Structure of PDB 4n9e Chain A Binding Site BS02

Receptor Information
>4n9e Chain A (length=471) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EFNILLATDSYKVTHYKQYPPNTSKVYSYFECREKKKYEETVFYGLQYIL
NKYLKGKVVTKEKIQEAKDVYKEHFQDDVFNEKGWNYILEKYDGHLPIEI
KAVPEGFVIPRGNVLFTVENTDPECYWLTNWIETILVQSWYPITVATNSR
EQKKILAKYLLETSGNLDGLEYKLHDFGYRGVSSQETAGIGASAHLVNFK
GTDTVAGLALIKKYYGTKDPVPGYSVPAAEHSTITAWGKDHEKDAFEHIV
TQFSSVPVSVVSDSYDIYNACEKIWGEDLRHLIVSRSTQAPLIIRPDSGN
PLDTVLKVLEILGKKFPVTENSKGYKLLPPYLRVIQGDGVDINTLQEIVE
GMKQKMWSIENIAFGSGGGLLQKLTRDLLNCSFKCSYVVTNGLGINVFKD
PVADPNKRSKKGRLSLHRTPAGNFVTLEEGKGDLEEYGQDLLHTVFKNGK
VTKSYSFDEIRKNAQLNIELE
Ligand information
Ligand ID2HL
InChIInChI=1S/C26H25N5O2/c32-25(29-22-7-4-12-27-16-22)21-8-9-24-23(15-21)28-18-31(24)17-19-10-13-30(14-11-19)26(33)20-5-2-1-3-6-20/h1-9,12,15-16,18-19H,10-11,13-14,17H2,(H,29,32)
InChIKeyUROBXDPDOFZURE-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385O=C(Nc1cccnc1)c2ccc3n(CC4CCN(CC4)C(=O)c5ccccc5)cnc3c2
OpenEye OEToolkits 1.7.6c1ccc(cc1)C(=O)N2CCC(CC2)Cn3cnc4c3ccc(c4)C(=O)Nc5cccnc5
ACDLabs 12.01O=C(c1ccccc1)N5CCC(Cn3c4ccc(C(=O)Nc2cccnc2)cc4nc3)CC5
FormulaC26 H25 N5 O2
Name1-[(1-benzoylpiperidin-4-yl)methyl]-N-(pyridin-3-yl)-1H-benzimidazole-5-carboxamide
ChEMBLCHEMBL3116399
DrugBank
ZINCZINC000098208176
PDB chain4n9e Chain B Residue 601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB4n9e Fragment-based design of 3-aminopyridine-derived amides as potent inhibitors of human nicotinamide phosphoribosyltransferase (NAMPT).
Resolution1.72 Å
Binding residue
(original residue number in PDB)		D16 Y18
Binding residue
(residue number reindexed from 1)		D9 Y11
Annotation score1
Binding affinityMOAD: ic50=0.015uM
PDBbind-CN: -logKd/Ki=7.82,IC50=0.015uM
BindingDB: IC50=15nM
Enzymatic activity
Enzyme Commision number 2.4.2.12: nicotinamide phosphoribosyltransferase.
Gene Ontology
Molecular Function
GO:0005125 cytokine activity
GO:0005515 protein binding
GO:0016757 glycosyltransferase activity
GO:0042802 identical protein binding
GO:0047280 nicotinamide phosphoribosyltransferase activity
Biological Process
GO:0007165 signal transduction
GO:0007267 cell-cell signaling
GO:0007623 circadian rhythm
GO:0008284 positive regulation of cell population proliferation
GO:0008286 insulin receptor signaling pathway
GO:0009435 NAD biosynthetic process
GO:0019363 pyridine nucleotide biosynthetic process
GO:0032922 circadian regulation of gene expression
GO:0034356 NAD biosynthesis via nicotinamide riboside salvage pathway
GO:0045944 positive regulation of transcription by RNA polymerase II
GO:0048511 rhythmic process
GO:0051770 positive regulation of nitric-oxide synthase biosynthetic process
GO:0060612 adipose tissue development
Cellular Component
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0016607 nuclear speck
GO:0030054 cell junction
GO:0070062 extracellular exosome

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4n9e, PDBe:4n9e, PDBj:4n9e
PDBsum4n9e
PubMed24433859
UniProtP43490|NAMPT_HUMAN Nicotinamide phosphoribosyltransferase (Gene Name=NAMPT)

[Back to BioLiP]