4KFP

Identification of 2,3-dihydro-1H-pyrrolo[3,4-c]pyridine-derived Ureas as Potent Inhibitors of Human Nicotinamide Phosphoribosyltransferase (NAMPT)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.143 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Identification of 2,3-dihydro-1H-pyrrolo[3,4-c]pyridine-derived ureas as potent inhibitors of human nicotinamide phosphoribosyltransferase (NAMPT).

Dragovich, P.S.Bair, K.W.Baumeister, T.Ho, Y.C.Liederer, B.M.Liu, X.Liu, Y.O'Brien, T.Oeh, J.Sampath, D.Skelton, N.Wang, L.Wang, W.Wu, H.Xiao, Y.Yuen, P.W.Zak, M.Zhang, L.Zheng, X.

(2013) Bioorg.Med.Chem.Lett. 23: 4875-4885

  • DOI: 10.1016/j.bmcl.2013.06.090

  • PubMed Abstract: 
  • Potent nicotinamide phosphoribosyltransferase (NAMPT) inhibitors containing 2,3-dihydro-1H-pyrrolo[3,4-c]pyridine-derived ureas were identified using structure-based design techniques. The new compounds displayed improved aqueous solubilities, determ ...

    Potent nicotinamide phosphoribosyltransferase (NAMPT) inhibitors containing 2,3-dihydro-1H-pyrrolo[3,4-c]pyridine-derived ureas were identified using structure-based design techniques. The new compounds displayed improved aqueous solubilities, determined using a high-throughput solubility assessment, relative to previously disclosed urea and amide-containing NAMPT inhibitors. An optimized 2,3-dihydro-1H-pyrrolo[3,4-c]pyridine-derived compound exhibited potent anti-NAMPT activity (18; BC NAMPT IC50 = 11 nM; PC-3 antiproliferative IC50 = 36 nM), satisfactory mouse PK properties, and was efficacious in a PC-3 mouse xenograft model. The crystal structure of another optimized compound (29; NAMPT IC50 = 10nM; A2780 antiproliferative IC50 = 7 nM) in complex with the NAMPT protein was also determined.


    Organizational Affiliation

    Genentech Inc, 1 DNA Way, South San Francisco, California 94080, USA. dragovich.peter@gene.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nicotinamide phosphoribosyltransferase
A, B
501Homo 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
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
1R7
Query on 1R7

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Download CCD File 
A, B
N-(4-{[1-(tetrahydro-2H-pyran-4-yl)piperidin-4-yl]sulfonyl}benzyl)-2H-pyrrolo[3,4-c]pyridine-2-carboxamide
C25 H30 N4 O4 S
MQRGBJFQXJYKOD-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1R7IC50: 10 nM BINDINGMOAD
1R7IC50: 10 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.143 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 60.550α = 90.00
b = 106.331β = 96.58
c = 82.931γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-08-14
    Type: Initial release
  • Version 1.1: 2013-08-21
    Type: Database references