4KFP

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

• PDB DOI: https://doi.org/10.2210/pdb4KFP/pdb

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


• Deposited: 2013-04-27 Released: 2013-08-14 
• Deposition Author(s): Dragovich, P.S., Bair, K.W., Baumeister, T., Ho, Y., Liederer, B.M., Liu, X., O'Brien, T., Oeh, J., Sampath, D., Skelton, N., Wang, L., Wang, W., Wu, H., Xiao, Y., Yuen, P., Zak, M., Zhang, L., Zheng, X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free: 0.171 
• R-Value Work: 0.143 
• R-Value Observed: 0.144 

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

• PubMed: 23899614 
• DOI: https://doi.org/10.1016/j.bmcl.2013.06.090
• Primary Citation of Related Structures:  
  4KFP


• 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, 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.

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Organizational Affiliation: 

Genentech Inc, 1 DNA Way, South San Francisco, California 94080, 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: 115.66 kDa 
• Atom Count: 8,461 
• Modelled Residue Count: 940 
• 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
1R7	C [auth A], K [auth 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
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]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
1R7	Binding MOAD:  4KFP	IC50: 10 (nM) from 1 assay(s)
	PDBBind:  4KFP	IC50: 10 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free: 0.171 
• R-Value Work: 0.143 
• R-Value Observed: 0.144 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.55	α = 90
b = 106.331	β = 96.58
c = 82.931	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: 2013-08-14 
Deposition Author(s): Dragovich, P.S., Bair, K.W., Baumeister, T., Ho, Y., Liederer, B.M., Liu, X., O'Brien, T., Oeh, J., Sampath, D., Skelton, N., Wang, L., Wang, W., Wu, H., Xiao, Y., Yuen, P., Zak, M., Zhang, L., Zheng, X.

Revision History  

• Version 1.0: 2013-08-14
  Type: Initial release
  
• Version 1.1: 2013-08-21
  Changes: Database references
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations