9GGN | pdb_00009ggn

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

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Arginase/deacetylase-like	8088484	3000260	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Arginase/deacetylase-like	8088484	3000260	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)
D	Beta-Casp	e9ggnD1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: Beta-Casp	ECOD (v295.2)
B	Beta-Casp	e9ggnB1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: Beta-Casp	ECOD (v295.2)
A	Beta-Casp	e9ggnA1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: Beta-Casp	ECOD (v295.2)
C	Beta-Casp	e9ggnC1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: Beta-Casp	ECOD (v295.2)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D	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
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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D	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 deacetylase activity protein lysine deacetylase activity catalytic activity, acting on a protein deacylase activity catalytic 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 deacetylase activity protein lysine deacetylase activity catalytic activity, acting on a protein deacylase activity catalytic activity transcription coregulator binding protein lysine delactylase activity histone deacetylase activity histone modifying activity chromatin binding 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	developmental process regulation of biological process regulation of cellular process regulation of developmental process cellular developmental process biological regulation regulation of cell differentiation stem cell differentiation cell differentiation regulation of stem cell differentiation cellular process regulation of neuron projection development multicellular organismal process regulation of cellular component organization developmental process regulation of biological process regulation of cellular process regulation of developmental process cellular developmental process biological regulation regulation of cell differentiation stem cell differentiation cell differentiation regulation of stem cell differentiation cellular process regulation of neuron projection development multicellular organismal process 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 animal gross anatomical part developmental process regulation of plasma membrane bounded cell projection organization regulation of biosynthetic process rhythmic process circadian regulation of gene expression circadian rhythm regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process positive regulation of protein metabolic process regulation of protein metabolic process positive regulation of biological process primary metabolic process regulation of primary metabolic process positive regulation of metabolic process regulation of proteolysis proteolysis positive regulation of proteolysis positive regulation of macromolecule metabolic process protein metabolic process positive regulation of cellular process cellular response to stimulus 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 response to 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 response to lipid 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 cellular response to chemical stimulus response to chemical cellular response to lipid 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 regulation of multicellular organismal process 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 macromolecule biosynthetic process positive regulation of biosynthetic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process 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 positive regulation of developmental process positive regulation of stem cell population maintenance positive regulation of multicellular organismal process cell population proliferation positive regulation of cell population proliferation regulation of cell population proliferation dendrite development cellular component biogenesis cellular component assembly chromatin organization chromatin remodeling heterochromatin formation epigenetic regulation of gene expression heterochromatin organization negative regulation of gene expression negative regulation of gene expression, epigenetic regulation of embryonic development regulation of multicellular organismal development embryo development eyelid development in camera-type eye sensory organ development eye development visual system development camera-type eye development sensory system development 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 limb development appendage development embryonic limb morphogenesis embryonic morphogenesis embryonic appendage morphogenesis appendage morphogenesis embryonic digit morphogenesis limb morphogenesis	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 transcription repressor complex
A, C	Isoform 1 of Kelch repeat and BTB domain-containing protein 4	-	catabolic process primary metabolic process proteasomal protein catabolic process protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process metabolic process cellular process protein metabolic process macromolecule metabolic process	cullin-RING ubiquitin ligase complex protein-containing complex ubiquitin ligase complex catalytic complex transferase complex Cul3-RING ubiquitin ligase complex intracellular protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D	IPR023801	Histone deacetylase domain	Domain
B, D	IPR000286	Histone deacetylase HDAC	Family
B, D	IPR003084	Class I/II Histone deacetylase HDAC	Family
B, D	IPR037138	Histone deacetylase domain superfamily	Homologous Superfamily
B, D	IPR023696	Ureohydrolase domain superfamily	Homologous Superfamily
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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B, D	: Q92769	myeloid leukemia squamous cell carcinoma melanoma Microsatellite Instability chronic monocytic leukemia cirrhosis of liver endometriosis plasma cell myeloma prostate adenocarcinoma schizophrenia acute T cell leukemia 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 schizophrenia acute T cell leukemia 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
A, C	: Q9NVX7	endogenous depression malignant ependymoma osteosarcoma hypertensive disorder medulloblastoma ovarian cancer lung cancer metabolic syndrome X subependymal giant cell astrocytoma