4WUY | pdb_00004wuy

Crystal Structure of Protein Lysine Methyltransferase SMYD2 in complex with LLY-507, a Cell-Active, Potent and Selective Inhibitor

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		e4wuyA1	A: Four-helical up-and-down bundle	X: Glycosyl hydrolase domain	H: Glycosyl hydrolase domain	T: Paramyxo_ncap	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.170.270.10	Mainly Beta	Beta Complex	Beta-clip-like	SET domain	CATH (4.3.0)
A	1.25.40.10	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat	Tetratricopeptide repeat domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00856	SET domain (SET)	SET domain	-	Family
A	PF01753	MYND finger (zf-MYND)	MYND finger		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	N-lysine methyltransferase SMYD2	p53 binding protein binding binding protein-lysine N-methyltransferase activity catalytic activity, acting on a protein transferase activity, transferring one-carbon groups lysine N-methyltransferase activity protein methyltransferase activity N-methyltransferase activity transferase activity methyltransferase activity catalytic activity S-adenosylmethionine-dependent methyltransferase activity histone H3 methyltransferase activity p53 binding protein binding binding protein-lysine N-methyltransferase activity catalytic activity, acting on a protein transferase activity, transferring one-carbon groups lysine N-methyltransferase activity protein methyltransferase activity N-methyltransferase activity transferase activity methyltransferase activity catalytic activity S-adenosylmethionine-dependent methyltransferase activity histone H3 methyltransferase activity histone modifying activity histone methyltransferase activity histone H3K4 methyltransferase activity histone H3K4 trimethyltransferase activity basal transcription machinery binding RNA polymerase binding RNA polymerase II complex binding basal RNA polymerase II transcription machinery binding RNA polymerase core enzyme binding enzyme binding histone H3K36 methyltransferase activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	developmental process heart development multicellular organism development multicellular organismal process anatomical structure development animal organ development circulatory system development system development peptidyl-lysine methylation protein methylation peptidyl-lysine modification primary metabolic process macromolecule methylation protein alkylation developmental process heart development multicellular organism development multicellular organismal process anatomical structure development animal organ development circulatory system development system development peptidyl-lysine methylation protein methylation peptidyl-lysine modification primary metabolic process macromolecule methylation protein alkylation methylation macromolecule modification peptidyl-amino acid modification metabolic process cellular process protein metabolic process macromolecule metabolic process protein modification process peptidyl-lysine dimethylation cellular response to stimulus regulation of cellular process response to stimulus signaling regulation of cellular response to stress regulation of signal transduction DNA damage response, signal transduction by p53 class mediator intracellular signal transduction cell communication cellular response to stress regulation of intracellular signal transduction response to stress regulation of response to stress regulation of signal transduction by p53 class mediator signal transduction regulation of DNA damage response, signal transduction by p53 class mediator regulation of biological process regulation of signaling biological regulation signal transduction by p53 class mediator regulation of response to stimulus DNA damage response regulation of cell communication signal transduction in response to DNA damage peptidyl-lysine monomethylation negative regulation of cell population proliferation cell population proliferation regulation of cell population proliferation negative regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process	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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR046341	SET domain superfamily	Homologous Superfamily
A	IPR011990	Tetratricopeptide-like helical domain superfamily	Homologous Superfamily
A	IPR001214	SET domain	Domain
A	IPR050869	Histone-lysine N-methyltransferase	Family
A	IPR002893	Zinc finger, MYND-type	Domain
A	IPR044419	SMYD2, SET domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q9NRG4	esophageal cancer abdominal aortic aneurysm oligodendroglioma astrocytic tumor lung cancer Pick disease attention deficit hyperactivity disorder, inattentive type neoplasm of esophagus pilocytic astrocytoma

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.