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

  • Resolution: 1.75 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 

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This is version 1.3 of the entry. See complete history


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: https://doi.org/10.1016/j.bmcl.2013.08.074
  • Primary Citation of Related Structures:  
    4LV9, 4LVA, 4LVB, 4LVD, 4LVF, 4LVG, 4M6P, 4M6Q

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nicotinamide phosphoribosyltransferaseA [auth B],
B [auth A]
501Homo 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
Binding Affinity Annotations 
IDSourceBinding Affinity
1EB BindingDB:  4LVD Kd: 5.10e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.75 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.423α = 90
b = 106.039β = 96.26
c = 83.055γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2013-09-25
    Type: Initial release
  • Version 1.1: 2013-10-02
    Changes: Database references
  • Version 1.2: 2018-01-24
    Changes: Advisory, Structure summary
  • Version 1.3: 2024-02-28
    Changes: Advisory, Data collection, Database references, Derived calculations