MultifacetedProtDB - Bologna Biocomputing Group

EC number	EC number description
3.5.1.-	Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides;
3.5.1.98	Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides; histone deacetylase

Structure

PDB	Resolution (Å)	PDB name
3MAX	2.05	Crystal Structure of Human HDAC2 complexed with an N-(2-aminophenyl)benzamide
4LXZ	1.85	Structure of Human HDAC2 in complex with SAHA (vorinostat)
4LY1	1.57	Structure of Human HDAC2 in complex with inhibitor 4-(acetylamino)-N-[2-amino-5-(thiophen-2-yl)phenyl]benzamide
5IWG	1.66	HDAC2 WITH LIGAND BRD4884
5IX0	1.72	HDAC2 WITH LIGAND BRD7232
6G3O	2.27	Crystal structure of human HDAC2 in complex with (R)-6-[3,4-Dioxo-2-(4-trifluoromethoxy-phenylamino)-cyclobut-1-enylamino]-heptanoic acid hydroxyamide
6WBW	1.46	Structure of Human HDAC2 in complex with an ethyl ketone inhibitor
6WBZ	1.32	Structure of Human HDAC2 in complex with an ethyl ketone inhibitor containing a spiro-bicyclic group
6WHN	1.54	Histone deacetylases complex with peptide macrocycles
6WHO	2.2	Histone deacetylases complex with peptide macrocycles
6WHQ	2.35	Histone deacetylases complex with peptide macrocycles
6WHZ	2.9	Histone deacetylases complex with peptide macrocycles
6WI3	2.35	Histone deacetylases complex with peptide macrocycles
6XDM	1.56	STRUCTURE OF HUMAN HDAC2 IN COMPLEX WITH AN ARYL KETONE INHIBITOR
6XEB	1.5	STRUCTURE OF HUMAN HDAC2 IN COMPLEX WITH KETONE INHIBITOR (COMPOUND E)
6XEC	1.701	STRUCTURE OF HUMAN HDAC2 IN COMPLEX WITH KETONE INHIBITOR (COMPOUND O)
7JS8	1.634	STRUCTURE OF HUMAN HDAC2 IN COMPLEX WITH AN ETHYL KETONE INHIBITOR CONTAINING A SPIRO-BICYCLIC GROUP (COMPOUND 22)
7KBG	1.26	Structure of Human HDAC2 in complex with a 2-substituted benzamide inhibitor (compound 20)
7KBH	2.68	Structure of Human HDAC2 in complex with a 2-substituted benzamide inhibitor (compound 16)
7LTG	1.8	STRUCTURE OF HUMAN HDAC2 IN COMPLEX WITH APICIDIN
7LTK	1.59	STRUCTURE OF HUMAN HDAC2 IN COMPLEX WITH AN INHIBITOR THAT LACKS A ZINC BINDING GROUP (COMPOUND 12)
7LTL	1.49	STRUCTURE OF HUMAN HDAC2 IN COMPLEX WITH AN INHIBITOR LACKING A ZINC BINDING GROUP (COMPOUND 19)
7MOS	1.704	Structure of HDAC2 in complex with a macrocyclic inhibitor (compound 4)
7MOT	1.54	Structure of HDAC2 in complex with an inhibitor (compound 9)
7MOX	1.69	Structure of HDAC2 in complex with an inhibitor (compound 14)
7MOY	1.78	Structure of HDAC2 in complex with an inhibitor (compound 19)
7MOZ	1.543	Structure of HDAC2 in complex with a macrocyclic inhibitor (compound 25)
7ZZO	2.0	HDAC2 in complex with an inhibitor
7ZZP	1.52	Structure of HDAC2 complexed with an inhibitory ligand
7ZZR	2.168	HDAC2 in complex with inhibitory ligand
7ZZS	1.88	HDAC2 complexed with an inhibitory ligand
7ZZT	1.56	Ligand binding to HDAC2
7ZZU	1.85	Inhibitory Ligand binding to HDAC2
7ZZW	1.73	Ligand binding to HDAC2
8A0B	1.746	Inhibitor binding to HDAC2

