9I2C | pdb_00009i2c

Cryo-EM structure of KBTBD4 WT-HDAC2-CoREST1 2:1:1 complex mediated by molecular glue UM171

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Arginase/deacetylase-like	8088484	3000260	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C	PF07707	BTB And C-terminal Kelch (BACK)	BTB And C-terminal Kelch	This domain is found associated with Pfam:PF00651 and Pfam:PF01344 [1]. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues [1]. This family appears to be closely related to the BTB domain (Finn RD, ...	This domain is found associated with Pfam:PF00651 and Pfam:PF01344 [1]. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues [1]. This family appears to be closely related to the BTB domain (Finn RD, personal observation).	Domain
A, C	PF07646	Kelch motif (Kelch_2)	Kelch motif	-	Repeat
A, C	PF00651	BTB/POZ domain (BTB)	BTB/POZ domain	The BTB (for BR-C, ttk and bab) [1] or POZ (for Pox virus and Zinc finger) [2] domain is present near the N-terminus of a fraction of zinc finger (Pfam:PF00096) proteins and in proteins that contain the Pfam:PF01344 motif such as Kelch and a family o ...	The BTB (for BR-C, ttk and bab) [1] or POZ (for Pox virus and Zinc finger) [2] domain is present near the N-terminus of a fraction of zinc finger (Pfam:PF00096) proteins and in proteins that contain the Pfam:PF01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation [2]. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule [3]. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT [4,5,6]. The POZ or BTB domain is also known as BR-C/Ttk or ZiN.	Domain
B	PF00850	Histone deacetylase domain (Hist_deacetyl)	Histone deacetylase domain	Histones can be reversibly acetylated on several lysine residues. Regulation of transcription is caused in part by this mechanism. Histone deacetylases catalyse the removal of the acetyl group. Histone deacetylases are related to other proteins [1]. ...	Histones can be reversibly acetylated on several lysine residues. Regulation of transcription is caused in part by this mechanism. Histone deacetylases catalyse the removal of the acetyl group. Histone deacetylases are related to other proteins [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C	Isoform 1 of Kelch repeat and BTB domain-containing protein 4	-	-	-
B	Histone deacetylase 2	protein binding binding histone binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding DNA-binding transcription factor binding NF-kappaB binding histone deacetylase binding enzyme binding heat shock protein binding deacetylase activity protein lysine deacetylase activity catalytic activity, acting on a protein deacylase activity protein binding binding histone binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding DNA-binding transcription factor binding NF-kappaB binding histone deacetylase binding enzyme binding heat shock protein binding deacetylase activity protein lysine deacetylase activity catalytic activity, acting on a protein deacylase activity catalytic activity transcription coregulator binding protein lysine delactylase activity chromatin binding promoter-specific chromatin binding histone deacetylase activity histone modifying activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides protein de-2-hydroxyisobutyrylase activity hydrolase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds RNA binding nucleic acid binding protein decrotonylase activity histone decrotonylase activity histone deacetylase activity, hydrolytic mechanism	response to stimulus response to chemical response to xenobiotic stimulus multicellular organismal process regulation of cellular process interleukin-1 production positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process regulation of cytokine production cytokine production positive regulation of interleukin-1 production regulation of multicellular organismal process response to stimulus response to chemical response to xenobiotic stimulus multicellular organismal process regulation of cellular process interleukin-1 production positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process regulation of cytokine production cytokine production positive regulation of interleukin-1 production regulation of multicellular organismal process positive regulation of macromolecule metabolic process positive regulation of cellular process regulation of biosynthetic process regulation of biological process regulation of interleukin-1 production biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process positive regulation of gene expression positive regulation of multicellular organismal process regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process positive regulation of cytokine production regulation of metabolic process macromolecule modification primary metabolic process protein metabolic process protein modification process developmental process regulation of developmental process cellular developmental process regulation of cell differentiation stem cell differentiation cell differentiation regulation of stem cell differentiation cellular