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
3C5K	1.55	Crystal structure of human HDAC6 zinc finger domain
3GV4	1.72	Crystal structure of human HDAC6 zinc finger domain and ubiquitin C-terminal peptide RLRGG
3PHD	3.0	Crystal structure of human HDAC6 in complex with ubiquitin
5B8D	1.05	Crystal structure of a low occupancy fragment candidate (N-(4-Methyl-1,3-thiazol-2-yl)propanamide) bound adjacent to the ubiquitin binding pocket of the HDAC6 zinc-finger domain
5EDU	2.79	Crystal structure of human histone deacetylase 6 catalytic domain 2 in complex with trichostatin A
5KH3	1.6	Crystal structure of fragment (3-(5-Chloro-1,3-benzothiazol-2-yl)propanoic acid) bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain
5KH7	1.7	Crystal structure of fragment (3-[6-Oxo-3-(3-pyridinyl)-1(6H)-pyridazinyl]propanoic acid) bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain
5KH9	1.07	Crystal structure of a low occupancy fragment candidate (5-[(4-Isopropylphenyl)amino]-6-methyl-1,2,4-triazin-3(2H)-one) bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain
5WBN	1.64	Crystal structure of fragment 3-(3-Benzyl-2-oxo-2H-[1,2,4]triazino[2,3-c]quinazolin-6-yl)propanoic acid bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain
5WPB	1.55	Crystal structure of fragment 3-(3-(pyridin-2-ylmethoxy)quinoxalin-2-yl)propanoic acid bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain
6CE6	1.6	Structure of HDAC6 zinc-finger ubiquitin binding domain soaked with 3,3'-(benzo[1,2-d:5,4-d']bis(thiazole)-2,6-diyl)dipropionic acid
6CE8	1.55	Crystal structure of fragment 2-(Benzo[d]thiazol-2-yl)acetic acid bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain
6CEA	1.6	Crystal structure of fragment 3-(quinolin-2-yl)propanoic acid bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain
6CEC	1.55	Crystal structure of fragment 3-(3-Methoxy-2-quinoxalinyl)propanoic acid bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain
6CED	1.7	Crystal structure of fragment 3-(3-Methyl-4-oxo-3,4-dihydroquinazolin-2-yl)propanoic acid bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain
6CEE	1.55	Crystal structure of fragment 3-(1-Methyl-2-oxo-1,2-dihydroquinoxalin-3-yl)propionic acid bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain
6CEF	1.8	Crystal structure of fragment 3-(1,3-Benzothiazol-2-yl)propanoic acid bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain
7ZYU	2.43	HDAC6 ZnF domain inhibitor - DARPin (Designed Ankyrin repeat protein) F10

