MultifacetedProtDB - Bologna Biocomputing Group

EC number	EC number description
2.7.1.137	Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor; phosphatidylinositol 3-kinase
2.7.1.153	Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor; phosphatidylinositol-4,5-bisphosphate 3-kinase

Structure

PDB	Resolution (Å)	PDB name
5DXU	2.64	p110delta/p85alpha with GDC-0326
5M6U	2.85	HUMAN PI3KDELTA IN COMPLEX WITH LASW1579
5T8F	2.91	p110delta/p85alpha with taselisib (GDC-0032)
5UBT	2.83	CRYSTAL STRUCTURE OF PI3K DELTA IN COMPLEX WITH A 7-(3-(PIPERAZIN-1-YL)PHENYL)PYRROLO[2,1-F][1,2,4] TRIAZIN-4-AMINE DERIVIATINE
5VLR	2.8	CRYSTAL STRUCTURE OF PI3K DELTA IN COMPLEX WITH A TRIFLUORO-ETHYL-PYRAZOL-PYROLOTRIAZINE INHIBITOR
6G6W	2.72	HUMAN PI3KDELTA IN COMPLEX WITH LIGAND LASW1976
6OCO	2.58	HUMAN PI3KDELTA IN COMPLEX WITH COMPOUND 6
6OCU	2.77	HUMAN PI3KDELTA IN COMPLEX WITH COMPOUND 29
6PYR	2.21	Human PI3Kdelta in complex with Compound 2-10 ((3S)-3-benzyl-3-methyl-5-[5-(2-methylpyrimidin-5-yl)pyrazolo[1,5-a]pyrimidin-3-yl]-1,3-dihydro-2H-indol-2-one)
6PYU	2.54	Human PI3Kdelta in complex with Compound 4-2 ((3S)-1'-(cyclopropanecarbonyl)-5-(quinoxalin-6-yl)spiro[indole-3,2'-pyrrolidin]-2(1H)-one)
7JIS	2.42	HUMAN PI3KDELTA IN COMPLEX WITH COMPOUND 2F
7LM2	2.79	HUMAN PI3KDELTA IN COMPLEX WITH COMPOUND 3C
7LQ1	2.96	HUMAN PI3KDELTA IN COMPLEX WITH COMPOUND 28

GO term

GO ontology	GO term	GO description
Biological Process	GO:0042113	B cell activation
Biological Process	GO:0035754	B cell chemotaxis
Biological Process	GO:0030183	B cell differentiation
Biological Process	GO:0050853	B cell receptor signaling pathway
Biological Process	GO:0042110	T cell activation
Biological Process	GO:0010818	T cell chemotaxis
Biological Process	GO:0030217	T cell differentiation
Biological Process	GO:0050852	T cell receptor signaling pathway
Biological Process	GO:0002250	adaptive immune response
Biological Process	GO:0016477	cell migration
Biological Process	GO:0006955	immune response
Biological Process	GO:0006954	inflammatory response
Biological Process	GO:0045087	innate immune response
Biological Process	GO:0002551	mast cell chemotaxis
Biological Process	GO:0043303	mast cell degranulation
Biological Process	GO:0060374	mast cell differentiation
Biological Process	GO:0030101	natural killer cell activation
Biological Process	GO:0035747	natural killer cell chemotaxis
Biological Process	GO:0001779	natural killer cell differentiation
Biological Process	GO:0030593	neutrophil chemotaxis
Biological Process	GO:0072672	neutrophil extravasation
Biological Process	GO:0014065	phosphatidylinositol 3-kinase signaling
Biological Process	GO:0036092	phosphatidylinositol-3-phosphate biosynthetic process
Biological Process	GO:0016310	phosphorylation
Biological Process	GO:0045766	positive regulation of angiogenesis
Biological Process	GO:0030335	positive regulation of cell migration
Biological Process	GO:0038089	positive regulation of cell migration by vascular endothelial growth factor signaling pathway
Biological Process	GO:0001819	positive regulation of cytokine production
Biological Process	GO:0010595	positive regulation of endothelial cell migration
Biological Process	GO:0001938	positive regulation of endothelial cell proliferation
Biological Process	GO:1905278	positive regulation of epithelial tube formation
Biological Process	GO:0010628	positive regulation of gene expression
Biological Process	GO:0033031	positive regulation of neutrophil apoptotic process
Biological Process	GO:0051897	positive regulation of protein kinase B signaling
Biological Process	GO:0006468	protein phosphorylation
Biological Process	GO:0002679	respiratory burst involved in defense response
Biological Process	GO:0007165	signal transduction
Molecular Function	GO:0016303	1-phosphatidylinositol-3-kinase activity
Molecular Function	GO:0035005	1-phosphatidylinositol-4-phosphate 3-kinase activity
Molecular Function	GO:0005524	ATP binding
Molecular Function	GO:0016301	kinase activity
Molecular Function	GO:0035004	phosphatidylinositol 3-kinase activity
Molecular Function	GO:0052812	phosphatidylinositol-3,4-bisphosphate 5-kinase activity
Molecular Function	GO:0046934	phosphatidylinositol-4,5-bisphosphate 3-kinase activity
Cellular Component	GO:0005737	cytoplasm
Cellular Component	GO:0005829	cytosol
Cellular Component	GO:0005942	phosphatidylinositol 3-kinase complex
Cellular Component	GO:0005943	phosphatidylinositol 3-kinase complex, class IA
Cellular Component	GO:0005886	plasma membrane

