6V6L | pdb_00006v6l

Co-structure of human glycogen synthase kinase beta with 1-(6-((2-((6-amino-5-nitropyridin-2-yl)amino)ethyl)amino)-2-(2,4-dichlorophenyl)pyridin-3-yl)-4-methylpiperazin-2-one

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	d6v6la_	Alpha and beta proteins (a+b)	Protein kinase-like (PK-like)	Protein kinase-like (PK-like)	Protein kinases, catalytic subunit	Glycogen synthase kinase-3 beta (Gsk3b)	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	Protein kinase-like (PK-like)	8036019	3000066	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	Pkinase_Tyr	e6v6lA1	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: Pkinase_Tyr	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00069	Protein kinase domain (Pkinase)	Protein kinase domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Glycogen synthase kinase-3 beta	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 ubiquitin protein ligase binding protein binding ubiquitin-like protein ligase binding enzyme binding protease binding scaffold protein binding kinase binding protein kinase binding protein serine/threonine kinase activity catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups beta-catenin binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding DNA-binding transcription factor binding NF-kappaB binding tau-protein kinase activity cytoskeletal protein binding tau protein binding dynactin binding p53 binding protein serine kinase activity protein kinase A catalytic subunit binding protein kinase A binding	positive regulation of cell communication regulation of cellular process modulation of chemical synaptic transmission signaling positive regulation of biological process cell communication long-term synaptic potentiation synaptic signaling regulation of biological quality positive regulation of cellular process regulation of synaptic plasticity trans-synaptic signaling regulation of biological process regulation of signaling positive regulation of cell communication regulation of cellular process modulation of chemical synaptic transmission signaling positive regulation of biological process cell communication long-term synaptic potentiation synaptic signaling regulation of biological quality positive regulation of cellular process regulation of synaptic plasticity trans-synaptic signaling regulation of biological process regulation of signaling biological regulation cell-cell signaling positive regulation of synaptic transmission chemical synaptic transmission regulation of trans-synaptic signaling anterograde trans-synaptic signaling regulation of long-term synaptic potentiation regulation of cell communication cellular process positive regulation of signaling cellular response to stimulus cell surface receptor signaling pathway response to stimulus canonical Wnt signaling pathway signal transduction Wnt signaling pathway multicellular organismal process cellular developmental process regulation of developmental process negative regulation of biological process regulation of cell differentiation neurogenesis multicellular organism development neuron differentiation cell differentiation regulation of dopaminergic neuron differentiation anatomical structure development negative regulation of cellular process negative regulation of dopaminergic neuron differentiation negative regulation of cell differentiation system development developmental process dopaminergic neuron differentiation negative regulation of developmental process nervous system development generation of neurons negative regulation of neuron differentiation regulation of neuron differentiation regulation of cell-substrate adhesion positive regulation of cell adhesion regulation of cell adhesion cell-substrate adhesion positive regulation of cell-matrix adhesion cell adhesion cell-matrix adhesion positive regulation of cell-substrate adhesion regulation of cell-matrix adhesion extrinsic apoptotic signaling pathway via death domain receptors negative regulation of signaling regulation of signal transduction regulation of programmed cell death extrinsic apoptotic signaling pathway negative regulation of cell communication negative regulation of extrinsic apoptotic signaling pathway negative regulation of apoptotic signaling pathway negative regulation of response to stimulus negative regulation of programmed cell death regulation of apoptotic process negative regulation of extrinsic apoptotic signaling pathway via death domain receptors cell death negative regulation of signal transduction regulation of extrinsic apoptotic signaling pathway apoptotic signaling pathway negative regulation of apoptotic process regulation of response to stimulus regulation of extrinsic apoptotic signaling pathway via death domain receptors apoptotic process programmed cell death regulation of apoptotic signaling pathway cellular response to nitrogen compound response to dopamine cellular response to dopamine response to monoamine response to catecholamine cellular response to catecholamine stimulus G protein-coupled dopamine receptor signaling pathway response to oxygen-containing compound response to nitrogen compound cellular response to oxygen-containing compound cellular response to chemical stimulus cellular response to monoamine stimulus response to chemical G protein-coupled receptor signaling pathway response to lipid response to retinoic acid cellular response to retinoic acid cellular response to lipid positive regulation of proteasomal protein catabolic process catabolic process positive regulation of protein metabolic process proteolysis involved in protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process regulation of ubiquitin-dependent protein catabolic process regulation of primary metabolic process positive regulation of metabolic process positive regulation of ubiquitin-dependent protein catabolic process regulation of proteolysis regulation of proteolysis involved in protein catabolic process modification-dependent macromolecule catabolic process proteolysis positive regulation of macromolecule metabolic process protein metabolic process regulation of protein metabolic process primary metabolic process proteasomal protein catabolic process regulation of macromolecule metabolic process protein catabolic process regulation of catabolic process positive regulation of protein catabolic process positive regulation of proteolysis involved in protein catabolic process positive regulation of catabolic process regulation of proteasomal ubiquitin-dependent protein catabolic process modification-dependent protein catabolic process positive regulation of proteolysis regulation of proteasomal protein catabolic process positive regulation of proteasomal ubiquitin-dependent protein catabolic process metabolic process ubiquitin-dependent protein catabolic process macromolecule metabolic process regulation of metabolic process regulation of protein catabolic process protein localization regulation of localization establishment of protein localization cellular localization nitrogen compound transport regulation of protein localization nucleocytoplasmic transport transport nuclear transport localization cellular macromolecule localization establishment of localization in cell regulation of protein export from nucleus nuclear export regulation of intracellular transport regulation of transport regulation of establishment of protein localization intracellular transport regulation of nucleocytoplasmic transport regulation of protein transport protein export from nucleus establishment of localization protein transport regulation of cellular localization macromolecule localization regulation of intracellular protein transport intracellular protein transport viral gene expression viral protein processing viral process regulation of glycogen biosynthetic process negative regulation of glycogen biosynthetic process glucan biosynthetic process energy derivation by oxidation of organic compounds regulation of glucan biosynthetic process regulation of generation of precursor metabolites and energy regulation of polysaccharide metabolic process polysaccharide metabolic process glucan metabolic process regulation of carbohydrate metabolic process negative regulation of carbohydrate metabolic process negative regulation of glycogen metabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process carbohydrate metabolic process polysaccharide biosynthetic process carbohydrate biosynthetic process glycogen metabolic process negative regulation of metabolic process generation of precursor metabolites and energy glycogen biosynthetic process macromolecule biosynthetic process biosynthetic process negative regulation of biosynthetic process regulation of polysaccharide biosynthetic process negative regulation of macromolecule biosynthetic process energy reserve metabolic process regulation of macromolecule biosynthetic process regulation of carbohydrate biosynthetic process regulation of glycogen metabolic process protein phosphorylation phosphorylation macromolecule modification phosphate-containing compound metabolic process protein modification process phosphorus metabolic process negative regulation of locomotion regulation of cell motility regulation of locomotion regulation of cell migration negative regulation of cell motility cell migration cell motility negative regulation of cell migration locomotion regulation of epithelial to mesenchymal transition mesenchyme development regulation of multicellular organismal process animal organ development tissue development negative regulation of epithelial to mesenchymal transition epithelial to mesenchymal transition mesenchymal cell differentiation negative regulation of multicellular organismal process response to biotic stimulus intracellular signal transduction cellular response to biotic stimulus ER overload response cellular response to stress response to stress ER-nucleus signaling pathway response to endoplasmic reticulum stress calcineurin-NFAT signaling cascade negative regulation of intracellular signal transduction negative regulation of calcineurin-NFAT signaling cascade regulation of intracellular signal transduction intracellular signaling cassette regulation of calcineurin-mediated signaling regulation of calcium-mediated signaling regulation of calcineurin-NFAT signaling cascade negative regulation of calcium-mediated signaling calcium-mediated signaling negative regulation of calcineurin-mediated signaling calcineurin-mediated signaling positive regulation of autophagy autophagy regulation of autophagy process utilizing autophagic mechanism regulation of protein binding positive regulation of molecular function regulation of molecular function positive regulation of protein binding regulation of binding positive regulation of binding rhythmic process circadian rhythm regulation of neuron projection development axonogenesis regulation of cellular component organization cell projection organization plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell morphogenesis cellular component organization cell projection morphogenesis neuron projection morphogenesis regulation of axonogenesis cellular component organization or biogenesis regulation of anatomical