GO term

GO ontology	GO term	GO description
Biological Process	GO:0048149	behavioral response to ethanol
Biological Process	GO:0003300	cardiac muscle hypertrophy
Biological Process	GO:1903351	cellular response to dopamine
Biological Process	GO:0034605	cellular response to heat
Biological Process	GO:0070301	cellular response to hydrogen peroxide
Biological Process	GO:0071300	cellular response to retinoic acid
Biological Process	GO:0071560	cellular response to transforming growth factor beta stimulus
Biological Process	GO:0006338	chromatin remodeling
Biological Process	GO:0032922	circadian regulation of gene expression
Biological Process	GO:0016358	dendrite development
Biological Process	GO:0042733	embryonic digit morphogenesis
Biological Process	GO:0009913	epidermal cell differentiation
Biological Process	GO:0061029	eyelid development in camera-type eye
Biological Process	GO:0061198	fungiform papilla formation
Biological Process	GO:0060789	hair follicle placode formation
Biological Process	GO:0070828	heterochromatin organization
Biological Process	GO:0070932	histone H3 deacetylation
Biological Process	GO:0016575	histone deacetylation
Biological Process	GO:0043392	negative regulation of DNA binding
Biological Process	GO:0043433	negative regulation of DNA-binding transcription factor activity
Biological Process	GO:0045892	negative regulation of DNA-templated transcription
Biological Process	GO:0045347	negative regulation of MHC class II biosynthetic process
Biological Process	GO:0043066	negative regulation of apoptotic process
Biological Process	GO:0030336	negative regulation of cell migration
Biological Process	GO:0061000	negative regulation of dendritic spine development
Biological Process	GO:0010977	negative regulation of neuron projection development
Biological Process	GO:2000757	negative regulation of peptidyl-lysine acetylation
Biological Process	GO:1902455	negative regulation of stem cell population maintenance
Biological Process	GO:0000122	negative regulation of transcription by RNA polymerase II
Biological Process	GO:0030512	negative regulation of transforming growth factor beta receptor signaling pathway
Biological Process	GO:0042475	odontogenesis of dentin-containing tooth
Biological Process	GO:0045893	positive regulation of DNA-templated transcription
Biological Process	GO:0008284	positive regulation of cell population proliferation
Biological Process	GO:0032967	positive regulation of collagen biosynthetic process
Biological Process	GO:0010718	positive regulation of epithelial to mesenchymal transition
Biological Process	GO:0032732	positive regulation of interleukin-1 production
Biological Process	GO:1902437	positive regulation of male mating behavior
Biological Process	GO:0048714	positive regulation of oligodendrocyte differentiation
Biological Process	GO:0045862	positive regulation of proteolysis
Biological Process	GO:2000273	positive regulation of signaling receptor activity
Biological Process	GO:1902459	positive regulation of stem cell population maintenance
Biological Process	GO:0045944	positive regulation of transcription by RNA polymerase II
Biological Process	GO:0032760	positive regulation of tumor necrosis factor production
Biological Process	GO:0042531	positive regulation of tyrosine phosphorylation of STAT protein
Biological Process	GO:0042659	regulation of cell fate specification
Biological Process	GO:2000736	regulation of stem cell differentiation
Biological Process	GO:0006357	regulation of transcription by RNA polymerase II
Biological Process	GO:0001975	response to amphetamine
Biological Process	GO:0031000	response to caffeine
Biological Process	GO:0042220	response to cocaine
Biological Process	GO:0055093	response to hyperoxia
Biological Process	GO:0032496	response to lipopolysaccharide
Biological Process	GO:0035094	response to nicotine
Biological Process	GO:0009410	response to xenobiotic stimulus
Molecular Function	GO:0051059	NF-kappaB binding
Molecular Function	GO:0003723	RNA binding
Molecular Function	GO:0061629	RNA polymerase II-specific DNA-binding transcription factor binding
Molecular Function	GO:0003682	chromatin binding
Molecular Function	GO:0019899	enzyme binding
Molecular Function	GO:0031072	heat shock protein binding
Molecular Function	GO:0004407	histone deacetylase activity
Molecular Function	GO:0042826	histone deacetylase binding
Molecular Function	GO:0160009	histone decrotonylase activity
Molecular Function	GO:1990841	promoter-specific chromatin binding
Molecular Function	GO:0160010	protein de-2-hydroxyisobutyrylase activity
Molecular Function	GO:0033558	protein lysine deacetylase activity
Molecular Function	GO:0043565	sequence-specific DNA binding
Cellular Component	GO:0035098	ESC/E(Z) complex
Cellular Component	GO:0016581	NuRD complex
Cellular Component	GO:0016580	Sin3 complex
Cellular Component	GO:0000785	chromatin
Cellular Component	GO:0000781	chromosome, telomeric region
Cellular Component	GO:0005737	cytoplasm
Cellular Component	GO:0000118	histone deacetylase complex
Cellular Component	GO:0005654	nucleoplasm
Cellular Component	GO:0005634	nucleus
Cellular Component	GO:0032991	protein-containing complex

