4DMX

Cathepsin K inhibitor

• PDB DOI:  https://doi.org/10.2210/pdb4DMX/pdb

• Classification: Hydrolase/Hydrolase inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-02-08 Released: 2012-07-11 
• Deposition Author(s): 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., Kenny, P.W., Martin, S., MacFaul, P.A., McGuire, T.M., Gutierrez, P.M., Morley, A.D., Morris, J.J., Page, K.M., Rosenbrier Ribeiro, L., Sawney, H., Steinbacher, S., Krapp, S., Jestel, A., Smith, C., Vickers, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.206 
• R-Value Work: 0.156 
• R-Value Observed: 0.158 

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

• PubMed: 22742641 
• DOI: https://doi.org/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 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.

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Organizational Affiliation: 

AstraZeneca R&D, Mereside, Alderley Park, Macclesfield, Cheshire, SK10 4TG, UK. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 24.01 kDa 
• Atom Count: 1,831 
• Modelled Residue Count: 215 
• Deposited Residue Count: 215 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cathepsin K	A	215	Homo sapiens	Mutation(s): 0  Gene Names: CTSK, CTSO, CTSO2 EC: 3.4.22.38
UniProt & NIH Common Fund Data Resources
Find proteins for P43235 (Homo sapiens) Explore P43235  Go to UniProtKB:  P43235
PHAROS:  P43235

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0LB	B [auth A]	(1R,2R)-N-(1-cyanocyclopropyl)-2-{[4-(4-fluorophenyl)piperazin-1-yl]carbonyl}cyclohexanecarboxamide C22 H27 F N4 O2 GHDIYQHGVKVLJX-RTBURBONSA-N
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
0LB	BindingDB:  4DMX	IC50: min: 15, max: 15.85 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.206 
• R-Value Work: 0.156 
• R-Value Observed: 0.158 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.362	α = 90
b = 83.958	β = 109.96
c = 35.999	γ = 90

Software Package:

Software Name	Purpose
PXSOFT	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-07-11 
Deposition Author(s): 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., Kenny, P.W., Martin, S., MacFaul, P.A., McGuire, T.M., Gutierrez, P.M., Morley, A.D., Morris, J.J., Page, K.M., Rosenbrier Ribeiro, L., Sawney, H., Steinbacher, S., Krapp, S., Jestel, A., Smith, C., Vickers, M.

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: 2018-01-24
  Changes: Advisory, Structure summary