structure morphogenesis plasma membrane bounded cell projection organization regulation of cell projection organization axon development cell morphogenesis involved in neuron differentiation anatomical structure morphogenesis neuron development regulation of plasma membrane bounded cell projection organization regulation of circadian rhythm regulation of protein modification process regulation of protein ubiquitination positive regulation of post-translational protein modification positive regulation of protein modification process protein ubiquitination regulation of protein modification by small protein conjugation or removal positive regulation of protein modification by small protein conjugation or removal positive regulation of protein ubiquitination regulation of post-translational protein modification post-translational protein modification protein modification by small protein conjugation protein modification by small protein conjugation or removal axon extension regulation of growth regulation of cellular component size developmental growth developmental growth involved in morphogenesis cell growth regulation of axon extension regulation of extent of cell growth regulation of cell size neuron projection extension regulation of developmental growth developmental cell growth growth regulation of cell growth regulation of anatomical structure size head development forebrain development brain development superior temporal gyrus development pallium development cerebral cortex development central nervous system development telencephalon development regulation of postsynaptic membrane potential system process chemical synaptic transmission, postsynaptic nervous system process excitatory postsynaptic potential regulation of membrane potential heart development heart valve development circulatory system development response to peptide hormone insulin receptor signaling pathway cell surface receptor protein tyrosine kinase signaling pathway cellular response to endogenous stimulus response to hormone enzyme-linked receptor protein signaling pathway cellular response to hormone stimulus response to endogenous stimulus cellular response to peptide hormone stimulus response to insulin cellular response to insulin stimulus dendrite development regulation of dendrite morphogenesis dendrite morphogenesis regulation of dendrite development positive regulation of organelle organization positive regulation of cellular component organization plasma membrane bounded cell projection assembly cellular component biogenesis cellular component assembly cilium assembly positive regulation of cell projection organization cilium organization organelle assembly positive regulation of cellular component biogenesis regulation of cell projection assembly regulation of cellular component biogenesis regulation of organelle organization regulation of plasma membrane bounded cell projection assembly positive regulation of cilium assembly organelle organization regulation of cilium assembly regulation of organelle assembly cell projection assembly positive regulation of plasma membrane bounded cell projection assembly positive regulation of organelle assembly regulation of protein localization to nucleus protein localization to nucleus negative regulation of protein localization to nucleus protein localization to organelle negative regulation of protein localization protein localization to microtubule cytoskeleton regulation of protein localization to centrosome protein localization to microtubule organizing center protein localization to cytoskeleton positive regulation of protein localization positive regulation of protein localization to centrosome protein localization to centrosome gene expression regulation of gene expression negative regulation of gene expression apoptotic mitochondrial changes positive regulation of membrane permeability positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway regulation of membrane permeability regulation of mitochondrial membrane permeability involved in apoptotic process mitochondrial outer membrane permeabilization involved in programmed cell death mitochondrial membrane organization positive regulation of mitochondrial membrane permeability involved in apoptotic process positive regulation of mitochondrial membrane permeability regulation of mitochondrial membrane permeability mitochondrial transport mitochondrion organization membrane organization positive regulation of transport regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway regulation of mitochondrion organization mitochondrial outer membrane permeabilization cellular response to amyloid-beta response to amyloid-beta presynaptic modulation of chemical synaptic transmission negative regulation of glycogen (starch) synthase activity regulation of catalytic activity negative regulation of transferase activity negative regulation of molecular function negative regulation of catalytic activity regulation of transferase activity regulation of glycogen (starch) synthase activity positive regulation of macromolecule biosynthetic process positive regulation of gene expression positive regulation of biosynthetic process protein-containing complex organization positive regulation of protein-containing complex assembly regulation of protein-containing complex assembly protein-containing complex assembly regulation of canonical Wnt signaling pathway negative regulation of Wnt signaling pathway regulation of Wnt signaling pathway negative regulation of canonical Wnt signaling pathway negative regulation of stem cell differentiation negative regulation of mesenchymal stem cell differentiation stem cell differentiation regulation of stem cell differentiation mesenchymal stem cell differentiation regulation of mesenchymal stem cell differentiation neuron apoptotic process positive regulation of programmed cell death positive regulation of apoptotic process positive regulation of neuron apoptotic process regulation of neuron apoptotic process regulation of cytoskeleton organization microtubule cytoskeleton organization regulation of microtubule-based process microtubule anchoring at centrosome microtubule anchoring microtubule anchoring at microtubule organizing center regulation of microtubule anchoring at centrosome microtubule-based process regulation of microtubule cytoskeleton organization cytoskeleton organization negative regulation of cellular component organization negative regulation of protein-containing complex assembly establishment of cell polarity establishment or maintenance of cell polarity positive regulation of developmental process positive regulation of cell differentiation protein autophosphorylation signal transduction in absence of ligand extrinsic apoptotic signaling pathway in absence of ligand negative regulation of TORC2 signaling negative regulation of TOR signaling TOR signaling regulation of TOR signaling regulation of TORC2 signaling TORC2 signaling response to peptide cellular response to interleukin-3 response to cytokine cellular response to cytokine stimulus response to interleukin-3 peptidyl-serine modification peptidyl-serine phosphorylation peptidyl-amino acid modification cellular response to heat regulation of cellular response to heat regulation of cellular response to stress response to heat response to temperature stimulus regulation of response to stress response to abiotic stimulus protein localization to cilium positive regulation of protein localization to cilium regulation of protein localization to cilium hippocampus development limbic system development regulation of osteoblast differentiation negative regulation of osteoblast differentiation osteoblast differentiation ossification neuron projection organization positive regulation of nucleocytoplasmic transport positive regulation of establishment of protein localization positive regulation of protein transport positive regulation of intracellular transport positive regulation of protein export from nucleus positive regulation of intracellular protein transport negative regulation of type B pancreatic cell development regulation of type B pancreatic cell development epithelial cell differentiation regulation of cell development pancreas development endocrine pancreas development type B pancreatic cell differentiation epithelium development endocrine system development type B pancreatic cell development negative regulation of cell development epithelial cell development enteroendocrine cell differentiation maintenance of cell polarity	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane protein-containing complex catalytic complex beta-catenin destruction complex intracellular protein-containing complex somatodendritic compartment cell projection dendrite cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane protein-containing complex catalytic complex beta-catenin destruction complex intracellular protein-containing complex somatodendritic compartment cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection synapse cell junction glutamatergic synapse axon postsynapse membrane-bounded organelle intracellular organelle mitochondrion organelle intracellular membrane-bounded organelle centrosome microtubule organizing center cytoskeleton membraneless organelle intracellular membraneless organelle microtubule cytoskeleton presynapse nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen Wnt signalosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR000719	Protein kinase domain	Domain
A	IPR017441	Protein kinase, ATP binding site	Binding Site
A	IPR050591	Glycogen Synthase Kinase-3	Family
A	IPR039192	Glycogen synthase kinase 3, catalytic domain	Domain
A	IPR008271	Serine/threonine-protein kinase, active site	Active Site
A	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P49841	Alzheimer disease peritonitis bipolar disorder muscular atrophy tauopathy congestive heart failure hypertensive disorder Arthritis, Experimental poisoning prostate cancer melancholia myocardial infarction endogenous depression schizophrenia mantle cell lymphoma Alzheimer disease peritonitis bipolar disorder muscular atrophy tauopathy congestive heart failure hypertensive disorder Arthritis, Experimental poisoning prostate cancer melancholia myocardial infarction endogenous depression schizophrenia mantle cell lymphoma malignant ependymoma psoriasis brain injury cancer medulloblastoma depressive disorder neuronal ceroid lipofuscinosis 6 acute kidney failure osteoarthritis pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia malignant glioma rheumatoid arthritis spina bifida tuberculosis acquired metabolic disease neurotic disorder glioblastoma osteosarcoma heart failure pancreatic intraductal papillary-mucinous carcinoma astrocytic tumor large cell medulloblastoma major depressive disorder breast cancer subependymal giant cell astrocytoma diabetes mellitus oligodendroglioma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm juvenile idiopathic arthritis Pick disease atypical teratoid rhabdoid tumor

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A	PTR	Parent Component: TYR RESID: AA0039 PSI-MOD : O4'-phospho-L-tyrosine MOD:00048

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.