InterPro / Pfam

InterPro	InterPro name
IPR000286	Histone deacetylase family
IPR003084	Histone deacetylase
IPR023696	Ureohydrolase domain superfamily
IPR023801	Histone deacetylase domain
IPR037138	Histone deacetylase domain superfamily

Pfam	Pfam name
PF00850	Histone deacetylase domain

Reactome

Reactome	Reactome Name	Node type	Reactome Root	Reactome Root Name
R-HSA-193670	p75NTR negatively regulates cell cycle via SC1	Leaf	R-HSA-162582	Signal Transduction
R-HSA-2122947	NOTCH1 Intracellular Domain Regulates Transcription	Leaf	R-HSA-162582	Signal Transduction
R-HSA-2644606	Constitutive Signaling by NOTCH1 PEST Domain Mutants	Leaf	R-HSA-1643685	Disease
R-HSA-2894862	Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants	Leaf	R-HSA-1643685	Disease
R-HSA-3214815	HDACs deacetylate histones	Leaf	R-HSA-4839726	Chromatin organization
R-HSA-350054	Notch-HLH transcription pathway	Leaf	R-HSA-74160	Gene expression (Transcription)
R-HSA-427389	ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression	Leaf	R-HSA-74160	Gene expression (Transcription)
R-HSA-427413	NoRC negatively regulates rRNA expression	Leaf	R-HSA-74160	Gene expression (Transcription)
R-HSA-4551638	SUMOylation of chromatin organization proteins	Leaf	R-HSA-392499	Metabolism of proteins
R-HSA-6804758	Regulation of TP53 Activity through Acetylation	Internal node	R-HSA-74160	Gene expression (Transcription)
R-HSA-73762	RNA Polymerase I Transcription Initiation	Leaf	R-HSA-74160	Gene expression (Transcription)
R-HSA-8943724	Regulation of PTEN gene transcription	Leaf	R-HSA-162582	Signal Transduction
R-HSA-9022692	Regulation of MECP2 expression and activity	Leaf	R-HSA-74160	Gene expression (Transcription)
R-HSA-9022699	MECP2 regulates neuronal receptors and channels	Leaf	R-HSA-74160	Gene expression (Transcription)
R-HSA-9615017	FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes	Leaf	R-HSA-74160	Gene expression (Transcription)
R-HSA-9619665	EGR2 and SOX10-mediated initiation of Schwann cell myelination	Leaf	R-HSA-1266738	Developmental Biology
R-HSA-9679191	Potential therapeutics for SARS	Leaf	R-HSA-1643685	Disease
R-HSA-9701898	STAT3 nuclear events downstream of ALK signaling	Leaf	R-HSA-162582	Signal Transduction
R-HSA-983231	Factors involved in megakaryocyte development and platelet production	Internal node	R-HSA-109582	Hemostasis

Subcellular location

Location	ECO term	Pubmed
Cytoplasm	ECO:0000269	PubMed:24970816
Nucleus	ECO:0000269	PubMed:20523938
Nucleus	ECO:0000269	PubMed:24970816
Nucleus	ECO:0000269	PubMed:28977666
Nucleus	ECO:0000269	PubMed:33283408

Interactor | Variant | Drug

Phenotype

Tissue and cell type

Tissue	Cell type	Expression level	Reliability
adipose tissue	adipocytes	High	Supported
adrenal gland	glandular cells	High	Supported
appendix	glandular cells	High	Supported
appendix	lymphoid tissue	High	Supported
bone marrow	hematopoietic cells	High	Supported
breast	adipocytes	Low	Supported
breast	glandular cells	Medium	Supported
breast	myoepithelial cells	Medium	Supported
bronchus	respiratory epithelial cells	High	Supported
caudate	glial cells	High	Supported
caudate	neuronal cells	High	Supported
cerebellum	Purkinje cells	High	Supported
cerebellum	cells in granular layer	High	Supported
cerebellum	cells in molecular layer	High	Supported
cerebral cortex	endothelial cells	Medium	Supported
cerebral cortex	glial cells	High	Supported
cerebral cortex	neuronal cells	High	Supported
cerebral cortex	neuropil	Medium	Supported
cervix	glandular cells	Medium	Supported
cervix	squamous epithelial cells	High	Supported
colon	endothelial cells	Medium	Supported
colon	glandular cells	High	Supported
colon	peripheral nerve/ganglion	Medium	Supported
duodenum	glandular cells	High	Supported
endometrium 1	cells in endometrial stroma	High	Supported
endometrium 1	glandular cells	High	Supported
endometrium 2	cells in endometrial stroma	High	Supported
endometrium 2	glandular cells	High	Supported
epididymis	glandular cells	High	Supported
esophagus	squamous epithelial cells	High	Supported
fallopian tube	glandular cells	High	Supported
gallbladder	glandular cells	High	Supported
heart muscle	cardiomyocytes	High	Supported
hippocampus	glial cells	High	Supported
hippocampus	neuronal cells	High	Supported
kidney	cells in glomeruli	High	Supported
kidney	cells in tubules	High	Supported
liver	cholangiocytes	Low	Supported
liver	hepatocytes	Low	Supported
lung	alveolar cells type I	High	Supported
lung	alveolar cells type II	High	Supported
lung	endothelial cells	High	Supported
lung	macrophages	High	Supported
lymph node	germinal center cells	High	Supported
lymph node	non-germinal center cells	High	Supported
nasopharynx	respiratory epithelial cells	High	Supported
oral mucosa	squamous epithelial cells	High	Supported
ovary	ovarian stroma cells	High	Supported
pancreas	exocrine glandular cells	High	Supported
pancreas	pancreatic endocrine cells	High	Supported
parathyroid gland	glandular cells	High	Supported
placenta	decidual cells	High	Supported
placenta	trophoblastic cells	High	Supported
prostate	glandular cells	High	Supported
rectum	glandular cells	Medium	Supported
salivary gland	glandular cells	High	Supported
seminal vesicle	glandular cells	Medium	Supported
skeletal muscle	myocytes	High	Supported
skin 1	cells in basal layer	High	Supported
skin 1	cells in granular layer	High	Supported
skin 1	cells in spinous layer	High	Supported
skin 1	endothelial cells	High	Supported
skin 1	fibrohistiocytic cells	High	Supported
skin 1	langerhans cells	High	Supported
skin 1	lymphocytes	High	Supported
skin 1	melanocytes	High	Supported
skin 1	vascular mural cells	Medium	Supported
skin 2	cells in basal layer	High	Supported
skin 2	cells in granular layer	High	Supported
skin 2	cells in spinous layer	High	Supported
skin 2	endothelial cells	High	Supported
skin 2	fibrohistiocytic cells	High	Supported
skin 2	langerhans cells	High	Supported
skin 2	lymphocytes	High	Supported
skin 2	melanocytes	High	Supported
skin 2	vascular mural cells	High	Supported
small intestine	glandular cells	Medium	Supported
smooth muscle	smooth muscle cells	High	Supported
soft tissue 1	chondrocytes	Medium	Supported
soft tissue 1	fibroblasts	Medium	Supported
soft tissue 1	peripheral nerve	High	Supported
soft tissue 2	fibroblasts	High	Supported
soft tissue 2	peripheral nerve	Medium	Supported
spleen	cells in red pulp	High	Supported
spleen	cells in white pulp	Medium	Supported
stomach 1	glandular cells	High	Supported
stomach 2	glandular cells	High	Supported
testis	Leydig cells	Medium	Supported
testis	pachytene spermatocytes	High	Supported
testis	peritubular cells	Low	Supported
testis	preleptotene spermatocytes	Medium	Supported
testis	round or early spermatids	Medium	Supported
testis	sertoli cells	Medium	Supported
testis	spermatogonia cells	High	Supported
thyroid gland	glandular cells	Medium	Supported
tonsil	germinal center cells	High	Supported
tonsil	non-germinal center cells	High	Supported
tonsil	squamous epithelial cells	High	Supported
urinary bladder	urothelial cells	High	Supported
vagina	squamous epithelial cells	Medium	Supported

Summary of Q92769

Gene: HDAC2
Protein: Histone deacetylase 2

Structure

GO term

InterPro / Pfam

Reactome

Subcellular location

Interactor | Variant | Drug

Phenotype

Tissue and cell type

Disease

Summary of Q92769

Gene: HDAC2 Protein: Histone deacetylase 2

Structure

GO term

InterPro / Pfam

Reactome

Subcellular location

Interactor | Variant | Drug

Phenotype

Tissue and cell type

Disease

Gene: HDAC2
Protein: Histone deacetylase 2