ASpdb: an integrative knowledgebase of human protein isoforms from experimental and AI-predicted structures

Home

Download

Statistics

Examples

Help

Contact

	Protein Summary
	AS Summary
	Protein Functional Features
	Gene Isoform Structures and Expression Levels
	Protein Structures
	pLDDT Score Distribution
	Ramachandran Plot of Protein Structures
	Potential Active Site Information
	Protein Structure and Feature Comparision
	Protein-Protein Interaction
	Related Drugs
	Related Diseases
	Clinically Important Variants

Protein:HDAC8

Protein Summary

Gene summary

Gene name: HDAC8
ASpdb.0 ID: 55869
	Gene
Gene symbol	HDAC8
Gene ID	55869
Gene name	histone deacetylase 8
Synonyms	CDA07\|CDLS5\|HD8\|HDACL1\|KDAC8\|MRXS6\|RPD3\|WTS
Cytomap	Xq13.1
Type of gene	protein-coding
Description	histone deacetylase 8histone deacetylase-like 1protein deacetylase HDAC8protein decrotonylase HDAC8
Modification date	20240411
UniProtAcc	Q9BY41

Gene ontology of this gene with evidence of Inferred from Direct Assay (IDA) from Entrez

Partner	Gene	GO ID	GO term	PubMed ID
Gene	HDAC8	GO:0004407	histone deacetylase activity	28497810
Gene	HDAC8	GO:0031397	negative regulation of protein ubiquitination	16809764
Gene	HDAC8	GO:0031647	regulation of protein stability	16809764
Gene	HDAC8	GO:0033558	protein lysine deacetylase activity	22885700
Gene	HDAC8	GO:0160009	histone decrotonylase activity	28497810

AS Summary

Information of the canonical protein with experimentally identified structure from PDB (2023).

UniProt Acc	File name	PDB ID	Method	Resolution	Chain	Start	End
Q9BY41-1	Q9BY41-1_2v5w_B.pdb	2V5W	X-ray	2.0	B	10	376

ASpdb's canonical and alternatively spliced isoform information.

accession_id	gene_name	canonical_id	alternative_id	canonical_length	alternative_length	canonical_start	canonical_end	type	originalSEQ	variationSEQ	alternative_start	alternative_end
Q9BY41	HDAC8	Q9BY41-1	Q9BY41-4	377	286	56	146	Deletion	none	none	55	55
Q9BY41	HDAC8	Q9BY41-1	Q9BY41-5	377	256	246	272	Substitution	SVLKEVYQAFNPKAVVLQLGADTIAGD	RYEPPAPNPGL	246	256
Q9BY41	HDAC8	Q9BY41-1	Q9BY41-5	377	256	273	377	Deletion	none	none	256	256
Q9BY41	HDAC8	Q9BY41-1	Q9BY41-6	377	139	56	146	Deletion	none	none	55	55
Q9BY41	HDAC8	Q9BY41-1	Q9BY41-6	377	139	185	210	Deletion	none	none	93	93
Q9BY41	HDAC8	Q9BY41-1	Q9BY41-6	377	139	246	256	Substitution	SVLKEVYQAFN	RYEPPAPNPGL	129	139
Q9BY41	HDAC8	Q9BY41-1	Q9BY41-6	377	139	257	377	Deletion	none	none	139	139
Q9BY41	HDAC8	Q9BY41-1	Q9BY41-7	377	158	147	158	Substitution	DEASGFCYLNDA	ETCVYVALYKAF	147	158
Q9BY41	HDAC8	Q9BY41-1	Q9BY41-7	377	158	159	377	Deletion	none	none	158	158
Q9BY41	HDAC8	Q9BY41-1	Q9BY41-8	377	146	147	377	Deletion	none	none	146	146

Multiple sequence alignment of our canonical and alternatively spliced HDAC8

Matched gene isoform IDs with Ensembl and RefSeq of our canonical and alternative spliced genes of HDAC8

UniProt-id	ENSG	ENST	ENSP
Q9BY41-1	ENSG00000147099.21	ENST00000373573.9	ENSP00000362674.3
Q9BY41-4	ENSG00000147099.21	ENST00000373589.9	ENSP00000362691.4
Q9BY41-5	ENSG00000147099.21	ENST00000439122.7	ENSP00000414486.2
Q9BY41-6	ENSG00000147099.21	ENST00000373559.8	ENSP00000362660.4
Q9BY41-7	ENSG00000147099.21	ENST00000373556.8	ENSP00000362657.3
Q9BY41-8	ENSG00000147099.21	ENST00000373554.6	ENSP00000362655.1
Q9BY41-8	ENSG00000147099.21	ENST00000649116.1	ENSP00000497925.1

