Structure of PDB 5vlr Chain A

Receptor sequence
>5vlrA (length=926) Species: 9606 (Homo sapiens) [Search protein sequence]
NQSVVVDFLLPTGVYLNFPVSRNANLSTIKQLLWHRAQYEPLFHMLSGPE
AYVFTCINQTAEQQELEDEQRRLCDVQPFLPVLRLVAREGDRVKKLINSQ
ISLLIGKGLHEFDSLCDPEVNDFRAKMCQFCEEAAARRQQLGWEAWLQYS
FPLQLEPSLPNRALLVNVKFEGSEESFTFQVSTKDVPLALMACALRKKAT
EDYTLQVNGRHEYLYGSYPLCQFQYICSCLHSGLTPHLTMVHSSSILAMR
DLWSLEQPFRIELIQGSKVNADERMKLVVQAGLFHGNEMLCKTVSSSEVS
VCSEPVWKQRLEFDINICDLPRMARLCFALYAVIEKAKADCPIAWANLML
FDYKDQLKTGERCLYMWPSVPDEKGELLNPTGTVRSNPNTDSAAALLICL
PEVAPHPVYYPALEKILELGRHTEEEQLQLREILEGELYEHEKDLVWKLR
HEVQEHFPEALARLLLVTKWNKHEDVAQMLYLLCSWPELPVLSALELLDF
SFPDCHVGSFAIKSLRKLTDDELFQYLLQLVQVLKYESYLDCELTKFLLD
RALANRKIGHFLFWHLRSEMHVPSVALRFGLILEAYCRGSTHHMKVLMKQ
GEALSKLKALNDFVKLSSQKTPKPQTKELMHLCMRQEAYLEALSHLQSPL
DPSTLLAEVCVEQCTFMDSKMKPLWIMYSNEEASVGIIFKNGDDLRQDML
TLQMIQLMDVLWKQEGLDLRMTPYGCLPTGDRTGLIEVVLRSDTIANIQL
NFNKDALLNWLKSKNPGEALDRAIEEFTLSCAGYCVATYVLGIGDRHSDN
IMIRESGQLFHIDFGHFLGNFINRERVPFILTYDFVHVIQQGKTNNSEKF
ERFRGYCERAYTILRRHGLLFLHLFALMRAAGLPELSCSKDIQYLKDSLA
LGKTEEEALKHFRVKFNEALRESWKT
3D structure
PDB5vlr Identification of a Potent, Selective, and Efficacious Phosphatidylinositol 3-Kinase delta (PI3K delta ) Inhibitor for the Treatment of Immunological Disorders.
ChainA
Resolution2.8 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 9EM A T750 M752 W760 I777 K779 Y813 I825 E826 V828 T833 M900 I910 D911 T665 M667 W675 I688 K690 Y724 I736 E737 V739 T744 M802 I812 D813 PDBbind-CN: -logKd/Ki=8.52,IC50=3nM
BindingDB: IC50=3.00nM
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5vlr, PDBe:5vlr, PDBj:5vlr
PDBsum5vlr
PubMed28541707
UniProtO00329|PK3CD_HUMAN Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform (Gene Name=PIK3CD)

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