4O1D

Structural Basis for Resistance to Diverse Classes of NAMPT Inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural Basis for Resistance to Diverse Classes of NAMPT Inhibitors.

Wang, W.Elkins, K.Oh, A.Ho, Y.C.Wu, J.Li, H.Xiao, Y.Kwong, M.Coons, M.Brillantes, B.Cheng, E.Crocker, L.Dragovich, P.S.Sampath, D.Zheng, X.Bair, K.W.O'Brien, T.Belmont, L.D.

(2014) PLoS One 9: e109366-e109366

  • DOI: 10.1371/journal.pone.0109366
  • Primary Citation of Related Structures:  
    4O13, 4O14, 4O15, 4O1A, 4O1B, 4O1C, 4O1D, 4O16, 4O17, 4O18

  • PubMed Abstract: 
  • Inhibiting NAD biosynthesis by blocking the function of nicotinamide phosphoribosyl transferase (NAMPT) is an attractive therapeutic strategy for targeting tumor metabolism. However, the development of drug resistance commonly limits the efficacy of cancer therapeutics ...

    Inhibiting NAD biosynthesis by blocking the function of nicotinamide phosphoribosyl transferase (NAMPT) is an attractive therapeutic strategy for targeting tumor metabolism. However, the development of drug resistance commonly limits the efficacy of cancer therapeutics. This study identifies mutations in NAMPT that confer resistance to a novel NAMPT inhibitor, GNE-618, in cell culture and in vivo, thus demonstrating that the cytotoxicity of GNE-618 is on target. We determine the crystal structures of six NAMPT mutants in the apo form and in complex with various inhibitors and use cellular, biochemical and structural data to elucidate two resistance mechanisms. One is the surprising finding of allosteric modulation by mutation of residue Ser165, resulting in unwinding of an α-helix that binds the NAMPT substrate 5-phosphoribosyl-1-pyrophosphate (PRPP). The other mechanism is orthosteric blocking of inhibitor binding by mutations of Gly217. Furthermore, by evaluating a panel of diverse small molecule inhibitors, we unravel inhibitor structure activity relationships on the mutant enzymes. These results provide valuable insights into the design of next generation NAMPT inhibitors that offer improved therapeutic potential by evading certain mechanisms of resistance.


    Organizational Affiliation

    Genentech, Inc., South San Francisco, California, United States of America.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nicotinamide phosphoribosyltransferaseA, B501Homo sapiensMutation(s): 1 
Gene Names: NAMPTPBEFPBEF1
EC: 2.4.2.12
UniProt & NIH Common Fund Data Resources
Find proteins for P43490 (Homo sapiens)
Explore P43490 
Go to UniProtKB:  P43490
PHAROS:  P43490
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DGB
Query on DGB

Download Ideal Coordinates CCD File 
C [auth A], M [auth B](2E)-N-{4-[1-(benzenecarbonyl)piperidin-4-yl]butyl}-3-(pyridin-3-yl)prop-2-enamide
C24 H29 N3 O2
KPBNHDGDUADAGP-VAWYXSNFSA-N
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
D [auth A], L [auth A], N [auth B], W [auth B]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
E [auth A] , F [auth A] , G [auth A] , H [auth A] , I [auth A] , J [auth A] , K [auth A] , O [auth B] , 
E [auth A],  F [auth A],  G [auth A],  H [auth A],  I [auth A],  J [auth A],  K [auth A],  O [auth B],  P [auth B],  Q [auth B],  R [auth B],  S [auth B],  T [auth B],  U [auth B],  V [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DGBIC50:  3   nM  BindingDB
DGBKi:  0.30000001192092896   nM  BindingDB
DGBIC50:  4.900000095367432   nM  BindingDB
DGBIC50:  24   nM  Binding MOAD
DGBIC50:  2.200000047683716   nM  BindingDB
DGBIC50:  1   nM  BindingDB
DGBIC50:  0.14000000059604645   nM  BindingDB
DGBIC50:  5   nM  BindingDB
DGBIC50:  9   nM  BindingDB
DGBKi:  3   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.658α = 90
b = 106.599β = 96.42
c = 83.376γ = 90
Software Package:
Software NamePurpose
B3data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-22
    Type: Initial release
  • Version 1.1: 2016-11-09
    Changes: Non-polymer description