6PEB

Crystal Structure of human NAMPT in complex with NVP-LTM976


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.161 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

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: 10.1021/acsmedchemlett.9b00325
  • Primary Citation of Related Structures:  
    6PEB

  • 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 ...

    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

    Chemical Biology and Therapeutics, Novartis Institute for Biomedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nicotinamide phosphoribosyltransferaseA, B, C, D500Homo sapiensMutation(s): 0 
Gene Names: NAMPTPBEFPBEF1
EC: 2.4.2.12
UniProt & NIH Common Fund Data Resources
Find proteins for P43490 (Homo sapiens)
Explore P43490 
Go to UniProtKB:  P43490
PHAROS:  P43490
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / 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]N-{4-[(1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)methyl]phenyl}-3-(pyridin-3-yl)azetidine-1-carboxamide
C24 H20 N4 O3
BXJQNJNBPGVHBT-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
BUSTER-TNTphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

  • Deposited Date: 2019-06-20 
  • Released Date: 2019-12-04 
  • Deposition Author(s): Weihofen, W.A.

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-04
    Type: Initial release