4N9D

Fragment-based Design of 3-Aminopyridine-derived Amides as Potent Inhibitors of Human Nicotinamide Phosphoribosyltransferase (NAMPT)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.701 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.152 

wwPDB Validation 3D Report Full Report


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Literature

Fragment-based design of 3-aminopyridine-derived amides as potent inhibitors of human nicotinamide phosphoribosyltransferase (NAMPT).

Dragovich, P.S.Zhao, G.Baumeister, T.Bravo, B.Giannetti, A.M.Ho, Y.C.Hua, R.Li, G.Liang, X.Ma, X.O'Brien, T.Oh, A.Skelton, N.J.Wang, C.Wang, W.Wang, Y.Xiao, Y.Yuen, P.W.Zak, M.Zhao, Q.Zheng, X.

(2014) Bioorg.Med.Chem.Lett. 24: 954-962

  • DOI: 10.1016/j.bmcl.2013.12.062
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The fragment-based identification of two novel and potent biochemical inhibitors of the nicotinamide phosphoribosyltransferase (NAMPT) enzyme is described. These compounds (51 and 63) incorporate an amide moiety derived from 3-aminopyridine, and are ...

    The fragment-based identification of two novel and potent biochemical inhibitors of the nicotinamide phosphoribosyltransferase (NAMPT) enzyme is described. These compounds (51 and 63) incorporate an amide moiety derived from 3-aminopyridine, and are thus structurally distinct from other known anti-NAMPT agents. Each exhibits potent inhibition of NAMPT biochemical activity (IC50=19 and 15 nM, respectively) as well as robust antiproliferative properties in A2780 cell culture experiments (IC50=121 and 99 nM, respectively). However, additional biological studies indicate that only inhibitor 51 exerts its A2780 cell culture effects via a NAMPT-mediated mechanism. The crystal structures of both 51 and 63 in complex with NAMPT are also independently described.


    Organizational Affiliation

    Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA. Electronic address: dragovich.peter@gene.com.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nicotinamide phosphoribosyltransferase
A, B
501Homo sapiensMutation(s): 0 
Gene Names: NAMPT (PBEF, PBEF1)
EC: 2.4.2.12
Find proteins for P43490 (Homo sapiens)
Go to Gene View: NAMPT
Go to UniProtKB:  P43490
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
2HJ
Query on 2HJ

Download SDF File 
Download CCD File 
A, B
4-({[(4-tert-butylphenyl)sulfonyl]amino}methyl)-N-(pyridin-3-yl)benzamide
C23 H25 N3 O3 S
NGQPRVWTFNBUHA-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
2HJIC50: 19 - 24 nM (100) BINDINGDB
2HJIC50: 19 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.701 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.152 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 60.413α = 90.00
b = 106.337β = 96.57
c = 83.205γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHENIXrefinement
PHASERphasing
DENZOdata reduction
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-02-19
    Type: Initial release