Structure of PDB 3dgr Chain B Binding Site BS01

Receptor Information
>3dgr Chain B (length=464) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
FNILLATDSYKVTHYKQYPPNTSKVYSYFECREYEETVFYGLQYILNKYL
KGKVVTKEKIQEAKDVYKEHFQDDVFNEKGWNYILEKYDGHLPIEIKAVP
EGFVIPRGNVLFTVENTDPECYWLTNWIETILVQSWYPITVATNSREQKK
ILAKYLLETSGNLDGLEYKLHDFGYRGVSSQETAGIGASAHLVNFKGTDT
VAGLALIKKYYGTKDPVPGYSVPAAEHSTITAWGKDHEKDAFEHIVTQFS
SVPVSVVSDSYDIYNACEKIWGEDLRHLIVSRSTQAPLIIRPDSGNPLDT
VLKVLEILGKKFPVTENSKGYKLLPPYLRVIQGDGVDINTLQEIVEGMKQ
KMWSIENIAFGSGGGLLQKLTRDLLNCSFKCSYVVTNGLGINVFKDPVAD
PNKRSKKGRLSLHRTPAGNFVTLEEGKGDLEEYGQDLLHTVFKNGKVTKS
YSFDEIRKNAQLNI
Ligand information
Ligand IDA12
InChIInChI=1S/C11H17N5O9P2/c12-9-6-10(14-2-13-9)16(3-15-6)11-8(18)7(17)5(25-11)1-24-27(22,23)4-26(19,20)21/h2-3,5,7-8,11,17-18H,1,4H2,(H,22,23)(H2,12,13,14)(H2,19,20,21)/t5-,7-,8-,11-/m1/s1
InChIKeyOLCWZBFDIYXLAA-IOSLPCCCSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(CP(=O)(O)O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)C[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)CP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(CP(=O)(O)O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)C[P](O)(O)=O)[C@@H](O)[C@H]3O
FormulaC11 H17 N5 O9 P2
NamePHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER;
ALPHA,BETA-METHYLENEADENOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL583969
DrugBankDB03148
ZINCZINC000013527614
PDB chain3dgr Chain A Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB3dgr A phosphoenzyme mimic, overlapping catalytic sites and reaction coordinate motion for human NAMPT.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		Y18 R392 S398 K400
Binding residue
(residue number reindexed from 1)		Y10 R372 S378 K380
Annotation score1
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

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3dgr, PDBe:3dgr, PDBj:3dgr
PDBsum3dgr
PubMed19666527
UniProtP43490|NAMPT_HUMAN Nicotinamide phosphoribosyltransferase (Gene Name=NAMPT)

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