4O10

Structural and Biochemical Analyses of the Catalysis and Potency Impact of Inhibitor Phosphoribosylation by Human Nicotinamide Phosphoribosyltransferase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.152 

wwPDB Validation 3D Report Full Report



Literature

Structural and biochemical analyses of the catalysis and potency impact of inhibitor phosphoribosylation by human nicotinamide phosphoribosyltransferase.

Oh, A.Ho, Y.C.Zak, M.Liu, Y.Chen, X.Yuen, P.W.Zheng, X.Liu, Y.Dragovich, P.S.Wang, W.

(2014) Chembiochem 15: 1121-1130

  • DOI: 10.1002/cbic.201402023
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Prolonged inhibition of nicotinamide phosphoribosyltransferase (NAMPT) is a strategy for targeting cancer metabolism. Many NAMPT inhibitors undergo NAMPT-catalyzed phosphoribosylation (pRib), a property often correlated with their cellular potency. T ...

    Prolonged inhibition of nicotinamide phosphoribosyltransferase (NAMPT) is a strategy for targeting cancer metabolism. Many NAMPT inhibitors undergo NAMPT-catalyzed phosphoribosylation (pRib), a property often correlated with their cellular potency. To understand this phenomenon and facilitate drug design, we analyzed a potent cellularly active NAMPT inhibitor (GNE-617). A crystal structure of pRib-GNE-617 in complex with NAMPT protein revealed a relaxed binding mode. Consistently, the adduct formation resulted in tight binding and strong product inhibition. In contrast, a biochemically equipotent isomer of GNE-617 (GNE-643) also formed pRib adducts but displayed significantly weaker cytotoxicity. Structural analysis revealed an altered ligand conformation of GNE-643, thus suggesting weak association of the adducts with NAMPT. Our data support a model for cellularly active NAMPT inhibitors that undergo NAMPT-catalyzed phosphoribosylation to produce pRib adducts that retain efficient binding to the enzyme.


    Organizational Affiliation

    Genentech, Inc., Department of Structural Biology, 1 DNA Way, South San Francisco, California 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
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2QF
Query on 2QF

Download CCD File 
A, B
N-{4-[(3,5-difluorophenyl)sulfonyl]benzyl}indolizine-7-carboxamide
C22 H16 F2 N2 O3 S
XVCMNEXVVACQMR-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 %)
2QFIC50:  78   nM  BindingDB
2QFIC50:  78   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.152 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.473α = 90
b = 106.358β = 96.35
c = 82.791γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2013-12-14 
  • Released Date: 2014-06-18 
  • Deposition Author(s): Oh, A., Wang, W.

Revision History 

  • Version 1.0: 2014-06-18
    Type: Initial release