4JNM

Discovery of Potent and Efficacious Urea-containing Nicotinamide Phosphoribosyltransferase (NAMPT) Inhibitors with Reduced CYP2C9 Inhibition Properties


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Discovery of potent and efficacious urea-containing nicotinamide phosphoribosyltransferase (NAMPT) inhibitors with reduced CYP2C9 inhibition properties.

Gunzner-Toste, J.Zhao, G.Bauer, P.Baumeister, T.Buckmelter, A.J.Caligiuri, M.Clodfelter, K.H.Fu, B.Han, B.Ho, Y.C.Kley, N.Liang, X.Liederer, B.M.Lin, J.Mukadam, S.O'Brien, T.Oh, A.Reynolds, D.J.Sharma, G.Skelton, N.Smith, C.C.Sodhi, J.Wang, W.Wang, Z.Xiao, Y.Yuen, P.W.Zak, M.Zhang, L.Zheng, X.Bair, K.W.Dragovich, P.S.

(2013) Bioorg Med Chem Lett 23: 3531-3538

  • DOI: 10.1016/j.bmcl.2013.04.040
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Potent, reversible inhibition of the cytochrome P450 CYP2C9 isoform was observed in a series of urea-containing nicotinamide phosphoribosyltransferase (NAMPT) inhibitors. This unwanted property was successfully removed from the described inhibitors t ...

    Potent, reversible inhibition of the cytochrome P450 CYP2C9 isoform was observed in a series of urea-containing nicotinamide phosphoribosyltransferase (NAMPT) inhibitors. This unwanted property was successfully removed from the described inhibitors through a combination of structure-based design and medicinal chemistry activities. An optimized compound which did not inhibit CYP2C9 exhibited potent anti-NAMPT activity (17; BC NAMPT IC50=3 nM; A2780 antiproliferative IC50=70 nM), good mouse PK properties, and was efficacious in an A2780 mouse xenograft model. The crystal structure of this compound in complex with the NAMPT protein is also described.


    Organizational Affiliation

    Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nicotinamide phosphoribosyltransferase
A, B
501Homo sapiensMutation(s): 0 
Gene Names: NAMPTPBEFPBEF1
EC: 2.4.2.12
Find proteins for P43490 (Homo sapiens)
Go to UniProtKB:  P43490
NIH Common Fund Data Resources
PHAROS  P43490
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1LJ
Query on 1LJ

Download CCD File 
A, B
1-[(6-aminopyridin-3-yl)methyl]-3-[4-(phenylsulfonyl)phenyl]urea
C19 H18 N4 O3 S
CYPHXCMPISHSDL-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

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

Download CCD File 
A, B
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1LJIC50:  3   nM  PDBBind
1LJIC50:  3   nM  BindingDB
1LJIC50:  70   nM  BindingDB
1LJIC50:  3   nM  Binding MOAD
1LJIC50:  30   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.44α = 90
b = 106.323β = 96.34
c = 82.824γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Revision History 

  • Version 1.0: 2013-05-29
    Type: Initial release
  • Version 1.1: 2013-06-05
    Changes: Database references