3N3G

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


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 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


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

  • DOI: 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-c ...

    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.


    Organizational Affiliation

    Merck Research Laboratories, MSD, Newhouse, Lanarkshire, UK. jiaqiang.cai@merck.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cathepsin SAB217Homo sapiensMutation(s): 0 
Gene Names: CTSS
EC: 3.4.22.27
Find proteins for P25774 (Homo sapiens)
Explore P25774 
Go to UniProtKB:  P25774
NIH Common Fund Data Resources
PHAROS  P25774
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
935
Query on 935

Download CCD File 
A, 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
 Ligand Interaction
93N
Query on 93N

Download CCD File 
A
6-{4-[3-(4-methylpiperazin-1-yl)propoxy]-3-(trifluoromethyl)phenyl}pyridine-2-carbonitrile
C21 H23 F3 N4 O
CWICZCHZPOSFKO-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

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A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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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
DMS
Query on DMS

Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
93NIC50:  58   nM  BindingDB
93NKi :  58   nM  PDBBind
93NEC50:  138   nM  BindingDB
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 = 85.757α = 90
b = 85.757β = 90
c = 150.902γ = 90
Software Package:
Software NamePurpose
d*TREKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
d*TREKdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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