response to stimulus cellular response to heat cellular response to stress response to stress response to heat response to abiotic stimulus response to temperature stimulus response to nitrogen compound response to purine-containing compound response to caffeine response to alkaloid response to lipid response to oxygen-containing compound cellular response to oxygen-containing compound response to retinoic acid cellular response to chemical stimulus cellular response to retinoic acid cellular response to lipid regulation of neuron projection development regulation of cellular component organization cell projection organization negative regulation of biological process cell development neuron projection development cellular component organization neurogenesis multicellular organism development neuron differentiation anatomical structure development negative regulation of cellular process cellular component organization or biogenesis negative regulation of cell projection organization system development plasma membrane bounded cell projection organization negative regulation of cellular component organization regulation of cell projection organization nervous system development negative regulation of neuron projection development generation of neurons neuron development regulation of plasma membrane bounded cell projection organization rhythmic process circadian regulation of gene expression circadian rhythm positive regulation of protein metabolic process regulation of protein metabolic process regulation of primary metabolic process regulation of proteolysis proteolysis positive regulation of proteolysis negative regulation of transforming growth factor beta receptor signaling pathway cell surface receptor protein serine/threonine kinase signaling pathway cellular response to growth factor stimulus negative regulation of signaling signaling cellular response to transforming growth factor beta stimulus regulation of transmembrane receptor protein serine/threonine kinase signaling pathway regulation of signal transduction negative regulation of cell communication cell communication regulation of transforming growth factor beta receptor signaling pathway cellular response to endogenous stimulus signal transduction enzyme-linked receptor protein signaling pathway regulation of signaling cell surface receptor signaling pathway negative regulation of response to stimulus regulation of cellular response to transforming growth factor beta stimulus response to endogenous stimulus regulation of cellular response to growth factor stimulus negative regulation of signal transduction response to transforming growth factor beta regulation of response to stimulus transforming growth factor beta receptor signaling pathway regulation of cell communication response to growth factor transforming growth factor beta receptor superfamily signaling pathway negative regulation of transmembrane receptor protein serine/threonine kinase signaling pathway 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 epithelium development epidermal cell differentiation epidermis development tissue development epithelial cell differentiation intracellular receptor signaling pathway progesterone receptor signaling pathway hormone-mediated signaling pathway intracellular signal transduction response to hormone response to steroid hormone nuclear receptor-mediated steroid hormone signaling pathway cellular response to steroid hormone stimulus steroid hormone receptor signaling pathway cellular response to hormone stimulus nuclear receptor-mediated signaling pathway negative regulation of developmental process regulation of stem cell population maintenance stem cell population maintenance negative regulation of stem cell population maintenance maintenance of cell number negative regulation of multicellular organismal process RNA 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 transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process positive regulation of DNA-templated transcription positive regulation of nucleobase-containing compound metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process cellular response to nitrogen compound response to dopamine cellular response to dopamine response to monoamine response to catecholamine cellular response to monoamine stimulus cellular response to catecholamine stimulus negative regulation of dendritic spine development regulation of dendritic spine development dendrite development dendritic spine development ectodermal placode morphogenesis molting cycle process hair cycle animal organ development hair follicle placode formation ectodermal placode formation anatomical structure morphogenesis skin development skin epidermis development hair follicle development molting cycle anatomical structure formation involved in morphogenesis ectodermal placode development hair cycle process regulation of cell fate commitment cell fate specification regulation of cell fate specification cell fate commitment odontogenesis of dentin-containing tooth odontogenesis animal organ morphogenesis negative regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death cell death negative regulation of apoptotic process apoptotic process programmed cell death regulation of epithelial to mesenchymal transition positive regulation of epithelial to mesenchymal transition mesenchyme development positive regulation of developmental process positive regulation of cell differentiation epithelial to mesenchymal transition mesenchymal cell differentiation positive regulation of stem cell population maintenance behavior adult behavior response to alcohol behavioral response to ethanol response to ethanol cell population proliferation positive regulation of cell population proliferation regulation of cell population proliferation response to amyloid-beta cellular response to oxidative stress cellular response to chemical stress cellular response to hydrogen peroxide response to reactive oxygen species response to hydrogen peroxide response to oxidative stress cellular response to reactive oxygen species negative regulation of transcription by competitive promoter binding muscle hypertrophy system process cardiac muscle hypertrophy striated muscle hypertrophy muscle system process chromatin organization chromatin remodeling heterochromatin formation epigenetic regulation of gene expression negative regulation of gene expression negative regulation of gene expression, epigenetic response to amine response to amphetamine positive regulation of nervous system development regulation of neurogenesis regulation of gliogenesis positive regulation of gliogenesis regulation of cell development regulation of nervous system development gliogenesis positive regulation of neurogenesis positive regulation of oligodendrocyte differentiation regulation of multicellular organismal development positive regulation of cell development regulation of glial cell differentiation positive regulation of glial cell differentiation central nervous system development oligodendrocyte differentiation glial cell differentiation regulation of oligodendrocyte differentiation eyelid development in camera-type eye sensory organ development eye development visual system development camera-type eye development sensory system development regulation of tumor necrosis factor production positive regulation of tumor necrosis factor superfamily cytokine production tumor necrosis factor superfamily cytokine production positive regulation of tumor necrosis factor production tumor necrosis factor production regulation of tumor necrosis factor superfamily cytokine production response to nicotine positive regulation of cell communication positive regulation of signal transduction positive regulation of intracellular estrogen receptor signaling pathway positive regulation of response to stimulus regulation of intracellular signal transduction regulation of intracellular estrogen receptor signaling pathway regulation of intracellular steroid hormone receptor signaling pathway positive regulation of intracellular signal transduction estrogen receptor signaling pathway positive regulation of intracellular steroid hormone receptor signaling pathway positive regulation of signaling tongue development fungiform papilla formation fungiform papilla development sensory organ morphogenesis fungiform papilla morphogenesis tongue morphogenesis regulation of reproductive process reproductive process male mating behavior multicellular organismal reproductive process mating behavior positive regulation of male mating behavior regulation of behavior positive regulation of behavior reproductive behavior regulation of male mating behavior positive regulation of reproductive process biological process involved in interspecies interaction between organisms response to other organism response to external stimulus response to lipopolysaccharide response to biotic stimulus response to bacterium response to external biotic stimulus response to molecule of bacterial origin response to cocaine limb development appendage development embryonic limb morphogenesis embryonic morphogenesis embryonic appendage morphogenesis embryo development appendage morphogenesis embryonic digit morphogenesis limb morphogenesis response to oxygen levels response to hyperoxia response to increased oxygen levels	membrane-bounded organelle protein-containing complex histone methyltransferase complex intracellular anatomical structure catalytic complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle transferase complex intracellular organelle lumen PcG protein complex intracellular organelle cellular anatomical structure membrane-bounded organelle protein-containing complex histone methyltransferase complex intracellular anatomical structure catalytic complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle transferase complex intracellular organelle lumen PcG protein complex intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle methyltransferase complex ESC/E(Z) complex nuclear lumen cytoplasm membraneless organelle intracellular membraneless organelle chromatin chromosome ATPase complex transcription regulator complex histone deacetylase complex NuRD complex SWI/SNF superfamily-type complex CHD-type complex chromosome, telomeric region chromosomal region Sin3-type complex nuclear chromosome
