4BFR | pdb_00004bfr

Discovery and Optimization of Pyrimidone Indoline Amide PI3Kbeta Inhibitors for the Treatment of Phosphatase and TENsin homologue (PTEN)-Deficient Cancers

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	PI3_PI4_kinase	e4bfrB4	A: a/b three-layered sandwiches	X: Transmembrane heme-binding four-helical bundle	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: PI3_PI4_kinase	ECOD (v294.1)
B	E1_FCCH	e4bfrB1	A: a/b three-layered sandwiches	X: Transmembrane heme-binding four-helical bundle	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: E1_FCCH	ECOD (v294.1)
A	PI3K_C2	e4bfrA1	A: a/b three-layered sandwiches	X: YrdC/RibB	H: SH3	T: SH3	F: PI3K_C2	ECOD (v294.1)
A	Topoisom_bac	e4bfrA4	A: a/b three-layered sandwiches	X: YrdC/RibB	H: SH3	T: SH3	F: Topoisom_bac	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	1.25.40.70	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat	Phosphatidylinositol 3-kinase, accessory domain (PIK)	CATH (4.3.0)
B	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
B	2.60.40.150	Mainly Beta	Sandwich	Immunoglobulin-like	C2 domain	CATH (4.3.0)
B	3.30.1010.10	Alpha Beta	2-Layer Sandwich	Phosphatidylinositol 3-kinase Catalytic Subunit	Chain A, domain 4	CATH (4.3.0)
B	1.10.1070.11	Mainly Alpha	Orthogonal Bundle	Phosphatidylinositol 3-kinase Catalytic Subunit	Chain A, Domain 5	CATH (4.3.0)
A	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
A	2.60.40.150	Mainly Beta	Sandwich	Immunoglobulin-like	C2 domain	CATH (4.3.0)
A	1.25.40.70	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat	Phosphatidylinositol 3-kinase, accessory domain (PIK)	CATH (4.3.0)
A	3.30.1010.10	Alpha Beta	2-Layer Sandwich	Phosphatidylinositol 3-kinase Catalytic Subunit	Chain A, domain 4	CATH (4.3.0)
A	1.10.1070.11	Mainly Alpha	Orthogonal Bundle	Phosphatidylinositol 3-kinase Catalytic Subunit	Chain A, Domain 5	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00794	PI3-kinase family, ras-binding domain (PI3K_rbd)	PI3-kinase family, ras-binding domain	Certain members of the PI3K family possess Ras-binding domains in their N-termini. These regions show some similarity (although not highly significant similarity) to Ras-binding Pfam:PF00788 domains (unpublished observation).	Domain
A, B	PF00454	Phosphatidylinositol 3- and 4-kinase (PI3_PI4_kinase)	Phosphatidylinositol 3- and 4-kinase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	PHOSPHATIDYLINOSITOL 4,5-BISPHOSPHATE 3-KINASE CATALYTIC S SUBUNIT BETA ISOFORM	protein binding binding insulin receptor substrate binding phosphatidylinositol kinase activity kinase activity lipid kinase activity transferase activity catalytic activity 1-phosphatidylinositol-3-kinase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups 1-phosphatidylinositol-4-phosphate 3-kinase activity adenyl ribonucleotide binding nucleotide binding protein binding binding insulin receptor substrate binding phosphatidylinositol kinase activity kinase activity lipid kinase activity transferase activity catalytic activity 1-phosphatidylinositol-3-kinase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups 1-phosphatidylinositol-4-phosphate 3-kinase activity adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding 1-phosphatidylinositol-4,5-bisphosphate 3-kinase activity catalytic activity, acting on a protein protein kinase activity protein serine kinase activity protein serine/threonine kinase activity	regulation of biosynthetic process regulation of nitric oxide biosynthetic process regulation of biological process regulation of cellular process biological regulation positive regulation of biological process reactive nitrogen species metabolic process nitric oxide metabolic process positive regulation of metabolic process nitric oxide biosynthetic process biosynthetic process positive regulation of biosynthetic process cellular process metabolic process regulation of biosynthetic process regulation of nitric oxide biosynthetic process regulation of biological process regulation of cellular process biological regulation positive regulation of biological process reactive nitrogen species metabolic process nitric oxide metabolic process positive regulation of metabolic process nitric oxide biosynthetic process biosynthetic process positive regulation of biosynthetic process cellular process metabolic process regulation of nitric oxide metabolic process positive regulation of nitric oxide biosynthetic process regulation of metabolic process positive regulation of cellular process developmental process multicellular organism development multicellular organismal process embryonic cleavage anatomical structure development cell division embryo development homeostatic process leukocyte apoptotic process regulation of programmed cell death regulation of neutrophil apoptotic process positive regulation of myeloid cell apoptotic process positive regulation of