5YJI

Co-crystal structure of Mouse Nicotinamide N-methyltransferase (NNMT) with small molecule analog of Nicotinamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

A small molecule inhibitor of Nicotinamide N-methyltransferase for the treatment of metabolic disorders.

Kannt, A.Rajagopal, S.Kadnur, S.V.Suresh, J.Bhamidipati, R.K.Swaminathan, S.Hallur, M.S.Kristam, R.Elvert, R.Czech, J.Pfenninger, A.Rudolph, C.Schreuder, H.Chandrasekar, D.V.Mane, V.S.Birudukota, S.Shaik, S.Zope, B.R.Burri, R.R.Anand, N.N.Thakur, M.K.Singh, M.Parveen, R.Kandan, S.Mullangi, R.Yura, T.Gosu, R.Ruf, S.Dhakshinamoorthy, S.

(2018) Sci Rep 8: 3660-3660

  • DOI: 10.1038/s41598-018-22081-7
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Nicotinamide N-methyltransferase (NNMT) is a cytosolic enzyme that catalyzes the transfer of a methyl group from the co-factor S-adenosyl-L-methionine (SAM) onto the substrate, nicotinamide (NA) to form 1-methyl-nicotinamide (MNA). Higher NNMT expres ...

    Nicotinamide N-methyltransferase (NNMT) is a cytosolic enzyme that catalyzes the transfer of a methyl group from the co-factor S-adenosyl-L-methionine (SAM) onto the substrate, nicotinamide (NA) to form 1-methyl-nicotinamide (MNA). Higher NNMT expression and MNA concentrations have been associated with obesity and type-2 diabetes. Here we report a small molecule analog of NA, JBSNF-000088, that inhibits NNMT activity, reduces MNA levels and drives insulin sensitization, glucose modulation and body weight reduction in animal models of metabolic disease. In mice with high fat diet (HFD)-induced obesity, JBSNF-000088 treatment caused a reduction in body weight, improved insulin sensitivity and normalized glucose tolerance to the level of lean control mice. These effects were not seen in NNMT knockout mice on HFD, confirming specificity of JBSNF-000088. The compound also improved glucose handling in ob/ob and db/db mice albeit to a lesser extent and in the absence of weight loss. Co-crystal structure analysis revealed the presence of the N-methylated product of JBSNF-000088 bound to the NNMT protein. The N-methylated product was also detected in the plasma of mice treated with JBSNF-000088. Hence, JBSNF-000088 may act as a slow-turnover substrate analog, driving the observed metabolic benefits.


    Organizational Affiliation

    Sanofi Research and Development, Industriepark Hoechst, H823, D-65926, Frankfurt am Main, Germany. aimo.kannt@sanofi.com.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nicotinamide N-methyltransferase
A, B
284Mus musculusMutation(s): 0 
Gene Names: Nnmt
EC: 2.1.1.1
Find proteins for O55239 (Mus musculus)
Go to UniProtKB:  O55239
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAH
Query on SAH

Download SDF File 
Download CCD File 
A, B
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
8WO
Query on 8WO

Download SDF File 
Download CCD File 
A, B
6-methoxy-1-methyl-2H-pyridine-3-carboxamide
C8 H12 N2 O2
XDTUJYQFSMEIJT-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.210 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 47.356α = 90.00
b = 71.622β = 90.00
c = 157.408γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
XDSdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-03-21
    Type: Initial release