4LVB

Fragment-based Identification of Amides Derived From trans-2-(Pyridin-3-yl)cyclopropanecarboxylic Acid as Potent Inhibitors of Human Nicotinamide Phosphoribosyltransferase (NAMPT)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.836 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Identification of amides derived from 1H-pyrazolo[3,4-b]pyridine-5-carboxylic acid as potent inhibitors of human nicotinamide phosphoribosyltransferase (NAMPT).

Zheng, X.Bair, K.W.Bauer, P.Baumeister, T.Bowman, K.K.Buckmelter, A.J.Caligiuri, M.Clodfelter, K.H.Feng, Y.Han, B.Ho, Y.C.Kley, N.Li, H.Liang, X.Liederer, B.M.Lin, J.Ly, J.O'Brien, T.Oeh, J.Oh, A.Reynolds, D.J.Sampath, D.Sharma, G.Skelton, N.Smith, C.C.Tremayne, J.Wang, L.Wang, W.Wang, Z.Wu, H.Wu, J.Xiao, Y.Yang, G.Yuen, P.W.Zak, M.Dragovich, P.S.

(2013) Bioorg.Med.Chem.Lett. 23: 5488-5497

  • DOI: 10.1016/j.bmcl.2013.08.074
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Potent, 1H-pyrazolo[3,4-b]pyridine-containing inhibitors of the human nicotinamide phosphoribosyltransferase (NAMPT) enzyme were identified using structure-based design techniques. Many of these compounds exhibited nanomolar antiproliferation activit ...

    Potent, 1H-pyrazolo[3,4-b]pyridine-containing inhibitors of the human nicotinamide phosphoribosyltransferase (NAMPT) enzyme were identified using structure-based design techniques. Many of these compounds exhibited nanomolar antiproliferation activities against human tumor lines in in vitro cell culture experiments, and a representative example (compound 26) demonstrated encouraging in vivo efficacy in a mouse xenograft tumor model derived from the A2780 cell line. This molecule also exhibited reduced rat retinal exposures relative to a previously studied imidazo-pyridine-containing NAMPT inhibitor. Somewhat surprisingly, compound 26 was only weakly active in vitro against mouse and monkey tumor cell lines even though it was a potent inhibitor of NAMPT enzymes derived from these species. The compound also exhibited only minimal effects on in vivo NAD levels in mice, and these changes were considerably less profound than those produced by an imidazo-pyridine-containing NAMPT inhibitor. The crystal structures of compound 26 and the corresponding PRPP-derived ribose adduct in complex with NAMPT were also obtained.


    Organizational Affiliation

    Forma Therapeutics, Inc., 500 Arsenal Street, Watertown, MA 02472, USA.




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

Download SDF File 
Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
20N
Query on 20N

Download SDF File 
Download CCD File 
A, B
N-[4-(acetylamino)phenyl]cyclopropanecarboxamide
C12 H14 N2 O2
XJFJFROTOPBZCO-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
20NKd: 78000 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.836 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.175 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 60.612α = 90.00
b = 106.681β = 96.39
c = 83.142γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling
Blu-Icedata collection
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2013-09-25
    Type: Initial release
  • Version 1.1: 2013-10-02
    Type: Database references
  • Version 1.2: 2018-01-24
    Type: Structure summary