5VSE

Structure of human G9a SET-domain (EHMT2) in complex with inhibitor 17: N~2~-cyclopentyl-6,7-dimethoxy-N~2~-methyl-N~4~-(1-methylpiperidin-4-yl)quinazoline-2,4-diamine

External Resource: Annotation

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d5vseb1	All beta proteins	beta-clip	SET domain	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d5vseb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d5vsea_	All beta proteins	beta-clip	SET domain	automated matches	automated matches	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)
B	SCOP2B Superfamily	CXC domain-like	8092240	3002037	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	SET domain	8088641	3000162	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	SET domain	8088641	3000162	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	CXC domain-like	8092240	3002037	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)
B	SET	e5vseB1	A: beta barrels	X: beta-clip	H: SET domain-like (From Topology)	T: SET domain-like	F: SET	ECOD (1.6)
B	Pre-SET	e5vseB2	A: few secondary structure elements	X: Zn3Cys9 preSET domain-related (From Topology)	H: Zn3Cys9 preSET domain-related (From Topology)	T: Zn3Cys9 preSET domain-related	F: Pre-SET	ECOD (1.6)
A	SET	e5vseA1	A: beta barrels	X: beta-clip	H: SET domain-like (From Topology)	T: SET domain-like	F: SET	ECOD (1.6)
A	Pre-SET	e5vseA2	A: few secondary structure elements	X: Zn3Cys9 preSET domain-related (From Topology)	H: Zn3Cys9 preSET domain-related (From Topology)	T: Zn3Cys9 preSET domain-related	F: Pre-SET	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	2.170.270.10	Mainly Beta	Beta Complex	Beta-clip-like	SET domain	CATH (4.3.0)
A	2.170.270.10	Mainly Beta	Beta Complex	Beta-clip-like	SET domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00856	SET domain (SET)	SET domain	-	Family
A, B	PF05033	Pre-SET motif (Pre-SET)	Pre-SET motif	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Histone-lysine N-methyltransferase EHMT2	p53 binding protein binding binding transcription factor binding transcription coregulator binding transcription corepressor 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 p53 binding protein binding binding transcription factor binding transcription coregulator binding transcription corepressor 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 H3K56 methyltransferase activity histone methyltransferase activity histone modifying activity histone H3K9me2 methyltransferase activity histone H3K9 methyltransferase activity chromatin binding promoter-specific chromatin binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA binding organic cyclic compound binding nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription regulatory region nucleic acid binding C2H2 zinc finger domain binding protein domain specific binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding histone H3K27 methyltransferase activity enzyme binding	developmental process multicellular organismal process cellular developmental process neuron fate commitment nervous system development cell fate specification generation of neurons neurogenesis multicellular organism development neuron differentiation cell differentiation anatomical structure development cellular process neuron fate specification developmental process multicellular organismal process cellular developmental process neuron fate commitment nervous system development cell fate specification generation of neurons neurogenesis multicellular organism development neuron differentiation cell differentiation anatomical structure development cellular process neuron fate specification cell fate commitment system development adult behavior response to stimulus response to oxygen-containing compound response to nitrogen compound response to alkaloid behavior behavioral response to cocaine response to chemical response to organic cyclic compound response to cocaine regulation of cellular process negative regulation of biological process negative regulation of gene expression via chromosomal CpG island methylation cellular component organization chromatin organization negative regulation of cellular process chromatin remodeling cellular component organization or biogenesis negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process epigenetic regulation of gene expression negative regulation of metabolic process biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of gene expression, epigenetic regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process developmental growth growth organ growth sexual reproduction reproductive process fertilization peptidyl-lysine methylation protein methylation peptidyl-lysine modification primary metabolic process macromolecule methylation protein alkylation methylation macromolecule modification peptidyl-amino acid modification protein metabolic process protein modification process peptidyl-lysine dimethylation