3N4C

6-Phenyl-1H-imidazo[4,5-c]pyridine-4-carbonitrile as cathepsin S inhibitors

• PDB DOI: https://doi.org/10.2210/pdb3N4C/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2010-05-21 Released: 2011-04-06 
• Deposition Author(s): Fradera, X., Uitdehaag, J.C.M., van Zeeland, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.286 
• R-Value Work: 0.249 
• R-Value Observed: 0.251 

Starting Model: experimental

Literature

6-Phenyl-1H-imidazo[4,5-c]pyridine-4-carbonitrile as cathepsin S inhibitors.

Cai, J., Baugh, M., Black, D., Long, C., Jonathan Bennett, D., Dempster, M., Fradera, X., Gillespie, J., Andrews, F., Boucharens, S., Bruin, J., Cameron, K.S., Cumming, I., Hamilton, W., Jones, P.S., Kaptein, A., Kinghorn, E., Maidment, M., Martin, I., Mitchell, A., Rankovic, Z., Robinson, J., Scullion, P., Uitdehaag, J.C., Vink, P., Westwood, P., van Zeeland, M., van Berkom, L., Bastiani, M., Meulemans, T.

(2010) Bioorg Med Chem Lett 20: 4350-4354

• PubMed: 20598883 
• DOI: https://doi.org/10.1016/j.bmcl.2010.06.072
• Primary Citation of Related Structures:  
  3N4C


• PubMed Abstract: 
  

  6-Phenyl-1H-imidazo[4,5-c]pyridine-4-carbonitrile analogues were identified as potent and selective cathepsin S inhibitor against both purified enzyme and in human JY cell based cellular assays. This core has a very stable thio-trapping nitrile war-head in comparison with the well reported pyrimidine-2-carbonitrile cysteine cathepsin inhibitors. Compound 47 is also very potent in in vivo mouse spleenic Lip10 accumulation assays.

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Organizational Affiliation: 

Merck Research Laboratories, Newhouse, Lanarkshire ML1 5SH, UK. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 49.19 kDa 
• Atom Count: 3,665 
• Modelled Residue Count: 434 
• Deposited Residue Count: 434 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cathepsin S	A, B	217	Homo sapiens	Mutation(s): 0  Gene Names: CTSS, Homo sapiens 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 GTEx:  ENSG00000163131

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EF3	C [auth A], E [auth B]	(E)-1-(1-methyl-6-{4-[3-(4-methylpiperazin-1-yl)propoxy]-3-(trifluoromethyl)phenyl}-1H-imidazo[4,5-c]pyridin-4-yl)methanimine C23 H27 F3 N6 O MZJARPQAOGJEES-MZJWZYIUSA-N
SO4	F [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
DMS	D [auth A], G [auth B]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
EF3	PDBBind:  3N4C	IC50: 9.5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.286 
• R-Value Work: 0.249 
• R-Value Observed: 0.251 
• Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.629	α = 90
b = 85.629	β = 90
c = 150.573	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
d*TREK	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-04-06 
Deposition Author(s): Fradera, X., Uitdehaag, J.C.M., van Zeeland, M.

Revision History  

• Version 1.0: 2011-04-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-11-06
  Changes: Structure summary