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): Yes 

  • 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 
  • R-Value Observed: 0.224 

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
  • Primary Citation of Related Structures:  
    6ORR

  • 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 rational design led to the development of potent and selective alkynyl bisubstrate inhibitors of NNMT ...

    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 cocrystal 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 --: --

    Organizational Affiliation

    Jubilant Biosys Ltd. , Yeshwantpur, Bangalore , 560 022 Karnataka , India.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NNMT proteinA, B, C, D283Homo sapiensMutation(s): 3 
Gene Names: NNMThCG_39357
EC: 2.1.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P40261 (Homo sapiens)
Explore P40261 
Go to UniProtKB:  P40261
PHAROS:  P40261
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
N37
Query on N37

Download Ideal Coordinates CCD File 
E [auth A], J [auth B], K [auth C], M [auth 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
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A], G [auth A], H [auth A], I [auth A], L [auth C]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
N37Ki:  0.5   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 
  • Space Group: P 1
  • Diffraction Data DOI: 10.15785/SBGRID/731 SBGrid
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.074α = 82.519
b = 62.203β = 81.844
c = 108.202γ = 68.353
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



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  (Full details and data files)

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