InterPro / Pfam

InterPro	InterPro name
IPR000341	Phosphatidylinositol 3-kinase Ras-binding (PI3K RBD) domain
IPR000403	Phosphatidylinositol 3-/4-kinase, catalytic domain
IPR001263	Phosphoinositide 3-kinase, accessory (PIK) domain
IPR002420	C2 phosphatidylinositol 3-kinase-type domain
IPR003113	Phosphatidylinositol 3-kinase, adaptor-binding domain
IPR011009	Protein kinase-like domain superfamily
IPR015433	Phosphatidylinositol kinase
IPR016024	Armadillo-type fold
IPR018936	Phosphatidylinositol 3/4-kinase, conserved site
IPR029071	Ubiquitin-like domain superfamily
IPR035892	C2 domain superfamily
IPR036940	Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily
IPR037703	PI3Kdelta, catalytic domain
IPR042236	Phosphoinositide 3-kinase, accessory (PIK) domain superfamily

Pfam	Pfam name
PF00454	Phosphatidylinositol 3- and 4-kinase
PF00613	Phosphoinositide 3-kinase family, accessory domain (PIK domain)
PF00792	Phosphoinositide 3-kinase C2
PF00794	PI3-kinase family, ras-binding domain
PF02192	PI3-kinase family, p85-binding domain

Reactome

Reactome	Reactome Name	Node type	Reactome Root	Reactome Root Name
R-HSA-1257604	PIP3 activates AKT signaling	Internal node	R-HSA-162582	Signal Transduction
R-HSA-1660499	Synthesis of PIPs at the plasma membrane	Leaf	R-HSA-1430728	Metabolism
R-HSA-2219530	Constitutive Signaling by Aberrant PI3K in Cancer	Leaf	R-HSA-1643685	Disease
R-HSA-512988	Interleukin-3, Interleukin-5 and GM-CSF signaling	Internal node	R-HSA-168256	Immune System
R-HSA-6811558	PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling	Leaf	R-HSA-162582	Signal Transduction
R-HSA-8853659	RET signaling	Leaf	R-HSA-1266738	Developmental Biology
R-HSA-9027276	Erythropoietin activates Phosphoinositide-3-kinase (PI3K)	Leaf	R-HSA-162582	Signal Transduction
R-HSA-912526	Interleukin receptor SHC signaling	Leaf	R-HSA-168256	Immune System
R-HSA-912631	Regulation of signaling by CBL	Leaf	R-HSA-168256	Immune System
R-HSA-983695	Antigen activates B Cell Receptor (BCR) leading to generation of second messengers	Leaf	R-HSA-168256	Immune System