D	REST corepressor 1	transcription corepressor activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity chromatin binding binding protein binding enzyme binding	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 negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process 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 negative regulation of cellular process 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 negative regulation of DNA-templated transcription regulation of biological process negative regulation of metabolic process biological regulation primary 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 metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process multicellular organismal process cellular developmental process regulation of developmental process regulation of megakaryocyte differentiation positive regulation of biological process megakaryocyte differentiation cell development regulation of cell differentiation regulation of cell development positive regulation of developmental process multicellular organism development positive regulation of cell differentiation cell differentiation anatomical structure development regulation of immune system process regulation of multicellular organismal process positive regulation of megakaryocyte differentiation positive regulation of cellular process developmental process regulation of multicellular organismal development hemopoiesis regulation of myeloid cell differentiation myeloid cell differentiation immune system process positive regulation of myeloid cell differentiation regulation of hemopoiesis homeostatic process erythrocyte differentiation multicellular organismal-level homeostasis homeostasis of number of cells myeloid cell homeostasis erythrocyte homeostasis transcription by RNA polymerase II regulation of transcription by RNA polymerase II negative regulation of gene expression cellular component organization chromatin organization cellular component organization or biogenesis	protein-containing complex catalytic complex DNA repair complex membrane-bounded organelle histone methyltransferase complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure protein-containing complex catalytic complex DNA repair complex membrane-bounded organelle histone methyltransferase complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle methyltransferase complex nuclear lumen transcription regulator complex histone deacetylase complex transcription repressor complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR042884	Kelch repeat and BTB domain-containing protein 4	Family
A, C	IPR011498	Kelch repeat type 2	Repeat
A, C	IPR042949	KBTBD4, BTB/POZ domain	Domain
A, C	IPR017096	BTB-kelch protein	Family
A, C	IPR011705	BTB/Kelch-associated	Domain
A, C	IPR000210	BTB/POZ domain	Domain
A, C	IPR011333	SKP1/BTB/POZ domain superfamily	Homologous Superfamily
A, C	IPR042950	KBTBD4, BACK domain	Domain
A, C	IPR015915	Kelch-type beta-propeller	Homologous Superfamily
B	IPR023801	Histone deacetylase domain	Domain
B	IPR000286	Histone deacetylase HDAC	Family
B	IPR003084	Class I/II Histone deacetylase HDAC	Family
B	IPR050284	HDAC_PDAC	Unknown
B	IPR037138	Histone deacetylase domain superfamily	Homologous Superfamily
B	IPR023696	Ureohydrolase domain superfamily	Homologous Superfamily
D	IPR051066	Transcriptional Regulator and Corepressor	Family
D	IPR009057	Homedomain-like superfamily	Homologous Superfamily
D	IPR049048	REST corepressor, helical domain	Domain
D	IPR017884	SANT domain	Domain
D	IPR001005	SANT/Myb domain	Domain
D	IPR000949	ELM2 domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, C	Pharos: Q9NVX7	endogenous depression malignant ependymoma osteosarcoma hypertensive disorder medulloblastoma ovarian cancer lung cancer metabolic syndrome X subependymal giant cell astrocytoma
B	Pharos: Q92769	myeloid leukemia squamous cell carcinoma melanoma Microsatellite Instability chronic monocytic leukemia cirrhosis of liver endometriosis plasma cell myeloma prostate adenocarcinoma acute T cell leukemia schizophrenia cancer chronic obstructive pulmonary disease large cell medulloblastoma medulloblastoma myeloid leukemia squamous cell carcinoma melanoma Microsatellite Instability chronic monocytic leukemia cirrhosis of liver endometriosis plasma cell myeloma prostate adenocarcinoma acute T cell leukemia schizophrenia cancer chronic obstructive pulmonary disease large cell medulloblastoma medulloblastoma primary cutaneous T-cell lymphoma adult T-cell leukemia/lymphoma lung cancer ovarian cancer primitive neuroectodermal tumor cutaneous melanoma mature T-cell and NK-cell non-Hodgkin lymphoma
D	Pharos: Q9UKL0	malignant colon neoplasm allergic rhinitis dermatomyositis ovarian cancer benign colon neoplasm IgA glomerulonephritis malignant glioma colonic neoplasm large cell medulloblastoma medulloblastoma