5KIT | pdb_00005kit

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.180 (Depositor), 0.174 (DCC) 
  • R-Value Work: 
    0.137 (Depositor), 0.130 (DCC) 
  • R-Value Observed: 
    0.139 (Depositor) 

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1021/acs.jmedchem.6b00697
  • Primary Citation Related Structures: 
    5KIT

  • 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 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.

Macromolecule Content 

  • Total Structure Weight: 113.09 kDa 
  • Atom Count: 8,832 
  • Modeled Residue Count: 940 
  • Deposited Residue Count: 982 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Nicotinamide phosphoribosyltransferase
A, B
491Homo 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
6TA

Query on 6TA



Download:Ideal Coordinates CCD File
C [auth A],
K [auth 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
PO4

Query on PO4



Download:Ideal Coordinates CCD File
D [auth A]
E [auth A]
J [auth A]
L [auth B]
M [auth B]
D [auth A],
E [auth A],
J [auth A],
L [auth B],
M [auth B],
R [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]
N [auth B]
F [auth A],
G [auth A],
H [auth A],
I [auth A],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
S [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
6TA BindingDB:  5KIT IC50: min: 1, max: 13 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.180 (Depositor), 0.174 (DCC) 
  • R-Value Work:  0.137 (Depositor), 0.130 (DCC) 
  • R-Value Observed: 0.139 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.748α = 90
b = 106.589β = 96.65
c = 83.32γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-31
    Type: Initial release
  • Version 1.1: 2016-10-05
    Changes: Database references
  • Version 1.2: 2024-03-06
    Changes: Data collection, Database references, Derived calculations