Crystal Structure of human NAMPT in complex with NVP-LTM976

Experimental Data Snapshot

  • Resolution: 2.46 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.161 

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Scaffold Morphing Identifies 3-Pyridyl Azetidine Ureas as Inhibitors of Nicotinamide Phosphoribosyltransferase (NAMPT).

Palacios, D.S.Meredith, E.L.Kawanami, T.Adams, C.M.Chen, X.Darsigny, V.Palermo, M.Baird, D.George, E.L.Guy, C.Hewett, J.Tierney, L.Thigale, S.Wang, L.Weihofen, W.A.

(2019) ACS Med Chem Lett 10: 1524-1529

  • DOI: https://doi.org/10.1021/acsmedchemlett.9b00325
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Small molecules that inhibit the metabolic enzyme NAMPT have emerged as potential therapeutics in oncology. As part of our effort in this area, we took a scaffold morphing approach and identified 3-pyridyl azetidine ureas as a potent NAMPT inhibiting motif. We explored the SAR of this series, including 5 and 6 amino pyridines, using a convergent synthetic strategy. This lead optimization campaign yielded multiple compounds with excellent in vitro potency and good ADME properties that culminated in compound 27 .

  • Organizational Affiliation

    Global Discovery Chemistry, Novartis Institute for Biomedical Research, 22 Windsor Street, Cambridge, Massachusetts 02139, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nicotinamide phosphoribosyltransferase
A, B, C, D
500Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P43490 (Homo sapiens)
Explore P43490 
Go to UniProtKB:  P43490
PHAROS:  P43490
GTEx:  ENSG00000105835 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43490
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OE4 (Subject of Investigation/LOI)
Query on OE4

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B],
M [auth C]
C24 H20 N4 O3
Query on PO4

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
J [auth B]
K [auth B]
F [auth A],
G [auth A],
H [auth A],
J [auth B],
K [auth B],
L [auth B],
N [auth C],
O [auth C],
P [auth C],
Q [auth D],
R [auth D],
S [auth D]
O4 P
Binding Affinity Annotations 
IDSourceBinding Affinity
OE4 Binding MOAD:  6PEB IC50: 2.7 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.46 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.161 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.74α = 90
b = 96.16β = 90
c = 246.84γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-04
    Type: Initial release
  • Version 1.1: 2023-10-11
    Changes: Data collection, Database references, Refinement description