UniProt-id	NM ID	NP ID
Q9BY41-1	NM_018486.2	NP_060956.1
Q9BY41-4	NM_001166418.1	NP_001159890.1
Q9BY41-5	NM_001166419.1	NP_001159891.1
Q9BY41-6	NM_001166448.1	NP_001159920.1
Q9BY41-7	NM_001166422.1	NP_001159894.1
Q9BY41-8	NM_001166420.1	NP_001159892.1

Amino acid sequences of our canonical and alternatively spliced HDAC8

accession_id	Protein sequence
Q9BY41-1	MEEPEEPADSGQSLVPVYIYSPEYVSMCDSLAKIPKRASMVHSLIEAYALHKQMRIVKPKVASMEEMATFHTDAYLQHLQKVSQEGDDDH PDSIEYGLGYDCPATEGIFDYAAAIGGATITAAQCLIDGMCKVAINWSGGWHHAKKDEASGFCYLNDAVLGILRLRRKFERILYVDLDLH HGDGVEDAFSFTSKVMTVSLHKFSPGFFPGTGDVSDVGLGKGRYYSVNVPIQDGIQDEKYYQICESVLKEVYQAFNPKAVVLQLGADTIA GDPMCSFNMTPVGIGKCLKYILQWQLATLILGGGGYNLANTARCWTYLTGVILGKTLSSEIPDHEFFTAYGPDYVLEITPSCRPDRNEPH
Q9BY41-4	MEEPEEPADSGQSLVPVYIYSPEYVSMCDSLAKIPKRASMVHSLIEAYALHKQMRDEASGFCYLNDAVLGILRLRRKFERILYVDLDLHH GDGVEDAFSFTSKVMTVSLHKFSPGFFPGTGDVSDVGLGKGRYYSVNVPIQDGIQDEKYYQICESVLKEVYQAFNPKAVVLQLGADTIAG DPMCSFNMTPVGIGKCLKYILQWQLATLILGGGGYNLANTARCWTYLTGVILGKTLSSEIPDHEFFTAYGPDYVLEITPSCRPDRNEPHR
Q9BY41-5	MEEPEEPADSGQSLVPVYIYSPEYVSMCDSLAKIPKRASMVHSLIEAYALHKQMRIVKPKVASMEEMATFHTDAYLQHLQKVSQEGDDDH PDSIEYGLGYDCPATEGIFDYAAAIGGATITAAQCLIDGMCKVAINWSGGWHHAKKDEASGFCYLNDAVLGILRLRRKFERILYVDLDLH
Q9BY41-6	MEEPEEPADSGQSLVPVYIYSPEYVSMCDSLAKIPKRASMVHSLIEAYALHKQMRDEASGFCYLNDAVLGILRLRRKFERILYVDLDLHH
Q9BY41-7	MEEPEEPADSGQSLVPVYIYSPEYVSMCDSLAKIPKRASMVHSLIEAYALHKQMRIVKPKVASMEEMATFHTDAYLQHLQKVSQEGDDDH
Q9BY41-8	MEEPEEPADSGQSLVPVYIYSPEYVSMCDSLAKIPKRASMVHSLIEAYALHKQMRIVKPKVASMEEMATFHTDAYLQHLQKVSQEGDDDH

Protein Functional Features

Main function of this protein. (from UniProt)

HDAC8 (go to UniProt):Q9BY41

Retention analysis result of protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at
download page
* Minus value of BPloci means that the break pointn is located before the CDS.

- Retained protein feature among the 13 regional features.

Accession_id	Subsection	Start	End	Funcitonal feature	Splicing information
Q9BY41	Region	14	324	Note=Histone deacetylase	Type=Deletion;Start=56;End=146
Q9BY41	Region	14	324	Note=Histone deacetylase	Type=Substitution;Start=246;End=272
Q9BY41	Region	14	324	Note=Histone deacetylase	Type=Deletion;Start=273;End=377
Q9BY41	Region	14	324	Note=Histone deacetylase	Type=Deletion;Start=56;End=146
Q9BY41	Region	14	324	Note=Histone deacetylase	Type=Deletion;Start=185;End=210
Q9BY41	Region	14	324	Note=Histone deacetylase	Type=Substitution;Start=246;End=256
Q9BY41	Region	14	324	Note=Histone deacetylase	Type=Deletion;Start=257;End=377
Q9BY41	Region	14	324	Note=Histone deacetylase	Type=Substitution;Start=147;End=158
Q9BY41	Region	14	324	Note=Histone deacetylase	Type=Deletion;Start=159;End=377
Q9BY41	Region	14	324	Note=Histone deacetylase	Type=Deletion;Start=147;End=377

Gene Isoform Structures and Expression Levels for HDAC8

Gene structures of our canonical and alternative spliced genes of HDAC8
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

Expression levels of gene isoforms across GTEx.

Expression levels of gene isoforms across TCGA.

Protein Structures

PDB and CIF files of the predicted protein structures
* Here we show the 3D structure of the proteins using Mol*. AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Model confidence is shown from the pLDDT values per residue. pLDDT corresponds to the model’s prediction of its score on the local Distance Difference Test. It is a measure of local accuracy (from AlphfaFold website). To color code individual residues, we transformed individual PDB files into CIF format.

3D view using mol* of Q9BY41-1

3D view using mol* of Q9BY41-4

3D view using mol* of Q9BY41-5

3D view using mol* of Q9BY41-6

3D view using mol* of Q9BY41-7

3D view using mol* of Q9BY41-8

pLDDT Score Distribution

pLDDT score distribution of the predicted protein structures from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.

pLDDT distribution across the protein length of Q9BY41-1

pLDDT distribution across the protein length of Q9BY41-4

pLDDT distribution across the protein length of Q9BY41-5

pLDDT distribution across the protein length of Q9BY41-6

pLDDT distribution across the protein length of Q9BY41-7

pLDDT distribution across the protein length of Q9BY41-8

Ramachandran Plot of Protein Structures

Ramachandran plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in this protein peptide.

Ramachandran plot of Q9BY41-1

Ramachandran plot of Q9BY41-4

Ramachandran plot of Q9BY41-6

Ramachandran plot of Q9BY41-8

Potential Active Site Information

The potential binding sites of these proteins were identified using SiteMap, a module of the Schrodinger suite.

UniProt-id	Site score	Size	D score	Volume	Exposure	Enclosure	Contact	Phobic	Philic	Balance	Don/Acc	Residues
Q9BY41-1	0.895	34	0.553	55.223	0.393	0.997	1.46	0.281	1.82	0.155	0.61	18,19,20,24,25,28,29,34,37,38,41,42,136,137,138,14 1,315
Q9BY41-4	1.066	341	1.126	1248.863	0.619	0.708	0.821	0.809	0.733	1.104	1.136	12,13,14,15,16,17,18,19,20,21,24,25,27,28,31,34,37 ,38,41,42,45,54,58,59,60,61,62,63,64,65,66,67,69,7 0,74,83,85,87,89,90,91,92,93,94,117,118,172,173,19 8,201,204,206,207,208,209,210,211,212,213,215,224, 227,228,231
Q9BY41-5	1.061	193	1.108	626.661	0.64	0.724	0.902	0.895	0.817	1.096	0.736	18,19,20,24,25,28,31,32,33,34,37,38,41,42,100,101, 103,111,115,119,122,123,126,134,135,136,137,138,13 9,140,141,142,143,151,152,153,154,157,158,161,162, 165,172,174,175,176,177,178,179,180,208
Q9BY41-6	1.007	459	1.038	1300.999	0.531	0.685	0.878	0.541	0.961	0.563	1.051	16,17,18,19,28,29,31,33,34,37,38,41,48,50,54,57,58 ,59,60,61,62,63,64,65,66,67,68,69,71,72,73,75,76,7 9,80,81,82,83,84,85,86,87,88,89,90,91,92,95,99,104 ,106,107,108,109,110,111,112,113,114,118,123,126,1 27,130,132,133,134,135,136,137,139
Q9BY41-7	1.018	103	1.061	345.744	0.637	0.676	0.923	1.023	0.875	1.169	0.684	70,115,119,120,122,123,126,133,134,135,136,139,140 ,141,142,144,152,153,154,155,156,157
Q9BY41-8	1.059	143	1.123	511.413	0.593	0.691	0.875	1.121	0.712	1.576	0.978	31,33,67,70,71,75,76,79,96,98,101,102,103,105,108, 111,112,115,116,119,120,139,140,141,142,143,144,14 5,146

Protein Structure and Feature Comparision

Protein Structure Comparision Using Template Modeling Scores (TM-score).

Protein Structure Comparision Visualization with mol*. between Canonical predicted structure (AF2)(orange) vs Canonical validated structure (PDB)(green)

3D view using mol* of Q9BY41-1_Q9BY41-1_2v5w_B.pdb

Protein Structure Comparision Visualization with mol*. between Canonical validated structure (PDB)(orange) vs Alternative predicted structure (AF2)(green)

3D view using mol* of Q9BY41-1_2v5w_B_Q9BY41-4.pdb

3D view using mol* of Q9BY41-1_2v5w_B_Q9BY41-5.pdb

3D view using mol* of Q9BY41-1_2v5w_B_Q9BY41-6.pdb

3D view using mol* of Q9BY41-1_2v5w_B_Q9BY41-7.pdb

3D view using mol* of Q9BY41-1_2v5w_B_Q9BY41-8.pdb

Protein Structure Comparision Visualization with mol*. between Canonical predicted structure (AF2)(orange) vs Alternative predicted structure (AF2)(green)

3D view using mol* of Q9BY41-1_Q9BY41-4.pdb

3D view using mol* of Q9BY41-1_Q9BY41-5.pdb

3D view using mol* of Q9BY41-1_Q9BY41-6.pdb

3D view using mol* of Q9BY41-1_Q9BY41-7.pdb

3D view using mol* of Q9BY41-1_Q9BY41-8.pdb

Protein Feature Comparison of the protein sequendary structures among the protiens.

./stats/secondary_structure/figure/Q9BY41-1_vs_Q9BY41-4.png

./stats/secondary_structure/figure/Q9BY41-1_vs_Q9BY41-5.png

./stats/secondary_structure/figure/Q9BY41-1_vs_Q9BY41-6.png

./stats/secondary_structure/figure/Q9BY41-1_vs_Q9BY41-7.png

./stats/secondary_structure/figure/Q9BY41-1_vs_Q9BY41-8.png

Protein Feature Comparison of the relative accessible surface area (ASA) among the protiens.

./stats/relative_asa/Q9BY41-1_vs_Q9BY41-4.png

./stats/relative_asa/Q9BY41-1_vs_Q9BY41-5.png

./stats/relative_asa/Q9BY41-1_vs_Q9BY41-6.png

./stats/relative_asa/Q9BY41-1_vs_Q9BY41-7.png

./stats/relative_asa/Q9BY41-1_vs_Q9BY41-8.png

Protein-Protein Interaction

Interactors from UniProt.

Accession_id

Subsection

Start

End

Funcitonal feature

Splicing information

Interactors from STRING.

Gene name

Interactors

Related Drugs to HDAC8

Drugs targeting this gene/protein.
(DrugBank)

UniProt accession	Gene name	DrugBank ID	Drug name	Drug group	Actions
Q9BY41	HDAC8	DB01592	Iron	approved	cofactor
Q9BY41	HDAC8	DB07350	(2E)-N-hydroxy-3-[1-methyl-4-(phenylacetyl)-1H-pyrrol-2-yl]prop-2-enamide	experimental
Q9BY41	HDAC8	DB08168	Coumarin 120	experimental
Q9BY41	HDAC8	DB02917	N-Hydroxy-4-(Methyl{[5-(2-Pyridinyl)-2-Thienyl]Sulfonyl}Amino)Benzamide	experimental
Q9BY41	HDAC8	DB01593	Zinc	approved, investigational	cofactor
Q9BY41	HDAC8	DB14533	Zinc chloride	approved, investigational	cofactor
Q9BY41	HDAC8	DB14548	Zinc sulfate, unspecified form	approved, experimental	cofactor
Q9BY41	HDAC8	DB14501	Ferrous glycine sulfate	approved
Q9BY41	HDAC8	DB04297	Trichostatin A	experimental
Q9BY41	HDAC8	DB14488	Ferrous gluconate	approved
Q9BY41	HDAC8	DB14489	Ferrous succinate	approved
Q9BY41	HDAC8	DB02546	Vorinostat	approved, investigational
Q9BY41	HDAC8	DB14487	Zinc acetate	approved, investigational
Q9BY41	HDAC8	DB14490	Ferrous ascorbate	approved
Q9BY41	HDAC8	DB14491	Ferrous fumarate	approved
Q9BY41	HDAC8	DB02565	4-(dimethylamino)-N-[7-(hydroxyamino)-7-oxoheptyl]benzamide	experimental
Q9BY41	HDAC8	DB07586	5-(4-METHYL-BENZOYLAMINO)-BIPHENYL-3,4'-DICARBOXYLIC ACID 3-DIMETHYLAMIDE-4'-HYDROXYAMIDE	experimental

Related Diseases to HDAC8

Previous studies relating to the alternative splicing of HDAC8 and disease information from the MeSH term (PubMed)

Gene

PMID

Title

Abstract

MeSH ID

MeSH term

Clinically important variants in HDAC8

(ClinVar, 04/20/2024)

accession_id

uniprot_id

gene_name

Type

Variant

Clinical_significance