6YM3 | pdb_00006ym3

Crystal structure of Compound 1 with PIP4K2A

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Protein Modification Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d6ym3a1	Alpha and beta proteins (a+b)	SAICAR synthase-like	SAICAR synthase-like	Phosphatidylinositol phosphate kinase IIbeta, PIPK IIbeta	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d6ym3a2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d6ym3b1	Alpha and beta proteins (a+b)	SAICAR synthase-like	SAICAR synthase-like	Phosphatidylinositol phosphate kinase IIbeta, PIPK IIbeta	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d6ym3b2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	SAICAR synthase-like	8083248	3000802	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	SAICAR synthase-like	8083248	3000802	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PIP5K	e6ym3A1	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: SAICAR synthase	F: PIP5K	ECOD (1.6)
B	PIP5K	e6ym3B1	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: SAICAR synthase	F: PIP5K	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF01504	Phosphatidylinositol-4-phosphate 5-Kinase (PIP5K)	Phosphatidylinositol-4-phosphate 5-Kinase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Phosphatidylinositol 5-phosphate 4-kinase type-2 alpha	binding 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 binding 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 phosphatidylinositol kinase activity kinase activity lipid kinase activity 1-phosphatidylinositol-5-phosphate 4-kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups identical protein binding protein binding protein homodimerization activity protein dimerization activity 1-phosphatidylinositol-4-phosphate 5-kinase activity	membrane organization catabolic process transport macroautophagy membrane fusion organelle membrane fusion autophagy establishment of localization vesicle-mediated transport vesicle organization cellular component organization organelle fusion localization organelle organization autophagosome-lysosome fusion membrane organization catabolic process transport macroautophagy membrane fusion organelle membrane fusion autophagy establishment of localization vesicle-mediated transport vesicle organization cellular component organization organelle fusion localization organelle organization autophagosome-lysosome fusion cellular process metabolic process cellular component organization or biogenesis vesicle fusion process utilizing autophagic mechanism developmental process cellular developmental process hemopoiesis megakaryocyte differentiation cell development myeloid cell differentiation cell differentiation megakaryocyte development anatomical structure development myeloid cell development phosphatidylinositol metabolic process glycerophospholipid biosynthetic process glycerophospholipid metabolic process lipid biosynthetic process primary metabolic process phosphatidylinositol phosphate biosynthetic process phospholipid biosynthetic process phosphatidylinositol biosynthetic process phospholipid metabolic process biosynthetic process glycerolipid biosynthetic process organophosphate metabolic process organophosphate biosynthetic process phosphate-containing compound metabolic process glycerolipid metabolic process phosphorus metabolic process lipid metabolic process cellular localization intracellular lipid transport intracellular cholesterol transport vesicle-mediated cholesterol transport lipid localization intracellular transport lipid transport organic hydroxy compound transport intracellular sterol transport cytosolic transport establishment of localization in cell macromolecule localization cholesterol transport sterol transport positive regulation of organelle organization regulation of cellular process regulation of cellular component organization positive regulation of cellular component organization positive regulation of vacuole organization positive regulation of biological process autophagosome organization regulation of autophagy cellular component biogenesis positive regulation of metabolic process cellular component assembly positive regulation of autophagosome assembly positive regulation of macroautophagy positive regulation of cellular process positive regulation of autophagy regulation of biological process autophagosome assembly organelle assembly vacuole organization positive regulation of cellular component biogenesis biological regulation regulation of autophagosome assembly regulation of catabolic process regulation of vacuole organization regulation of cellular component biogenesis regulation of organelle organization positive regulation of catabolic process regulation of macroautophagy regulation of organelle assembly regulation of metabolic process positive regulation of organelle assembly 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate metabolic process 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate biosynthetic process cellular response to stimulus cellular response to nitrogen compound response to stimulus negative regulation of signaling signaling response to peptide hormone negative regulation of biological process regulation of signal transduction insulin receptor signaling pathway regulation of cellular response to insulin stimulus negative regulation of cell communication cell surface receptor protein tyrosine kinase signaling pathway cell communication cellular response to endogenous stimulus response to hormone negative regulation of cellular process signal transduction enzyme-linked receptor protein signaling pathway cellular response to hormone stimulus regulation of signaling cell surface receptor signaling pathway negative regulation of response to stimulus response to endogenous stimulus regulation of insulin receptor signaling pathway response to oxygen-containing compound cellular response to peptide hormone stimulus response to nitrogen compound negative regulation of signal transduction cellular response to oxygen-containing compound cellular response to chemical stimulus negative regulation of cellular response to insulin stimulus regulation of response to stimulus negative regulation of insulin receptor signaling pathway response to chemical response to insulin regulation of cell communication cellular response to insulin stimulus	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure organelle vacuole autophagosome cytoplasm intracellular membrane-bounded organelle photoreceptor inner segment cytosol cell periphery plasma membrane membrane membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure organelle vacuole autophagosome cytoplasm intracellular membrane-bounded organelle photoreceptor inner segment cytosol cell periphery plasma membrane membrane nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen lytic vacuole lysosome non-motile cilium 9+0 non-motile cilium cilium neuron projection photoreceptor outer segment plasma membrane bounded cell projection cell projection photoreceptor cell cilium

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR027483	Phosphatidylinositol-4-phosphate 4/5-kinase, C-terminal domain superfamily	Homologous Superfamily
A, B	IPR002498	Phosphatidylinositol-4-phosphate 4/5-kinase, core	Domain
A, B	IPR023610	Phosphatidylinositol-4/5-phosphate 5/4-kinase	Family
A, B	IPR027484	Phosphatidylinositol-4-phosphate 5-kinase, N-terminal	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: P48426	melanoma Sjogren syndrome acute lymphoblastic leukemia bipolar disorder diabetes mellitus large cell medulloblastoma malignant glioma osteosarcoma primitive neuroectodermal tumor ulcerative colitis atypical teratoid rhabdoid tumor Burkitt lymphoma gastric carcinoma lung carcinoma medulloblastoma melanoma Sjogren syndrome acute lymphoblastic leukemia bipolar disorder diabetes mellitus large cell medulloblastoma malignant glioma osteosarcoma primitive neuroectodermal tumor ulcerative colitis atypical teratoid rhabdoid tumor Burkitt lymphoma gastric carcinoma lung carcinoma medulloblastoma ovarian cancer schizophrenia B-cell acute lymphoblastic leukemia cutaneous melanoma glioblastoma malignant ependymoma Precursor B-cell lymphoblastic leukemia

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, B	PHD	Parent Component: ASP RESID: AA0033 PSI-MOD : L-aspartic 4-phosphoric anhydride MOD:00042

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.