4O14 | pdb_00004o14

Structural Basis for Resistance to Diverse Classes of NAMPT Inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 
    0.188 (Depositor), 0.190 (DCC) 
  • R-Value Work: 
    0.151 (Depositor), 0.153 (DCC) 
  • R-Value Observed: 
    0.153 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4O14

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: https://doi.org/10.1371/journal.pone.0109366
  • Primary Citation Related Structures: 
    4O13, 4O14, 4O15, 4O16, 4O17, 4O18, 4O19, 4O1A, 4O1B, 4O1C, 4O1D, 4O28

  • 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. 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.

Macromolecule Content 

  • Total Structure Weight: 114.69 kDa 
  • Atom Count: 8,443 
  • Modeled Residue Count: 938 
  • Deposited Residue Count: 1,002 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Nicotinamide phosphoribosyltransferase
A, B
501Homo 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
GTEx:  ENSG00000105835 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43490
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PO4

Query on PO4



Download:Ideal Coordinates CCD File
C [auth A],
H [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO

Query on EDO



Download:Ideal Coordinates CCD File
D [auth A]
E [auth A]
F [auth A]
G [auth A]
I [auth B]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
I [auth B],
J [auth B],
K [auth B],
L [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free:  0.188 (Depositor), 0.190 (DCC) 
  • R-Value Work:  0.151 (Depositor), 0.153 (DCC) 
  • R-Value Observed: 0.153 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.318α = 90
b = 105.651β = 96.93
c = 83.329γ = 90
Software Package:
Software NamePurpose
BOSdata 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: 2024-02-28
    Changes: Data collection, Database references, Derived calculations