Structure of PDB 5m6u Chain A

Receptor sequence
>5m6uA (length=916) Species: 9606 (Homo sapiens) [Search protein sequence]
NQSVVVDFLLPTGVYLNFPVSRNANLSTIKQLLWHRAQYEPLFHMLSGPE
AYVFTCINQTAEQQELEDEQRRLCDVQPFLPVLRLVAREGDRVKKLINSQ
ISLLIGKGLHEFDSLCDPEVNDFRAKMCQFCEEAAARRQQLGWEAWLQYS
FPLQLEPLLVNVKFEGSEESFTFQVSTKDVPLALMACPEDYTLQVNGRHE
YLYGSYPLCQFQYICSCLHSGLTPHLTMVHSSSILAMRDESLWSLEQPFR
IELIQGSKVNADERMKLVVQAGLFHGNEMLCKTVSSSEVSVCSEPVWKQR
LEFDINICDLPRMARLCFALYAVIEDCPIAWANLMLFDYKDQLKTGERCL
YMWPSVPDEKGELLNPTGTVRSNPNTDSAAALLICLPEVAPHPVYYPALE
KILELGRHSVTEEEQLQLREILERRGSGELYEHEKDLVWKLRHEVQEHFP
EALARLLLVTKWNKHEDVAQMLYLLCSWPELPVLSALELLDFSFPDCHVG
SFAIKSLRKLTDDELFQYLLQLVQVLKYESYLDCELTKFLLDRALANRKI
GHFLFWHLRSEMHVPSVALRFGLILEAYCRGSTHHMKVLMKQGEALSKLK
ALNDFVKLSSQKTPKPQTKELMHLCMRQEAYLEALSHLQSPLDPSTLLAE
VCVEQCTFMDSKMKPLWIMYSNEEAGSGGSVGIIFKNGDDLRQDMLTLQM
IQLMDVLWKQEGLDLRMTPYGCLPTGDRTGLIEVVLRSDTIANIQLDALL
NWLKSKNPGEALDRAIEEFTLSCAGYCVATYVLGIGDRHSDNIMIRESGQ
LFHIDFGHFLGNFKTRERVPFILTYDFVHVIQQGKTNNSEKFERFRGYCE
RAYTILRRHGLLFLHLFALMRAAGLPELSCSKDIQYLKDSLALGKTEEEA
LKHFRVKFNEALRESW
3D structure
PDB5m6u Discovery of a Potent, Selective, and Orally Available PI3K delta Inhibitor for the Treatment of Inflammatory Diseases.
ChainA
Resolution2.85 Å
3D
structure
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Enzymatic activity
Enzyme Commision number 2.7.1.137: phosphatidylinositol 3-kinase.
2.7.1.153: phosphatidylinositol-4,5-bisphosphate 3-kinase.
Interaction with ligand
Site
#		 Ligand Ligand
chain		 Binding residues on receptor
(original residue number in PDB)		 Binding residues on receptor
(residue number reindexed from 1)		 Binding affinity
BS01 7KA A M752 P758 W760 Y813 E826 V828 D832 M900 I910 M659 P665 W667 Y720 E733 V735 D739 M794 I804 PDBbind-CN: -logKd/Ki=8.37,IC50=4.3nM
BindingDB: IC50=4.7nM
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0016303 1-phosphatidylinositol-3-kinase activity
GO:0035005 1-phosphatidylinositol-4-phosphate 3-kinase activity
GO:0046934 1-phosphatidylinositol-4,5-bisphosphate 3-kinase activity
Biological Process
GO:0001779 natural killer cell differentiation
GO:0001819 positive regulation of cytokine production
GO:0001938 positive regulation of endothelial cell proliferation
GO:0002250 adaptive immune response
GO:0002551 mast cell chemotaxis
GO:0002679 respiratory burst involved in defense response
GO:0006468 protein phosphorylation
GO:0006629 lipid metabolic process
GO:0006935 chemotaxis
GO:0006954 inflammatory response
GO:0006955 immune response
GO:0007165 signal transduction
GO:0010595 positive regulation of endothelial cell migration
GO:0010628 positive regulation of gene expression
GO:0010818 T cell chemotaxis
GO:0016310 phosphorylation
GO:0030101 natural killer cell activation
GO:0030154 cell differentiation
GO:0030183 B cell differentiation
GO:0030217 T cell differentiation
GO:0030335 positive regulation of cell migration
GO:0030593 neutrophil chemotaxis
GO:0033031 positive regulation of neutrophil apoptotic process
GO:0035747 natural killer cell chemotaxis
GO:0035754 B cell chemotaxis
GO:0036092 phosphatidylinositol-3-phosphate biosynthetic process
GO:0038084 vascular endothelial growth factor signaling pathway
GO:0042110 T cell activation
GO:0042113 B cell activation
GO:0043303 mast cell degranulation
GO:0043491 phosphatidylinositol 3-kinase/protein kinase B signal transduction
GO:0045087 innate immune response
GO:0045766 positive regulation of angiogenesis
GO:0046854 phosphatidylinositol phosphate biosynthetic process
GO:0048015 phosphatidylinositol-mediated signaling
GO:0050852 T cell receptor signaling pathway
GO:0050853 B cell receptor signaling pathway
GO:0060374 mast cell differentiation
GO:0072672 neutrophil extravasation
GO:1905278 positive regulation of epithelial tube formation
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0005942 phosphatidylinositol 3-kinase complex
GO:0005943 phosphatidylinositol 3-kinase complex, class IA

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Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5m6u, PDBe:5m6u, PDBj:5m6u
PDBsum5m6u
PubMed28105286
UniProtO00329|PK3CD_HUMAN Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform (Gene Name=PIK3CD)

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