3P97

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

• PDB DOI: https://doi.org/10.2210/pdb3P97/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): dengue virus type 3
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-10-16 Released: 2010-12-08 
• Deposition Author(s): Noble, C.G., Yap, L.J., Lescar, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.221 
• R-Value Work: 0.192 
• R-Value Observed: 0.194 

Starting Model: experimental

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

• PubMed: 21147775 
• DOI: https://doi.org/10.1074/jbc.M110.179184
• Primary Citation of Related Structures:  
  3P8Z, 3P97


• 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 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.

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Organizational Affiliation: 

Novartis Institute for Tropical Diseases, 05-01 Chromos, Singapore. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 60.94 kDa 
• Atom Count: 4,856 
• Modelled Residue Count: 512 
• Deposited Residue Count: 534 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 5	A, B [auth C]	267	dengue virus type 3	Mutation(s): 0  EC: 2.1.1.56 (PDB Primary Data), 2.1.1.57 (PDB Primary Data)
UniProt
Find proteins for P27915 (Dengue virus type 3 (strain Philippines/H87/1956)) Explore P27915  Go to UniProtKB:  P27915

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAM	C [auth A], D [auth C]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.221 
• R-Value Work: 0.192 
• R-Value Observed: 0.194 
• Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.818	α = 90
b = 61.097	β = 90
c = 186.035	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-12-08 
Deposition Author(s): Noble, C.G., Yap, L.J., Lescar, J.

Revision History  

• Version 1.0: 2010-12-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-09-28
  Changes: Database references
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description