5KIT

Crystal Structure of Nicotinamide Phosphoribosyltransferase (Nampt) in Complex with Inhibitors 37


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.137 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Minimizing CYP2C9 Inhibition of Exposed-Pyridine NAMPT (Nicotinamide Phosphoribosyltransferase) Inhibitors.

Zak, M.Yuen, P.W.Liu, X.Patel, S.Sampath, D.Oeh, J.Liederer, B.M.Wang, W.O'Brien, T.Xiao, Y.Skelton, N.Hua, R.Sodhi, J.Wang, Y.Zhang, L.Zhao, G.Zheng, X.Ho, Y.C.Bair, K.W.Dragovich, P.S.

(2016) J.Med.Chem. 59: 8345-8368

  • DOI: 10.1021/acs.jmedchem.6b00697

  • PubMed Abstract: 
  • NAMPT inhibitors may show potential as therapeutics for oncology. Throughout our NAMPT inhibitor program, we found that exposed pyridines or related heterocyclic systems in the left-hand portion of the inhibitors are necessary pharmacophores for pote ...

    NAMPT inhibitors may show potential as therapeutics for oncology. Throughout our NAMPT inhibitor program, we found that exposed pyridines or related heterocyclic systems in the left-hand portion of the inhibitors are necessary pharmacophores for potent cellular NAMPT inhibition. However, when combined with a benzyl group in the center of the inhibitors, such pyridine-like moieties also led to consistent and potent inhibition of CYP2C9. In an attempt to reduce CYP2C9 inhibition, a parallel synthesis approach was used to identify central benzyl group replacements with increased Fsp3. A spirocyclic central motif was thus discovered that was combined with left-hand pyridines (or pyridine-like systems) to provide cellularly potent NAMPT inhibitors with minimal CYP2C9 inhibition. Further optimization of potency and ADME properties led to the discovery of compound 68, a highly potent NAMPT inhibitor with outstanding efficacy in a mouse tumor xenograft model and lacking measurable CYP2C9 inhibition at the concentrations tested.


    Organizational Affiliation

    Genentech Inc. , 1 DNA Way, South San Francisco, California 94080, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nicotinamide phosphoribosyltransferase
A, B
491Homo sapiensMutation(s): 0 
Gene Names: NAMPT (PBEF, PBEF1)
EC: 2.4.2.12
Find proteins for P43490 (Homo sapiens)
Go to Gene View: NAMPT
Go to UniProtKB:  P43490
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
6TA
Query on 6TA

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Download CCD File 
A, B
~{tert}-butyl (2~{S})-2-[(1,3-dihydropyrrolo[3,4-c]pyridin-2-ylcarbonylamino)methyl]-6-azaspiro[2.5]octane-6-carboxylate
C21 H30 N4 O3
DLHHFYXNVIMXSY-QGZVFWFLSA-N
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
6TAIC50: 13 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.137 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 60.748α = 90.00
b = 106.589β = 96.65
c = 83.320γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2016-06-17 
  • Released Date: 2016-08-31 
  • Deposition Author(s): Li, D., Wang, W.

Revision History 

  • Version 1.0: 2016-08-31
    Type: Initial release
  • Version 1.1: 2016-10-05
    Type: Database references