3N3G

4-(3-Trifluoromethylphenyl)-pyrimidine-2-carbonitrile as cathepsin S inhibitors: N3, not N1 is critically important

• PDB DOI: https://doi.org/10.2210/pdb3N3G/pdb

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


• Deposited: 2010-05-20 Released: 2010-07-14 
• Deposition Author(s): Fradera, X., Uitdehaag, J.C.M., van Zeeland, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.264 
• R-Value Work: 0.223 
• R-Value Observed: 0.225 

Literature

4-(3-Trifluoromethylphenyl)-pyrimidine-2-carbonitrile as cathepsin S inhibitors: N3, not N1 is critically important.

Cai, J., Fradera, X., van Zeeland, M., Dempster, M., Cameron, K.S., Bennett, D.J., Robinson, J., Popplestone, L., Baugh, M., Westwood, P., Bruin, J., Hamilton, W., Kinghorn, E., Long, C., Uitdehaag, J.C.

(2010) Bioorg Med Chem Lett 20: 4507-4510

• PubMed: 20580231 
• DOI: https://doi.org/10.1016/j.bmcl.2010.06.043
• Primary Citation of Related Structures:  
  3N3G


• PubMed Abstract: 
  

  Using computer aided modelling studies, a new extended P2/S2 interaction was identified. This extended region can accommodate a variety of functional groups, such as aryls and basic amines. It was discovered that the N3 nitrogen of the pyrimidine-2-carbonitrile is critical for its cathepsin cysteine protease inhibition. N1 nitrogen also contributes to the inhibitory activity, but to a very limited degree. An 'in situ double activation' mechanism was proposed to explain these results.

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Organizational Affiliation: 

Merck Research Laboratories, MSD, Newhouse, Lanarkshire, 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: 49.7 kDa 
• Atom Count: 4,014 
• 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 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 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
935	E [auth A], J [auth B]	(E)-1-(6-{4-[3-(4-methylpiperazin-1-yl)propoxy]-3-(trifluoromethyl)phenyl}pyridin-2-yl)methanimine C21 H25 F3 N4 O BNDJQLLXZUKTHM-MFKUBSTISA-N
93N	F [auth A]	6-{4-[3-(4-methylpiperazin-1-yl)propoxy]-3-(trifluoromethyl)phenyl}pyridine-2-carbonitrile C21 H23 F3 N4 O CWICZCHZPOSFKO-UHFFFAOYSA-N
PEG	C [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4	G [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	H [auth B], I [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS	D [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
93N	PDBBind:  3N3G	Ki: 58 (nM) from 1 assay(s)
	BindingDB:  3N3G	IC50: 58 (nM) from 1 assay(s)
		EC50: 138 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.264 
• R-Value Work: 0.223 
• R-Value Observed: 0.225 
• Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.757	α = 90
b = 85.757	β = 90
c = 150.902	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: 2010-07-14 
Deposition Author(s): Fradera, X., Uitdehaag, J.C.M., van Zeeland, M.

Revision History  

• Version 1.0: 2010-07-14
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance