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

  • 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

  • Resolution: 2.25 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 

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Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


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: https://doi.org/10.1021/acs.jmedchem.9b01238
  • Primary Citation of Related Structures:  

  • 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. 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.

  • Organizational Affiliation

    BioKin Ltd. , Watertown , Massachusetts 02472 , United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NNMT protein
A, B, C, D
283Homo sapiensMutation(s): 3 
Gene Names: NNMThCG_39357
UniProt & NIH Common Fund Data Resources
Find proteins for P40261 (Homo sapiens)
Explore P40261 
Go to UniProtKB:  P40261
PHAROS:  P40261
GTEx:  ENSG00000166741 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40261
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
N37 (Subject of Investigation/LOI)
Query on N37

Download Ideal Coordinates CCD File 
E [auth A],
J [auth B],
K [auth C],
M [auth D]
C24 H27 N7 O6
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
H [auth A],
I [auth A],
L [auth C]
C3 H8 O3
Binding Affinity Annotations 
IDSourceBinding Affinity
N37 Binding MOAD:  6ORR Ki: 0.5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.074α = 82.519
b = 62.203β = 81.844
c = 108.202γ = 68.353
Software Package:
Software NamePurpose
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

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
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description