Structure of PDB 4n9e Chain B Binding Site BS02

Receptor Information
>4n9e Chain B (length=469) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EFNILLATDSYKVTHYKQYPPNTSKVYSYFECREKKYEETVFYGLQYILN
KYLKGKVVTKEKIQEAKDVYKEHFQDDVFNEKGWNYILEKYDGHLPIEIK
AVPEGFVIPRGNVLFTVENTDPECYWLTNWIETILVQSWYPITVATNSRE
QKKILAKYLLETSGNLDGLEYKLHDFGYRGVSSQETAGIGASAHLVNFKG
TDTVAGLALIKKYYGTKDPVPGYSVPAAEHSTITAWGKDHEKDAFEHIVT
QFSSVPVSVVSDSYDIYNACEKIWGEDLRHLIVSRSTQAPLIIRPDSGNP
LDTVLKVLEILGKKFPVTENSKGYKLLPPYLRVIQGDGVDINTLQEIVEG
MKQKMWSIENIAFGSGGGLLQKLTRDLLNCSFKCSYVVTNGLGINVFKDP
VADPNKRSKKGRLSLHRTPAGNFVTLEEGKGDLEEYGQDLLHTVFKNGKV
TKSYSFDEIRKNAQLNIEL
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)		K189 H191 F193 R196 D219 V242 A244 S275 I309 R311 R349 I351 E376 N377 I378 A379
Binding residue
(residue number reindexed from 1)		K172 H174 F176 R179 D202 V225 A227 S258 I292 R294 R332 I334 E359 N360 I361 A362
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]