atom Count: 3,949 
  • Modeled Residue Count: 430 
  • Deposited Residue Count: 430 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cathepsin K
A, B
215Homo sapiensMutation(s): 0 
Gene Names: CTSK, CTSO, CTSO2
EC: 3.4.22.38
👁 Image
UniProt & NIH Common Fund Data Resources
Find proteins for P43235 (Homo sapiens)
Explore P43235 
Go to UniProtKB:  P43235
PHAROS:  P43235
GTEx:  ENSG00000143387 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43235
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
0LC

Query on 0LC


Download:Ideal Coordinates CCD File
C [auth A],
F [auth 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		👁 Image
SO4

Query on SO4


Download:Ideal Coordinates CCD File
D [auth A],
E [auth A],
G [auth B],
H [auth B]		SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		👁 Image
GOL

Query on GOL


Download:Ideal Coordinates CCD File
I [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		👁 Image

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free:  0.190 (Depositor), 0.198 (DCC) 
  • R-Value Work:  0.128 (Depositor), 0.141 (DCC) 
  • R-Value Observed: 0.131 (Depositor) 
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

👁 Image


Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • 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
  • Version 1.5: 2024-11-20
    Changes: Data collection, Database references, Derived calculations, Structure summary

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.