Subcellular location

Location	ECO term	Pubmed
Cytoplasm	ECO:0000269	PubMed:22020336

Interactor | Variant | Drug

Phenotype

HPO ID	HPO name
HP:0000006	Autosomal dominant inheritance
HP:0000007	Autosomal recessive inheritance
HP:0000010	Recurrent urinary tract infections
HP:0000086	Ectopic kidney
HP:0000122	Unilateral renal agenesis
HP:0000306	Abnormality of the chin
HP:0000316	Hypertelorism
HP:0000348	High forehead
HP:0000411	Protruding ear
HP:0000431	Wide nasal bridge
HP:0000455	Broad nasal tip
HP:0000463	Anteverted nares
HP:0000470	Short neck
HP:0000490	Deeply set eye
HP:0000609	Optic nerve hypoplasia
HP:0000648	Optic atrophy
HP:0000924	Abnormality of the skeletal system
HP:0000938	Osteopenia
HP:0000953	Hyperpigmentation of the skin
HP:0000998	Hypertrichosis
HP:0001249	Intellectual disability
HP:0001251	Ataxia
HP:0001263	Global developmental delay
HP:0001319	Neonatal hypotonia
HP:0001369	Arthritis
HP:0001537	Umbilical hernia
HP:0001744	Splenomegaly
HP:0001761	Pes cavus
HP:0001894	Thrombocytosis
HP:0001974	Leukocytosis
HP:0001999	Abnormal facial shape
HP:0002007	Frontal bossing
HP:0002014	Diarrhea
HP:0002020	Gastroesophageal reflux
HP:0002028	Chronic diarrhea
HP:0002037	Inflammation of the large intestine
HP:0002058	Myopathic facies
HP:0002080	Intention tremor
HP:0002090	Pneumonia
HP:0002100	Recurrent aspiration pneumonia
HP:0002110	Bronchiectasis
HP:0002119	Ventriculomegaly
HP:0002123	Generalized myoclonic seizure
HP:0002162	Low posterior hairline
HP:0002205	Recurrent respiratory infections
HP:0002403	Positive Romberg sign
HP:0002583	Colitis
HP:0002643	Neonatal respiratory distress
HP:0002716	Lymphadenopathy
HP:0002718	Recurrent bacterial infections
HP:0002720	Decreased circulating IgA level
HP:0002721	Immunodeficiency
HP:0002841	Recurrent fungal infections
HP:0002850	Decreased circulating total IgM
HP:0003307	Hyperlordosis
HP:0003460	Decreased circulating total IgA
HP:0003496	Increased circulating IgM level
HP:0003593	Infantile onset
HP:0003621	Juvenile onset
HP:0003765	Psoriasiform dermatitis
HP:0004313	Decreased circulating antibody level
HP:0004315	Decreased circulating IgG level
HP:0004425	Flat forehead
HP:0004429	Recurrent viral infections
HP:0005280	Depressed nasal bridge
HP:0005387	Combined immunodeficiency
HP:0005403	T lymphocytopenia
HP:0005407	Decreased proportion of CD4-positive helper T cells
HP:0005425	Recurrent sinopulmonary infections
HP:0005764	Polyarticular arthritis
HP:0006532	Recurrent pneumonia
HP:0006610	Wide intermamillary distance
HP:0007678	Lacrimal duct stenosis
HP:0008348	Decreased circulating IgG2 level
HP:0009098	Chronic oral candidiasis
HP:0009650	Short distal phalanx of the thumb
HP:0009844	Broad middle phalanx of finger
HP:0009891	Underdeveloped supraorbital ridges
HP:0010049	Short metacarpal
HP:0010282	Thin lower lip vermilion
HP:0010579	Cone-shaped epiphysis
HP:0010743	Short metatarsal
HP:0010750	Dermatochalasis
HP:0010976	B lymphocytopenia
HP:0011108	Recurrent sinusitis
HP:0011463	Childhood onset
HP:0011897	Neutrophilia
HP:0012178	Reduced natural killer cell activity
HP:0012311	Monocytosis
HP:0012476	Decreased specific pneumococcal antibody level
HP:0025540	Abnormal T cell subset distribution
HP:0030381	Increased proportion of transitional B cells
HP:0030388	Decreased proportion of class-switched memory B cells
HP:0031014	Arteria lusoria
HP:0031381	Decreased lymphocyte proliferation in response to mitogen
HP:0031382	Decreased lymphocyte proliferation in response to anti-CD3
HP:0032132	Decreased circulating total IgG
HP:0032140	Decreased specific antibody response to vaccination
HP:0033351	Candida esophagitis
HP:0040022	Clinodactyly of the 2nd finger
HP:0040024	Clinodactyly of the 3rd finger
HP:0040025	Clinodactyly of the 4th finger
HP:0040218	Reduced natural killer cell count
HP:0040288	Nasogastric tube feeding
HP:0100540	Palpebral edema
HP:0100658	Cellulitis
HP:0100660	Dyskinesia
HP:0410018	Recurrent ear infections

Tissue and cell type

Tissue	Cell type	Expression level	Reliability
appendix	lymphoid tissue	Medium	Enhanced
bronchus	respiratory epithelial cells	Low	Enhanced
epididymis	glandular cells	Low	Enhanced
gallbladder	glandular cells	Low	Enhanced
lymph node	non-germinal center cells	Medium	Enhanced
nasopharynx	respiratory epithelial cells	Low	Enhanced
soft tissue 1	fibroblasts	Low	Enhanced
spleen	cells in red pulp	Low	Enhanced
spleen	cells in white pulp	Low	Enhanced
testis	Leydig cells	Medium	Enhanced
testis	preleptotene spermatocytes	Medium	Enhanced
testis	spermatogonia cells	Medium	Enhanced
tonsil	squamous epithelial cells	Medium	Enhanced

Disease

Disease name	MONDO ID	ICD10	ICD10 chapter	OMIM	Orphanet
combined immunodeficiency with faciooculoskeletal anomalies	MONDO:0013226	Q87	chapter17, Congenital malformations, deformations and chromosomal abnormalities	OMIM:613328	Orphanet:221139
immunodeficiency 14	MONDO:0014222	D81	chapter3, Diseases of the blood and blood-forming organs and certain disorders involving the immune mechanism	OMIM:615513
immunodeficiency 14b- autosomal recessive	MONDO:0023655	-	-	OMIM:619281

Summary of O00329

Gene: PIK3CD
Protein: Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform

Structure

GO term

InterPro / Pfam

Reactome

Subcellular location

Interactor | Variant | Drug

Phenotype

Tissue and cell type

Disease

Summary of O00329

Gene: PIK3CD Protein: Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform

Structure

GO term

InterPro / Pfam

Reactome

Subcellular location

Interactor | Variant | Drug

Phenotype

Tissue and cell type

Disease

Gene: PIK3CD
Protein: Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform