4JNM | pdb_00004jnm

Discovery of Potent and Efficacious Urea-containing Nicotinamide Phosphoribosyltransferase (NAMPT) Inhibitors with Reduced CYP2C9 Inhibition Properties

• PDB DOI: https://doi.org/10.2210/pdb4JNM/pdb

• Classification: Transferase/Transferase inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-03-15 Released: 2013-05-29 
• Deposition Author(s): Gunzner-Toste, J., Zhao, G., Bauer, P., Baumeister, T., Buckmelter, A.J., Caligiuri, M., Clodfelter, K.H., Fu, B., Han, B., Ho, Y., Kley, N., Liederer, B., Lin, J., Mukadam, S., O'Brien, T., Reynolds, D.J., Sharma, G., Skelton, N., Smith, C.C., Oh, A., Wang, W., Wang, Z., Xiao, Y., Yuen, P., Zak, M., Zhang, L., Zheng, X., Bair, K.W., Dragovich, P.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.249 (Depositor), 0.243 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Literature

Discovery of potent and efficacious urea-containing nicotinamide phosphoribosyltransferase (NAMPT) inhibitors with reduced CYP2C9 inhibition properties.

Gunzner-Toste, J., Zhao, G., Bauer, P., Baumeister, T., Buckmelter, A.J., Caligiuri, M., Clodfelter, K.H., Fu, B., Han, B., Ho, Y.C., Kley, N., Liang, X., Liederer, B.M., Lin, J., Mukadam, S., O'Brien, T., Oh, A., Reynolds, D.J., Sharma, G., Skelton, N., Smith, C.C., Sodhi, J., Wang, W., Wang, Z., Xiao, Y., Yuen, P.W., Zak, M., Zhang, L., Zheng, X., Bair, K.W., Dragovich, P.S.

(2013) Bioorg Med Chem Lett 23: 3531-3538

• PubMed: 23668988 
• DOI: https://doi.org/10.1016/j.bmcl.2013.04.040
• Primary Citation Related Structures: 
  4JNM


• PubMed Abstract: 
  

  Potent, reversible inhibition of the cytochrome P450 CYP2C9 isoform was observed in a series of urea-containing nicotinamide phosphoribosyltransferase (NAMPT) inhibitors. This unwanted property was successfully removed from the described inhibitors through a combination of structure-based design and medicinal chemistry activities. An optimized compound which did not inhibit CYP2C9 exhibited potent anti-NAMPT activity (17; BC NAMPT IC50=3 nM; A2780 antiproliferative IC50=70 nM), good mouse PK properties, and was efficacious in an A2780 mouse xenograft model. The crystal structure of this compound in complex with the NAMPT protein is also described.

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Organizational Affiliation: 
• Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 115.65 kDa 
• Atom Count: 8,280 
• Modeled Residue Count: 944 
• Deposited Residue Count: 1,002 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nicotinamide phosphoribosyltransferase	A, B	501	Homo sapiens	Mutation(s): 0  Gene Names: NAMPT, PBEF, PBEF1 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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1LJ	C [auth A], K [auth B]	1-[(6-aminopyridin-3-yl)methyl]-3-[4-(phenylsulfonyl)phenyl]urea C19 H18 N4 O3 S CYPHXCMPISHSDL-UHFFFAOYSA-N
PO4	D [auth A], E [auth A], L [auth B], M [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO	F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
1LJ	BindingDB:  4JNM	IC50: min: 3, max: 70 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.249 (Depositor), 0.243 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.44	α = 90
b = 106.323	β = 96.34
c = 82.824	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-05-29 
Deposition Author(s): Gunzner-Toste, J., Zhao, G., Bauer, P., Baumeister, T., Buckmelter, A.J., Caligiuri, M., Clodfelter, K.H., Fu, B., Han, B., Ho, Y., Kley, N., Liederer, B., Lin, J., Mukadam, S., O'Brien, T., Reynolds, D.J., Sharma, G., Skelton, N., Smith, C.C., Oh, A., Wang, W., Wang, Z., Xiao, Y., Yuen, P., Zak, M., Zhang, L., Zheng, X., Bair, K.W., Dragovich, P.S.

Revision History  

• Version 1.0: 2013-05-29
  Type: Initial release
  
• Version 1.1: 2013-06-05
  Changes: Database references
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations