7ET7

Co-crystal structure of Human Nicotinamide N-methyltransferase (NNMT) with tricyclic small molecule inhibitor JBSNF-000028


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.223 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Novel tricyclic small molecule inhibitors of Nicotinamide N-methyltransferase for the treatment of metabolic disorders.

Ruf, S.Rajagopal, S.Kadnur, S.V.Hallur, M.S.Rani, S.Kristam, R.Swaminathan, S.Zope, B.R.Gondrala, P.K.Swamy, I.Putta, V.P.R.K.Kandan, S.Zech, G.Schreuder, H.Rudolph, C.Elvert, R.Czech, J.Birudukota, S.Siddiqui, M.A.Anand, N.N.Mane, V.S.Dittakavi, S.Suresh, J.Gosu, R.Ramesh, M.Yura, T.Dhakshinamoorthy, S.Kannt, A.

(2022) Sci Rep 12: 15440-15440

  • DOI: https://doi.org/10.1038/s41598-022-19634-2
  • Primary Citation of Related Structures:  
    7ET7, 7EU5

  • PubMed Abstract: 

    Nicotinamide N-methyltransferase (NNMT) is a metabolic regulator that catalyzes the methylation of nicotinamide (Nam) using the co-factor S-adenosyl-L-methionine to form 1-methyl-nicotinamide (MNA). Overexpression of NNMT and the presence of the active metabolite MNA is associated with a number of diseases including metabolic disorders. We conducted a high-throughput screening campaign that led to the identification of a tricyclic core as a potential NNMT small molecule inhibitor series. Elaborate medicinal chemistry efforts were undertaken and hundreds of analogs were synthesized to understand the structure activity relationship and structure property relationship of this tricyclic series. A lead molecule, JBSNF-000028, was identified that inhibits human and mouse NNMT activity, reduces MNA levels in mouse plasma, liver and adipose tissue, and drives insulin sensitization, glucose modulation and body weight reduction in a diet-induced obese mouse model of diabetes. The co-crystal structure showed that JBSNF-000028 binds below a hairpin structural motif at the nicotinamide pocket and stacks between Tyr-204 (from Hairpin) and Leu-164 (from central domain). JBSNF-000028 was inactive against a broad panel of targets related to metabolism and safety. Interestingly, the improvement in glucose tolerance upon treatment with JBSNF-000028 was also observed in NNMT knockout mice with diet-induced obesity, pointing towards the glucose-normalizing effect that may go beyond NNMT inhibition. JBSNF-000028 can be a potential therapeutic option for metabolic disorders and developmental studies are warranted.


  • Organizational Affiliation

    Sanofi-Aventis Deutschland GmbH, R&D, Integrated Drug Discovery, Industriepark Hoechst, 65926, Frankfurt am Main, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nicotinamide N-methyltransferase
A, B, C, D
281Homo sapiensMutation(s): 3 
Gene Names: NNMT
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
GTEx:  ENSG00000166741 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40261
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SAH
Query on SAH

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B],
I [auth C],
K [auth D]
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
JCU (Subject of Investigation/LOI)
Query on JCU

Download Ideal Coordinates CCD File 
F [auth A],
H [auth B],
J [auth C],
L [auth D]
10-methyl-1,10-diazatricyclo[6.3.1.0^{4,12}]dodeca-4,6,8(12)-trien-11-imine
C11 H13 N3
QHQIGFVXRSNTKN-QXMHVHEDSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.223 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.934α = 108.031
b = 62.862β = 103.54
c = 75.6γ = 104.252
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-18
    Type: Initial release
  • Version 1.1: 2022-11-30
    Changes: Database references, Derived calculations
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description