3P97

Dengue 3 NS5 Methyltransferase bound to the substrate S-Adenosyl methionine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Small molecule inhibitors that selectively block dengue virus methyltransferase

Lim, S.P.Sonntag, L.S.Noble, C.Nilar, S.H.Ng, R.H.Zou, G.Monaghan, P.Chung, K.Y.Dong, H.Liu, B.Bodenreider, C.Lee, G.Ding, M.Chan, W.L.Wang, G.Jian, Y.L.Chao, A.T.Lescar, J.Yin, Z.Vedananda, T.R.Keller, T.H.Shi, P.Y.

(2011) J.Biol.Chem. 286: 6233-6240

  • DOI: 10.1074/jbc.M110.179184
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Crystal structure analysis of Flavivirus methyltransferases uncovered a flavivirus-conserved cavity located next to the binding site for its cofactor, S-adenosyl-methionine (SAM). Chemical derivatization of S-adenosyl-homocysteine (SAH), the product ...

    Crystal structure analysis of Flavivirus methyltransferases uncovered a flavivirus-conserved cavity located next to the binding site for its cofactor, S-adenosyl-methionine (SAM). Chemical derivatization of S-adenosyl-homocysteine (SAH), the product inhibitor of the methylation reaction, with substituents that extend into the identified cavity, generated inhibitors that showed improved and selective activity against dengue virus methyltransferase (MTase), but not related human enzymes. Crystal structure of dengue virus MTase with a bound SAH derivative revealed that its N6-substituent bound in this cavity and induced conformation changes in residues lining the pocket. These findings demonstrate that one of the major hurdles for the development of methyltransferase-based therapeutics, namely selectivity for disease-related methyltransferases, can be overcome.


    Organizational Affiliation

    Novartis Institute for Tropical Diseases, 05-01 Chromos, Singapore. siew_pheng.lim@novartis.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Non-structural protein 5
A, C
267Dengue virus type 3 (strain Philippines/H87/1956)Mutation(s): 0 
Find proteins for P27915 (Dengue virus type 3 (strain Philippines/H87/1956))
Go to UniProtKB:  P27915
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAM
Query on SAM

Download SDF File 
Download CCD File 
A, C
S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.192 
  • Space Group: P 2 21 21
Unit Cell:
Length (Å)Angle (°)
a = 51.818α = 90.00
b = 61.097β = 90.00
c = 186.035γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
MOSFLMdata reduction
MOLREPphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-12-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2011-09-28
    Type: Database references