GO term

GO ontology	GO term	GO description
Biological Process	GO:0070846	Hsp90 deacetylation
Biological Process	GO:0070842	aggresome assembly
Biological Process	GO:0006914	autophagy
Biological Process	GO:0019896	axonal transport of mitochondrion
Biological Process	GO:0070301	cellular response to hydrogen peroxide
Biological Process	GO:0071218	cellular response to misfolded protein
Biological Process	GO:0071374	cellular response to parathyroid hormone stimulus
Biological Process	GO:0035967	cellular response to topologically incorrect protein
Biological Process	GO:0060271	cilium assembly
Biological Process	GO:0061523	cilium disassembly
Biological Process	GO:0048668	collateral sprouting
Biological Process	GO:0060997	dendritic spine morphogenesis
Biological Process	GO:0040029	epigenetic regulation of gene expression
Biological Process	GO:0016575	histone deacetylation
Biological Process	GO:0006886	intracellular protein transport
Biological Process	GO:0032418	lysosome localization
Biological Process	GO:0045892	negative regulation of DNA-templated transcription
Biological Process	GO:0048843	negative regulation of axon extension involved in axon guidance
Biological Process	GO:0010727	negative regulation of hydrogen peroxide metabolic process
Biological Process	GO:0007026	negative regulation of microtubule depolymerization
Biological Process	GO:0051354	negative regulation of oxidoreductase activity
Biological Process	GO:1901984	negative regulation of protein acetylation
Biological Process	GO:0031333	negative regulation of protein-containing complex assembly
Biological Process	GO:0043242	negative regulation of protein-containing complex disassembly
Biological Process	GO:0045861	negative regulation of proteolysis
Biological Process	GO:0000122	negative regulation of transcription by RNA polymerase II
Biological Process	GO:0061734	parkin-mediated stimulation of mitophagy in response to mitochondrial depolarization
Biological Process	GO:0034983	peptidyl-lysine deacetylation
Biological Process	GO:0070845	polyubiquitinated misfolded protein transport
Biological Process	GO:1904056	positive regulation of cholangiocyte proliferation
Biological Process	GO:0050775	positive regulation of dendrite morphogenesis
Biological Process	GO:0010634	positive regulation of epithelial cell migration
Biological Process	GO:1901300	positive regulation of hydrogen peroxide-mediated programmed cell death
Biological Process	GO:1903223	positive regulation of oxidative stress-induced neuron death
Biological Process	GO:0033138	positive regulation of peptidyl-serine phosphorylation
Biological Process	GO:2000273	positive regulation of signaling receptor activity
Biological Process	GO:0051968	positive regulation of synaptic transmission, glutamatergic
Biological Process	GO:0090044	positive regulation of tubulin deacetylation
Biological Process	GO:0006476	protein deacetylation
Biological Process	GO:0031648	protein destabilization
Biological Process	GO:0000209	protein polyubiquitination
Biological Process	GO:0006515	protein quality control for misfolded or incompletely synthesized proteins
Biological Process	GO:0032984	protein-containing complex disassembly
Biological Process	GO:0060765	regulation of androgen receptor signaling pathway
Biological Process	GO:0010506	regulation of autophagy
Biological Process	GO:1903146	regulation of autophagy of mitochondrion
Biological Process	GO:0070201	regulation of establishment of protein localization
Biological Process	GO:0045598	regulation of fat cell differentiation
Biological Process	GO:0016241	regulation of macroautophagy
Biological Process	GO:0060632	regulation of microtubule-based movement
Biological Process	GO:0031647	regulation of protein stability
Biological Process	GO:0001975	response to amphetamine
Biological Process	GO:0051412	response to corticosterone
Biological Process	GO:0071548	response to dexamethasone
Biological Process	GO:0070848	response to growth factor
Biological Process	GO:0035902	response to immobilization stress
Biological Process	GO:0051788	response to misfolded protein
Biological Process	GO:0090042	tubulin deacetylation
Biological Process	GO:0043162	ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway
Molecular Function	GO:0051879	Hsp90 protein binding
Molecular Function	GO:0000978	RNA polymerase II cis-regulatory region sequence-specific DNA binding
Molecular Function	GO:0003779	actin binding
Molecular Function	GO:0043014	alpha-tubulin binding
Molecular Function	GO:0008013	beta-catenin binding
Molecular Function	GO:0048487	beta-tubulin binding
Molecular Function	GO:0070840	dynein complex binding
Molecular Function	GO:0019899	enzyme binding
Molecular Function	GO:0004407	histone deacetylase activity
Molecular Function	GO:0042826	histone deacetylase binding
Molecular Function	GO:0008017	microtubule binding
Molecular Function	GO:0051787	misfolded protein binding
Molecular Function	GO:0031593	polyubiquitin modification-dependent protein binding
Molecular Function	GO:0033558	protein lysine deacetylase activity
Molecular Function	GO:0048156	tau protein binding
Molecular Function	GO:0001222	transcription corepressor binding
Molecular Function	GO:0042903	tubulin deacetylase activity
Molecular Function	GO:0043130	ubiquitin binding
Molecular Function	GO:0031625	ubiquitin protein ligase binding
Molecular Function	GO:0008270	zinc ion binding
Cellular Component	GO:0016235	aggresome
Cellular Component	GO:0030424	axon
Cellular Component	GO:1904115	axon cytoplasm
Cellular Component	GO:0005901	caveola
Cellular Component	GO:0031252	cell leading edge
Cellular Component	GO:0005813	centrosome
Cellular Component	GO:0036064	ciliary basal body
Cellular Component	GO:0005737	cytoplasm
Cellular Component	GO:0005829	cytosol
Cellular Component	GO:0030425	dendrite
Cellular Component	GO:0000118	histone deacetylase complex
Cellular Component	GO:0016234	inclusion body
Cellular Component	GO:0005874	microtubule
Cellular Component	GO:0005875	microtubule associated complex
Cellular Component	GO:0005771	multivesicular body
Cellular Component	GO:0005654	nucleoplasm
Cellular Component	GO:0005634	nucleus
Cellular Component	GO:0043204	perikaryon
Cellular Component	GO:0048471	perinuclear region of cytoplasm

