4WQ6 | pdb_00004wq6

The crystal structure of human Nicotinamide phosphoribosyltransferase (NAMPT) in complex with N-(4-{(S)-[1-(2-methylpropyl)piperidin-4-yl]sulfinyl}benzyl)furo[2,3-c]pyridine-2-carboxamide inhibitor (compound 21)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 
    0.188 (Depositor), 0.209 (DCC) 
  • R-Value Work: 
    0.163 (Depositor) 
  • R-Value Observed: 
    0.164 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 4WQ6

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Identification of nicotinamide phosphoribosyltransferase (NAMPT) inhibitors with no evidence of CYP3A4 time-dependent inhibition and improved aqueous solubility.

Zak, M.Liederer, B.M.Sampath, D.Yuen, P.W.Bair, K.W.Baumeister, T.Buckmelter, A.J.Clodfelter, K.H.Cheng, E.Crocker, L.Fu, B.Han, B.Li, G.Ho, Y.C.Lin, J.Liu, X.Ly, J.O'Brien, T.Reynolds, D.J.Skelton, N.Smith, C.C.Tay, S.Wang, W.Wang, Z.Xiao, Y.Zhang, L.Zhao, G.Zheng, X.Dragovich, P.S.

(2015) Bioorg Med Chem Lett 25: 529-541

  • DOI: https://doi.org/10.1016/j.bmcl.2014.12.026
  • Primary Citation Related Structures: 
    4WQ6

  • PubMed Abstract: 

    Herein we report the optimization efforts to ameliorate the potent CYP3A4 time-dependent inhibition (TDI) and low aqueous solubility exhibited by a previously identified lead compound from our NAMPT inhibitor program (1, GNE-617). Metabolite identification studies pinpointed the imidazopyridine moiety present in 1 as the likely source of the TDI signal, and replacement with other bicyclic systems was found to reduce or eliminate the TDI finding. A strategy of reducing the number of aromatic rings and/or lowering cLogD7.4 was then employed to significantly improve aqueous solubility. These efforts culminated in the discovery of 42, a compound with no evidence of TDI, improved aqueous solubility, and robust efficacy in tumor xenograft studies.


  • Organizational Affiliation
    • Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA. Electronic address: mzak@gene.com.

Macromolecule Content 

  • Total Structure Weight: 115.95 kDa 
  • Atom Count: 8,277 
  • Modeled Residue Count: 939 
  • 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): 0 
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 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3TQ

Query on 3TQ



Download:Ideal Coordinates CCD File
C [auth A],
O [auth B]
N-(4-{(S)-[1-(2-methylpropyl)piperidin-4-yl]sulfinyl}benzyl)furo[2,3-c]pyridine-2-carboxamide
C24 H29 N3 O3 S
CIUHVWRNTOWXDH-WJOKGBTCSA-N
PO4

Query on PO4



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

Query on EDO



Download:Ideal Coordinates CCD File
F [auth A]
G [auth A]
H [auth A]
I [auth A]
J [auth A]
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
R [auth B],
S [auth B],
T [auth B],
U [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free:  0.188 (Depositor), 0.209 (DCC) 
  • R-Value Work:  0.163 (Depositor) 
  • R-Value Observed: 0.164 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.621α = 90
b = 106.839β = 96.64
c = 83.086γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-02-11
    Type: Initial release
  • Version 1.1: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy