5ANL

Crystal structure of VPS34 in complex with (2S)-8-((3R)-3- Methylmorpholin-4-yl)-1-(3-methyl-2-oxo- butyl)-2-(trifluoromethyl)-3, 4-dihydro-2H-pyrimido(1,2-a)pyrimidin-6- one, processed with the CrystalDirect automated mounting and cryo-cooling technology

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PF00613	e5anlA2	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: PF00613	ECOD (1.6)
A	PF00454	e5anlA1	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Protein kinase	F: PF00454	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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	PF00613	Phosphoinositide 3-kinase family, accessory domain (PIK domain) (PI3Ka)	Phosphoinositide 3-kinase family, accessory domain (PIK domain)	-	Repeat
A	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	PHOSPHATIDYLINOSITOL 3-KINASE CATALYTIC SUBUNIT TYPE 3	kinase activity transferase activity catalytic activity transferase activity, transferring phosphorus-containing groups phosphatidylinositol kinase activity lipid kinase activity 1-phosphatidylinositol-3-kinase activity phosphotransferase activity, alcohol group as acceptor binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding kinase activity transferase activity catalytic activity transferase activity, transferring phosphorus-containing groups phosphatidylinositol kinase activity lipid kinase activity 1-phosphatidylinositol-3-kinase activity phosphotransferase activity, alcohol group as acceptor binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding catalytic activity, acting on a protein protein kinase activity	biological process involved in interspecies interaction between organisms modulation by host of symbiont process viral life cycle modulation by host of viral genome replication biological process involved in symbiotic interaction modulation by host of viral process viral genome replication viral process positive regulation by host of viral process biological process involved in interaction with symbiont positive regulation by host of viral genome replication cellular biosynthetic process glycerophospholipid metabolic process lipid biosynthetic process biological process involved in interspecies interaction between organisms modulation by host of symbiont process viral life cycle modulation by host of viral genome replication biological process involved in symbiotic interaction modulation by host of viral process viral genome replication viral process positive regulation by host of viral process biological process involved in interaction with symbiont positive regulation by host of viral genome replication cellular biosynthetic process glycerophospholipid metabolic process lipid biosynthetic process phospholipid metabolic process organic substance metabolic process organic substance biosynthetic process phosphate-containing compound metabolic process phosphorus metabolic process phosphatidylinositol metabolic process glycerophospholipid biosynthetic process phosphatidylinositol-3-phosphate biosynthetic process cellular metabolic process primary metabolic process phosphatidylinositol phosphate biosynthetic process phospholipid biosynthetic process phosphatidylinositol biosynthetic process biosynthetic process glycerolipid biosynthetic process organophosphate metabolic process organophosphate biosynthetic process cellular lipid metabolic process metabolic process cellular process glycerolipid metabolic process lipid metabolic process cellular component disassembly catabolic process macroautophagy protein-containing complex organization autophagy protein-containing complex disassembly cellular catabolic process cellular component organization autophagosome maturation cellular component organization or biogenesis process utilizing autophagic mechanism regulation of biological process regulation of cellular process biological regulation regulation of cellular metabolic process regulation of catabolic process regulation of autophagy regulation of macroautophagy regulation of cellular catabolic process regulation of metabolic process cell division cellular response to stimulus cellular response to nutrient levels response to nutrient levels response to stimulus cellular response to stress response to stress response to starvation cellular response to glucose starvation cellular response to starvation signaling intracellular signal transduction cell communication phosphatidylinositol-mediated signaling signal transduction regulation of cytokinesis regulation of cell cycle process cytokinesis regulation of cell division cell cycle regulation of cell cycle cell cycle process phosphorylation protein localization cellular localization autophagosome organization cellular component biogenesis localization cellular component assembly cellular macromolecule localization autophagosome assembly organelle assembly vacuole organization organelle organization macromolecule localization protein localization to phagophore assembly site import into cell transport endocytosis establishment of localization vesicle-mediated transport organonitrogen compound metabolic process lipoprotein biosynthetic process lipoprotein metabolic process organonitrogen compound biosynthetic process macromolecule biosynthetic process protein lipidation macromolecule modification protein metabolic process macromolecule metabolic process protein modification process establishment of protein localization nitrogen compound transport protein targeting establishment of protein localization to vacuole lysosomal transport protein targeting to lysosome establishment of localization in cell protein targeting to vacuole organic substance transport intracellular transport protein localization to vacuole protein localization to lysosome establishment of protein localization to organelle protein transport protein localization to organelle vacuolar transport intracellular protein transport endosomal transport vesicle-mediated transport between endosomal compartments early endosome to late endosome transport	membrane cellular anatomical entity membrane-bounded organelle intracellular anatomical structure axoneme ciliary plasm cilium cytoplasmic region plasma membrane bounded cell projection cytoplasm plasma membrane bounded cell projection intracellular organelle cell projection cytoskeleton organelle membrane cellular anatomical entity membrane-bounded organelle intracellular anatomical structure axoneme ciliary plasm cilium cytoplasmic region plasma membrane bounded cell projection cytoplasm plasma membrane bounded cell projection intracellular organelle cell projection cytoskeleton organelle intracellular non-membrane-bounded organelle cytoplasm non-membrane-bounded organelle cytosol phosphatidylinositol 3-kinase complex, class III, type II protein-containing complex catalytic complex membrane protein complex transferase complex phosphatidylinositol 3-kinase complex transferase complex, transferring phosphorus-containing groups phosphatidylinositol 3-kinase complex, class III extrinsic component of membrane intracellular vesicle phagocytic vesicle intracellular membrane-bounded organelle phagocytic vesicle membrane cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane endocytic vesicle membrane vesicle organelle membrane endocytic vesicle peroxisome microbody autolysosome lytic vacuole vacuole secondary lysosome lysosome phagophore assembly site midbody endosome endomembrane system phosphatidylinositol 3-kinase complex, class III, type I late endosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR015433	Phosphatidylinositol kinase	Family
A	IPR016024	Armadillo-type fold	Homologous Superfamily
A	IPR008290	Phosphatidylinositol 3-kinase, Vps34 type	Family
A	IPR002420	C2 phosphatidylinositol 3-kinase-type domain	Domain
A	IPR018936	Phosphatidylinositol 3/4-kinase, conserved site	Conserved Site
A	IPR000403	Phosphatidylinositol 3-/4-kinase, catalytic domain	Domain
A	IPR001263	Phosphoinositide 3-kinase, accessory (PIK) domain	Domain
A	IPR042236	Phosphoinositide 3-kinase, accessory (PIK) domain superfamily	Homologous Superfamily
A	IPR036940	Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily	Homologous Superfamily
A	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
A	IPR035892	C2 domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q8NEB9	atypical teratoid rhabdoid tumor glioblastoma large cell medulloblastoma malignant colon neoplasm medulloblastoma schizophrenia bipolar disorder intellectual disability lung adenocarcinoma malignant ependymoma osteosarcoma breast cancer invasive ductal breast carcinoma lung cancer malignant glioma atypical teratoid rhabdoid tumor glioblastoma large cell medulloblastoma malignant colon neoplasm medulloblastoma schizophrenia bipolar disorder intellectual disability lung adenocarcinoma malignant ependymoma osteosarcoma breast cancer invasive ductal breast carcinoma lung cancer malignant glioma ovarian cancer

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 R01GM133198.