7DH3 | pdb_00007dh3

The co-crystal structure of DYRK2 with a small molecule inhibitor 5

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Protein kinase-like (PK-like)	8100342	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	Ion_trans, Ion_trans_2	e7dh3A1	A: alpha bundles	X: CNF1/YfiH-like putative cysteine hydrolases	H: CNF1/YfiH-like putative cysteine hydrolases	T: CNF1/YfiH-like putative cysteine hydrolases	F: Ion_trans, Ion_trans_2	ECOD (develop294)

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	Dual specificity tyrosine-phosphorylation-regulated kinase 2	protein serine/threonine/tyrosine 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 cation binding manganese ion binding transition metal ion binding ion binding binding metal ion binding protein serine/threonine/tyrosine 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 cation binding manganese ion binding transition metal ion binding ion binding binding metal ion binding small molecule binding protein serine kinase activity protein tyrosine kinase activity magnesium ion binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding protein serine/threonine kinase activity	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process regulation of biological process regulation of cellular process cell surface receptor signaling pathway signaling biological regulation smoothened signaling pathway cell communication signal transduction cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process regulation of biological process regulation of cellular process cell surface receptor signaling pathway signaling biological regulation smoothened signaling pathway cell communication signal transduction regulation of generation of precursor metabolites and energy positive regulation of macromolecule biosynthetic process regulation of primary metabolic process positive regulation of glycogen metabolic process positive regulation of metabolic process regulation of small molecule metabolic process small molecule metabolic process positive regulation of macromolecule metabolic process carbohydrate biosynthetic process primary metabolic process hexose metabolic process positive regulation of glucose metabolic process positive regulation of glycogen biosynthetic process biosynthetic process metabolic process energy reserve metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process positive regulation of carbohydrate metabolic process regulation of glycogen metabolic process regulation of metabolic process monosaccharide metabolic process regulation of glycogen biosynthetic process glucan biosynthetic process energy derivation by oxidation of organic compounds regulation of glucan biosynthetic process positive regulation of biological process regulation of polysaccharide metabolic process polysaccharide metabolic process glucan metabolic process positive regulation of biosynthetic process regulation of carbohydrate metabolic process regulation of glucose metabolic process positive regulation of cellular process regulation of biosynthetic process carbohydrate metabolic process polysaccharide biosynthetic process glycogen metabolic process generation of precursor metabolites and energy regulation of macromolecule metabolic process glycogen biosynthetic process macromolecule biosynthetic process regulation of polysaccharide biosynthetic process regulation of carbohydrate biosynthetic process positive regulation of small molecule metabolic process glucose metabolic process protein phosphorylation phosphorylation macromolecule modification phosphate-containing compound metabolic process protein metabolic process protein modification process phosphorus metabolic process signal transduction by p53 class mediator cell death intracellular signal transduction intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator apoptotic signaling pathway intrinsic apoptotic signaling pathway by p53 class mediator intrinsic apoptotic signaling pathway in response to DNA damage apoptotic process intrinsic apoptotic signaling pathway programmed cell death regulation of signaling regulation of signal transduction regulation of intracellular signal transduction regulation of response to stimulus regulation of signal transduction by p53 class mediator regulation of cell communication calcineurin-NFAT signaling cascade negative regulation of signaling negative regulation of intracellular signal transduction negative regulation of biological process negative regulation of cell communication negative regulation of calcineurin-NFAT signaling cascade intracellular signaling cassette regulation of calcineurin-mediated signaling negative regulation of cellular process regulation of calcium-mediated signaling regulation of calcineurin-NFAT signaling cascade negative regulation of response to stimulus negative regulation of calcium-mediated signaling negative regulation of signal transduction calcium-mediated signaling negative regulation of calcineurin-mediated signaling calcineurin-mediated signaling	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen cytoskeleton membraneless organelle intracellular membraneless organelle protein-containing complex ribonucleoprotein complex ubiquitin ligase complex catalytic complex transferase complex intracellular protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR017441	Protein kinase, ATP binding site	Binding Site
A	IPR042521	Dual specificity tyrosine-phosphorylation-regulated kinase	Homologous Superfamily
A	IPR050494	Serine/threonine and dual-specificity kinase	Family
A	IPR000719	Protein kinase domain	Domain
A	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
A	IPR008271	Serine/threonine-protein kinase, active site	Active Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q92630	gastrointestinal stromal tumor glioblastoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia psoriasis tuberculosis adrenal cortex carcinoma cystic fibrosis juvenile dermatomyositis malignant ependymoma oligodendroglioma pancreatic intraductal papillary-mucinous carcinoma Pick disease rheumatoid arthritis ulcerative colitis chronic kidney disease gastrointestinal stromal tumor glioblastoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia psoriasis tuberculosis adrenal cortex carcinoma cystic fibrosis juvenile dermatomyositis malignant ependymoma oligodendroglioma pancreatic intraductal papillary-mucinous carcinoma Pick disease rheumatoid arthritis ulcerative colitis chronic kidney disease dermatomyositis large cell medulloblastoma medulloblastoma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm primitive neuroectodermal tumor sarcoidosis Crohn disease gastric carcinoma IgA glomerulonephritis lung cancer non-small cell lung carcinoma ovarian cancer

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
A	SEP	Parent Component: SER RESID: AA0039 , AA0037 PSI-MOD : O4'-phospho-L-tyrosine MOD:00048 , O-phospho-L-serine MOD:00046

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.