meiotic chromosome segregation synaptonemal complex assembly meiotic cell cycle process cellular component biogenesis cellular component assembly meiosis I meiotic nuclear division cell cycle synaptonemal complex organization chromosome segregation cell cycle process meiotic cell cycle organelle fission chromosome organization chromosome organization involved in meiotic cell cycle organelle organization nuclear division meiosis I cell cycle process homologous chromosome pairing at meiosis nuclear chromosome segregation homologous chromosome segregation DNA metabolic process nucleic acid metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process DNA replication regulation of nucleobase-containing compound metabolic process regulation of DNA replication regulation of DNA metabolic process multicellular organismal reproductive process oogenesis cell development cellular process involved in reproduction in multicellular organism developmental process involved in reproduction female gamete generation gamete generation oocyte development germ cell development oocyte differentiation phenotypic switching heterochromatin formation constitutive heterochromatin formation DNA methylation-dependent constitutive heterochromatin formation response to alcohol response to ethanol system process learning or memory long-term memory nervous system process cognition memory regulation of protein modification process regulation of protein metabolic process cellular response to stimulus cellular response to nutrient levels response to nutrient levels cellular response to stress response to stress response to starvation cellular response to starvation spermatid development spermatid differentiation spermatogenesis male gamete generation response to antibiotic response to fungicide response to toxic substance cellular response to nitrogen compound cellular response to organic cyclic compound cellular response to oxygen-containing compound cellular response to chemical stimulus cellular response to cocaine cellular response to alkaloid catabolic process regulation of cellular component organization macroautophagy autophagy negative regulation of organelle assembly autophagosome organization regulation of autophagy process utilizing autophagic mechanism negative regulation of autophagosome assembly negative regulation of catabolic process autophagosome assembly organelle assembly vacuole organization negative regulation of cellular component organization regulation of autophagosome assembly regulation of vacuole organization regulation of catabolic process regulation of cellular component biogenesis regulation of organelle organization negative regulation of macroautophagy regulation of macroautophagy negative regulation of organelle organization negative regulation of autophagy regulation of organelle assembly cellular response to xenobiotic stimulus response to xenobiotic stimulus RNA metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic 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 RNA biosynthetic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck nuclear body intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck nuclear body intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle nuclear lumen membraneless organelle intracellular membraneless organelle chromatin chromosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR043550	Histone-lysine N-methyltransferase EHMT1/EHMT2	Family
A, B	IPR007728	Pre-SET domain	Domain
A, B	IPR046341	SET domain superfamily	Homologous Superfamily
A, B	IPR036770	Ankyrin repeat-containing domain superfamily	Homologous Superfamily
A, B	IPR001214	SET domain	Domain
A, B	IPR038034	Histone-lysine N-methyltransferase EHMT2, SET domain	Domain
A, B	IPR047762	EHMT1/2, cysteine-rich region	Domain
A, B	IPR002110	Ankyrin repeat	Repeat

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q96KQ7	acute myeloid leukemia cocaine abuse Neoplasm Metastasis vesicular stomatitis cocaine dependence lung cancer non-alcoholic fatty liver disease primary hyperoxaluria type 1 age-related macular degeneration squamous cell lung carcinoma systemic lupus erythematosus vitiligo hepatitis B virus infection infertility disorder lung carcinoma acute myeloid leukemia cocaine abuse Neoplasm Metastasis vesicular stomatitis cocaine dependence lung cancer non-alcoholic fatty liver disease primary hyperoxaluria type 1 age-related macular degeneration squamous cell lung carcinoma systemic lupus erythematosus vitiligo hepatitis B virus infection infertility disorder lung carcinoma membranous glomerulonephritis osteosarcoma psoriatic arthritis ulcerative colitis wet macular degeneration endometriosis Hashimoto thyroiditis hypertensive disorder lung benign neoplasm ovarian cancer skin basal cell carcinoma autism spectrum disorder cervical cancer eosinophilic esophagitis heart disease

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.