InterPro / Pfam

InterPro	InterPro name
IPR000286	Histone deacetylase family
IPR001607	Zinc finger, UBP-type
IPR013083	Zinc finger, RING/FYVE/PHD-type
IPR017320	Histone deacetylase class II, eukaryotic-type
IPR023696	Ureohydrolase domain superfamily
IPR023801	Histone deacetylase domain
IPR037138	Histone deacetylase domain superfamily

Pfam	Pfam name
PF00850	Histone deacetylase domain
PF02148	Zn-finger in ubiquitin-hydrolases and other protein

Reactome

Reactome	Reactome Name	Node type	Reactome Root	Reactome Root Name
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-3371511	HSF1 activation	Leaf	R-HSA-8953897	Cellular responses to stimuli
R-HSA-350054	Notch-HLH transcription pathway	Leaf	R-HSA-74160	Gene expression (Transcription)
R-HSA-5617833	Cilium Assembly	Internal node	R-HSA-1852241	Organelle biogenesis and maintenance
R-HSA-8878166	Transcriptional regulation by RUNX2	Internal node	R-HSA-74160	Gene expression (Transcription)
R-HSA-8940973	RUNX2 regulates osteoblast differentiation	Leaf	R-HSA-74160	Gene expression (Transcription)
R-HSA-9613829	Chaperone Mediated Autophagy	Leaf	R-HSA-9612973	Autophagy
R-HSA-9615710	Late endosomal microautophagy	Leaf	R-HSA-9612973	Autophagy
R-HSA-9646399	Aggrephagy	Leaf	R-HSA-9612973	Autophagy

Subcellular location

Location	ECO term	Pubmed
Cell projection, axon	ECO:0000250
Cell projection, cilium	ECO:0000269	PubMed:17604723
Cell projection, dendrite	ECO:0000250
Cytoplasm	ECO:0000269	PubMed:12024216
Cytoplasm	ECO:0000269	PubMed:24687993
Cytoplasm, cytoskeleton	ECO:0000269	PubMed:12024216
Nucleus	ECO:0000250
Perikaryon	ECO:0000250

Interactor | Variant | Drug

Phenotype

HPO ID	HPO name
HP:0000154	Wide mouth
HP:0000238	Hydrocephalus
HP:0000256	Macrocephaly
HP:0000322	Short philtrum
HP:0000347	Micrognathia
HP:0000369	Low-set ears
HP:0000457	Depressed nasal ridge
HP:0000568	Microphthalmia
HP:0000878	11 pairs of ribs
HP:0000883	Thin ribs
HP:0000926	Platyspondyly
HP:0000962	Hyperkeratosis
HP:0001249	Intellectual disability
HP:0001256	Intellectual disability, mild
HP:0001321	Cerebellar hypoplasia
HP:0001423	X-linked dominant inheritance
HP:0001511	Intrauterine growth retardation
HP:0001522	Death in infancy
HP:0001773	Short foot
HP:0002007	Frontal bossing
HP:0002866	Hypoplastic iliac wing
HP:0003021	Metaphyseal cupping
HP:0003196	Short nose
HP:0004279	Short palm
HP:0004322	Short stature
HP:0004331	Decreased skull ossification
HP:0005871	Metaphyseal chondrodysplasia
HP:0006028	Metaphyseal cupping of metacarpals
HP:0006208	Metaphyseal cupping of proximal phalanges
HP:0006402	Distal shortening of limbs
HP:0008364	Abnormality of the calcaneus
HP:0008905	Rhizomelia
HP:0012789	Hypoplasia of the calcaneus

Tissue and cell type

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

Summary of Q9UBN7

Gene: HDAC6, KIAA0901, JM21
Protein: Histone deacetylase 6

Structure

GO term

InterPro / Pfam

Reactome

Subcellular location

Interactor | Variant | Drug

Phenotype

Tissue and cell type

Disease

Summary of Q9UBN7

Gene: HDAC6, KIAA0901, JM21 Protein: Histone deacetylase 6

Structure

GO term

InterPro / Pfam

Reactome

Subcellular location

Interactor | Variant | Drug

Phenotype

Tissue and cell type

Disease

Gene: HDAC6, KIAA0901, JM21
Protein: Histone deacetylase 6