neutrophil apoptotic process regulation of immune system process myeloid cell homeostasis positive regulation of leukocyte apoptotic process positive regulation of immune system process regulation of leukocyte apoptotic process myeloid cell apoptotic process positive regulation of programmed cell death regulation of apoptotic process cell death positive regulation of apoptotic process neutrophil homeostasis neutrophil apoptotic process multicellular organismal-level homeostasis leukocyte homeostasis immune system process inflammatory cell apoptotic process homeostasis of number of cells apoptotic process programmed cell death regulation of myeloid cell apoptotic process glycerophospholipid biosynthetic process phosphatidylinositol-3-phosphate biosynthetic process glycerophospholipid metabolic process lipid biosynthetic process primary metabolic process phosphatidylinositol phosphate biosynthetic process phospholipid biosynthetic process phospholipid metabolic process glycerolipid biosynthetic process organophosphate metabolic process organophosphate biosynthetic process phosphate-containing compound metabolic process glycerolipid metabolic process phosphorus metabolic process lipid metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process positive regulation of macromolecule biosynthetic process regulation of gene expression positive regulation of gene expression regulation of macromolecule biosynthetic process positive regulation of macromolecule metabolic process macromolecule metabolic process response to stimulus response to stress response to ischemia catabolic process autophagy process utilizing autophagic mechanism inorganic ion homeostasis intracellular calcium ion homeostasis calcium ion homeostasis cellular homeostasis chemical homeostasis intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis cell migration cell motility cellular response to stimulus signaling intracellular signal transduction cell communication phosphatidylinositol-mediated signaling signal transduction regulation of body fluid levels wound healing cell activation hemostasis blood coagulation coagulation regulation of biological quality response to wounding platelet activation regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction negative regulation of signaling negative regulation of intracellular signal transduction negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction negative regulation of biological process regulation of signal transduction negative regulation of cell communication regulation of intracellular signal transduction intracellular signaling cassette negative regulation of cellular process regulation of signaling negative regulation of response to stimulus negative regulation of signal transduction regulation of response to stimulus regulation of cell communication phosphatidylinositol 3-kinase/protein kinase B signal transduction cellular response to growth factor stimulus negative regulation of vascular endothelial growth factor signaling pathway negative regulation of cellular response to growth factor stimulus cell surface receptor protein tyrosine kinase signaling pathway cellular response to endogenous stimulus regulation of vascular endothelial growth factor signaling pathway enzyme-linked receptor protein signaling pathway regulation of cellular response to vascular endothelial growth factor stimulus cell surface receptor signaling pathway response to endogenous stimulus regulation of cellular response to growth factor stimulus vascular endothelial growth factor signaling pathway cellular response to vascular endothelial growth factor stimulus response to growth factor negative regulation of cellular response to vascular endothelial growth factor stimulus cell adhesion cell-cell adhesion homophilic cell-cell adhesion sphingolipid mediated signaling pathway sphingosine-1-phosphate receptor signaling pathway G protein-coupled receptor signaling pathway blood vessel morphogenesis tube development angiogenesis involved in wound healing angiogenesis vasculature development circulatory system development anatomical structure morphogenesis tube morphogenesis anatomical structure formation involved in morphogenesis blood vessel development system development positive regulation of cell communication small GTPase-mediated signal transduction positive regulation of signal transduction regulation of small GTPase mediated signal transduction positive regulation of response to stimulus Rac protein signal transduction positive regulation of intracellular signal transduction regulation of Rac protein signal transduction positive regulation of Rac protein signal transduction positive regulation of small GTPase mediated signal transduction positive regulation of signaling cell population proliferation endothelial cell proliferation epithelial cell proliferation cell-matrix adhesion regulation of cell-matrix adhesion regulation of cell-substrate adhesion regulation of cell adhesion cell-substrate adhesion cellular response to oxygen levels cellular response to hypoxia regulation of cellular response to stress negative regulation of apoptotic signaling pathway intrinsic apoptotic signaling pathway response to decreased oxygen levels negative regulation of programmed cell death negative regulation of apoptotic process intrinsic apoptotic signaling pathway in response to hypoxia response to hypoxia response to chemical response to oxygen levels response to abiotic stimulus regulation of apoptotic signaling pathway regulation of cellular response to hypoxia cellular response to decreased oxygen levels regulation of intrinsic apoptotic signaling pathway cellular response to stress regulation of response to stress regulation of hypoxia-induced intrinsic apoptotic signaling pathway negative regulation of cellular response to hypoxia apoptotic signaling pathway negative regulation of intrinsic apoptotic signaling pathway cellular response to chemical stimulus negative regulation of hypoxia-induced intrinsic apoptotic signaling pathway positive regulation of locomotion regulation of cell motility endothelial cell migration positive regulation of cell migration regulation of locomotion positive regulation of endothelial cell migration positive regulation of cell motility regulation of cell migration regulation of endothelial cell migration locomotion regulation of sprouting angiogenesis regulation of developmental process regulation of vasculature development regulation of multicellular organismal process regulation of anatomical structure morphogenesis regulation of multicellular organismal development negative regulation of blood vessel morphogenesis negative regulation of developmental process negative regulation of angiogenesis sprouting angiogenesis negative regulation of vasculature development regulation of angiogenesis negative regulation of multicellular organismal process negative regulation of sprouting angiogenesis localization import into cell transport endocytosis establishment of localization vesicle-mediated transport lymphocyte mediated immunity biological process involved in interspecies interaction between organisms immune response response to other organism defense response defense response to symbiont response to external stimulus leukocyte mediated cytotoxicity response to biotic stimulus immune effector process defense response to other organism natural killer cell mediated cytotoxicity innate immune response leukocyte mediated immunity response to external biotic stimulus natural killer cell mediated immunity cell killing regulation of MAPK cascade MAPK cascade negative regulation of MAPK cascade	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex catalytic complex membrane phosphatidylinositol 3-kinase complex, class I membrane protein complex transferase complex phosphatidylinositol 3-kinase complex, class IA phosphatidylinositol 3-kinase complex transferase complex, transferring phosphorus-containing groups extrinsic component of membrane cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex catalytic complex membrane phosphatidylinositol 3-kinase complex, class I membrane protein complex transferase complex phosphatidylinositol 3-kinase complex, class IA phosphatidylinositol 3-kinase complex transferase complex, transferring phosphorus-containing groups extrinsic component of membrane midbody membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle membraneless organelle nuclear lumen cell periphery plasma membrane nucleoplasm brush border membrane cluster of actin-based cell projections plasma membrane bounded cell projection brush border cell projection apical part of cell plasma membrane region apical plasma membrane cell projection membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR016024	Armadillo-type fold	Homologous Superfamily
A, B	IPR037702	Phosphatidylinositol 3-kinase beta, catalytic domain	Domain
A, B	IPR015433	Phosphatidylinositol 3-/4-kinase	Family
A, B	IPR002420	C2 phosphatidylinositol 3-kinase-type domain	Domain
A, B	IPR000403	Phosphatidylinositol 3-/4-kinase, catalytic domain	Domain
A, B	IPR001263	Phosphoinositide 3-kinase, accessory (PIK) domain	Domain
A, B	IPR018936	Phosphatidylinositol 3-/4-kinase, conserved site	Conserved Site
A, B	IPR042236	Phosphoinositide 3-kinase, accessory (PIK) domain superfamily	Homologous Superfamily
A, B	IPR036940	Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily	Homologous Superfamily
A, B	IPR003113	Phosphatidylinositol 3-kinase, adaptor-binding domain	Domain
A, B	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
A, B	IPR000341	Phosphatidylinositol 3-kinase Ras-binding (PI3K RBD) domain	Domain
A, B	IPR035892	C2 domain superfamily	Homologous Superfamily
A, B	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.