6ORR

Co-crystal structure of human NicotinamideN-Methyltransferase (NNMT) in complex with High-Affinity Alkynyl Bisubstrate Inhibitor NS1

  • Classification: TRANSFERASE/TRANSFERASE INHIBITOR
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli BL21(DE3)
  • Mutation(s): 

  • Deposited: 2019-04-30 Released: 2019-10-23 
  • Deposition Author(s): May, E.J., Policarpo, R.L., Gaudet, R.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS); National Institutes of Health/National Center for Research Resources (NIH/NCRR); National Science Foundation (NSF, United States); Department of Energy (DOE, United States) 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

High-Affinity Alkynyl Bisubstrate Inhibitors of NicotinamideN-Methyltransferase (NNMT).

Policarpo, R.L.Decultot, L.May, E.Kuzmic, P.Carlson, S.Huang, D.Chu, V.Wright, B.A.Dhakshinamoorthy, S.Kannt, A.Rani, S.Dittakavi, S.Panarese, J.D.Gaudet, R.Shair, M.D.

(2019) J.Med.Chem. 62: 9837-9873

  • DOI: 10.1021/acs.jmedchem.9b01238

  • PubMed Abstract: 
  • Nicotinamide N-methyltransferase (NNMT) is a metabolic enzyme that methylates nicotinamide (NAM) using cofactor S-adenosylmethionine (SAM). NNMT overexpression has been linked to diabetes, obesity, and various cancers. In this work, structure-based r ...

    Nicotinamide N-methyltransferase (NNMT) is a metabolic enzyme that methylates nicotinamide (NAM) using cofactor S-adenosylmethionine (SAM). NNMT overexpression has been linked to diabetes, obesity, and various cancers. In this work, structure-based rational design led to the development of potent and selective alkynyl bisubstrate inhibitors of NNMT. The reported nicotinamide-SAM conjugate (named NS1 ) features an alkyne as a key design element that closely mimics the linear, 180° transition state geometry found in the NNMT-catalyzed SAM → NAM methyl transfer reaction. NS1 was synthesized in 14 steps and found to be a high-affinity, subnanomolar NNMT inhibitor. An X-ray co-crystal structure and SAR study revealed the ability of an alkynyl linker to span the methyl transfer tunnel of NNMT with ideal shape complementarity. The compounds reported in this work represent the most potent and selective NNMT inhibitors reported to date. The rational design principle described herein could potentially be extended to other methyltransferase enzymes.


    Related Citations: 
    • High-Affinity Alkynyl Bisubstrate Inhibitors of NicotinamideN-Methyltransferase (NNMT)
      Policarpo, R.L.,Decultot, L.,May, E.J.,Kuzmic, P.,Carlson, S.,Huang, D.,Chu, V.,Wright, B.,Dhakshinamoorthy, S.,Kannt, A.,Rani, S.,Dittakavi, S.,Panarese, J.D.,Gaudet, R.,Shair, M.D.
      (2019) ChemRxiv --: --



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NNMT protein
A, B, C, D
283Homo sapiensMutation(s): 3 
Gene Names: NNMT
EC: 2.1.1.1
Find proteins for P40261 (Homo sapiens)
Go to Gene View: NNMT
Go to UniProtKB:  P40261
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
N37
Query on N37

Download SDF File 
Download CCD File 
A, B, C, D
9-{9-amino-6-[(3-carbamoylphenyl)ethynyl]-5,6,7,8,9-pentadeoxy-D-glycero-alpha-L-talo-decofuranuronosyl}-9H-purin-6-amine
C24 H27 N7 O6
QRKSTGPKAQGBDD-GGPTZFPQSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.222 
  • Space Group: P 1
  • Diffraction Data DOI: 
    10.15785/SBGRID/731 SBGrid
Unit Cell:
Length (Å)Angle (°)
a = 46.074α = 82.52
b = 62.203β = 81.84
c = 108.202γ = 68.35
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP41 GM103403
National Institutes of Health/National Center for Research Resources (NIH/NCRR)United StatesS10 RR029205
National Science Foundation (NSF, United States)United StatesDGE1144152.
Department of Energy (DOE, United States)United StatesDE-AC02-06CH11357

Revision History 

  • Version 1.0: 2019-10-23
    Type: Initial release
  • Version 1.1: 2019-11-27
    Type: Author supporting evidence, Database references