4KFO | pdb_00004kfo

Structure-Based Discovery of Novel Amide-Containing Nicotinamide Phosphoribosyltransferase (Nampt) Inhibitors

• PDB DOI: https://doi.org/10.2210/pdb4KFO/pdb

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


• Deposited: 2013-04-27 Released: 2013-05-08 
• Deposition Author(s): Zheng, X., Bauer, P., Baumeister, T., Buckmelter, A.J., Caligiuri, M., Clodfelter, K.H., Han, B., Ho, Y., Kley, N., Lin, J., Reynolds, D.J., Sharma, G., Smith, C.C., Wang, Z., Dragovich, P.S., Gunzner-Tosteb, J., Liederer, B.M., Ly, J., O'Brien, T., Oh, A., Wang, L., Wang, W., Xiao, Y., Zak, M., Zhao, G., Yuen, P., Bair, K.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.181 (Depositor), 0.175 (DCC) 
• R-Value Work: 
  0.155 (Depositor), 0.149 (DCC) 
• R-Value Observed: 
  0.157 (Depositor) 

Literature

Structure-based identification of ureas as novel nicotinamide phosphoribosyltransferase (nampt) inhibitors.

Zheng, X., Bauer, P., Baumeister, T., Buckmelter, A.J., Caligiuri, M., Clodfelter, K.H., Han, B., Ho, Y.C., Kley, N., Lin, J., Reynolds, D.J., Sharma, G., Smith, C.C., Wang, Z., Dragovich, P.S., Oh, A., Wang, W., Zak, M., Gunzner-Toste, J., Zhao, G., Yuen, P.W., Bair, K.W.

(2013) J Med Chem 56: 4921-4937

• PubMed: 23617784 
• DOI: https://doi.org/10.1021/jm400186h
• Primary Citation Related Structures: 
  4JR5, 4KFN, 4KFO


• PubMed Abstract: 
  

  Nicotinamide phosphoribosyltransferase (Nampt) is a promising anticancer target. Virtual screening identified a thiourea analogue, compound 5, as a novel highly potent Nampt inhibitor. Guided by the cocrystal structure of 5, SAR exploration revealed that the corresponding urea compound 7 exhibited similar potency with an improved solubility profile. These studies also indicated that a 3-pyridyl group was the preferred substituent at one inhibitor terminus and also identified a urea moiety as the optimal linker to the remainder of the inhibitor structure. Further SAR optimization of the other inhibitor terminus ultimately yielded compound 50 as a urea-containing Nampt inhibitor which exhibited excellent biochemical and cellular potency (enzyme IC50 = 0.007 μM; A2780 IC50 = 0.032 μM). Compound 50 also showed excellent in vivo antitumor efficacy when dosed orally in an A2780 ovarian tumor xenograft model (TGI of 97% was observed on day 17).

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Organizational Affiliation: 
• Forma Therapeutics, Inc., 500 Arsenal Street, Watertown, Massachusetts 02472, USA. [e-mail]

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: 115.74 kDa 
• Atom Count: 8,712 
• Modeled Residue Count: 942 
• 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
1QS	C [auth A], M [auth B]	N-{4-[(3,5-difluorophenyl)sulfonyl]benzyl}imidazo[1,2-a]pyridine-6-carboxamide C21 H15 F2 N3 O3 S XRDVXQQZLHVEQZ-UHFFFAOYSA-N
PO4	D [auth A], E [auth A], N [auth B], O [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], K [auth A], L [auth A], 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
1QS	BindingDB:  4KFO	IC50: min: 2, max: 42 (nM) from 5 assay(s)
		EC50: min: 1.1, max: 1.3 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.181 (Depositor), 0.175 (DCC) 
• R-Value Work:  0.155 (Depositor), 0.149 (DCC) 
• R-Value Observed: 0.157 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.779	α = 90
b = 106.439	β = 96.55
c = 82.917	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-05-08 
Deposition Author(s): Zheng, X., Bauer, P., Baumeister, T., Buckmelter, A.J., Caligiuri, M., Clodfelter, K.H., Han, B., Ho, Y., Kley, N., Lin, J., Reynolds, D.J., Sharma, G., Smith, C.C., Wang, Z., Dragovich, P.S., Gunzner-Tosteb, J., Liederer, B.M., Ly, J., O'Brien, T., Oh, A., Wang, L., Wang, W., Xiao, Y., Zak, M., Zhao, G., Yuen, P., Bair, K.W.

Revision History  

• Version 1.0: 2013-05-08
  Type: Initial release
  
• Version 1.1: 2013-06-26
  Changes: Database references
• Version 1.2: 2013-07-10
  Changes: Database references
• Version 1.3: 2024-02-28
  Changes: Data collection, Database references, Derived calculations