3N3G | pdb_00003n3g

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 (Depositor), 0.266 (DCC) 
  • R-Value Work: 
    0.223 (Depositor), 0.226 (DCC) 
  • R-Value Observed: 
    0.225 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 935Click on this verticalbar to view detailsBest fitted 93NClick on this verticalbar to view details

This is version 1.2 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: 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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cathepsin S
A, B
217Homo sapiensMutation(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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25774
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
935
Query on 935

Download Ideal Coordinates CCD File 
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
Query on 93N

Download Ideal Coordinates CCD File 
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
Query on PEG

Download Ideal Coordinates CCD File 
C [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
G [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
H [auth B],
I [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
D [auth A]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
93N 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 (Depositor), 0.266 (DCC) 
  • R-Value Work:  0.223 (Depositor), 0.226 (DCC) 
  • R-Value Observed: 0.225 (Depositor) 
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



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 935Click on this verticalbar to view detailsBest fitted 93NClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-07-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2024-12-25
    Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary