mutated Ligand Binding Site gene DataBase





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Gene Summary

Ligand Binding Site Mutation Information

Protein Structure Related Information

Gene Expression and Gene-Gene Network

Phenotype Information

Pharmacological Information

Conservation Information for LBS

Gene summary for HDAC3
Gene summary
Basic gene Info.Gene symbolHDAC3
Gene namehistone deacetylase 3
CytomapUCSC genome browser: 5q31
Type of geneprotein-coding
Modification date20141222
dbXrefs MIM : 605166
Ensembl : ENSG00000171720
HPRD : 08950
Vega : OTTHUMG00000129629
ProteinUniProt: O15379
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_HDAC3
BioGPS: 8841
PathwayNCI Pathway Interaction Database: HDAC3
Pathway Commons: HDAC3
ContextiHOP: HDAC3
ligand binding site mutation search in PubMed: HDAC3
UCL Cancer Institute: HDAC3
Assigned class in mutLBSgeneDBB: This gene belongs to targetable_mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO:0000122negative regulation of transcription from RNA polymerase II promoter16569215
GO:0001934positive regulation of protein phosphorylation25190803
GO:0006476protein deacetylation17172643
GO:0031647regulation of protein stability25190803
GO:0042993positive regulation of transcription factor import into nucleus25190803
GO:0045944positive regulation of transcription from RNA polymerase II promoter25190803
GO:0071498cellular response to fluid shear stress25190803

Ligand binding site mutations for HDAC3
Lollipop-style diagram of mutations at LBS in amino-acid sequence.
We represented ligand binding site mutations only. (You can see big image via clicking.)
: non-synonymous mutation on LBS, Circle size denotes number of samples.

Cancer type specific mutLBS sorted by frequency
LBSAAchange of nsSNVCancer type# samples
cf) Cancer type abbreviation. BLCA: Bladder urothelial carcinoma, BRCA: Breast invasive carcinoma, CESC: Cervical squamous cell carcinoma and endocervical adenocarcinoma, COAD: Colon adenocarcinoma, GBM: Glioblastoma multiforme, LGG: Brain lower grade glioma, HNSC: Head and neck squamous cell carcinoma, KICH: Kidney chromophobe, KIRC: Kidney renal clear cell carcinoma, KIRP: Kidney renal papillary cell carcinoma, LAML: Acute myeloid leukemia, LUAD: Lung adenocarcinoma, LUSC: Lung squamous cell carcinoma, OV: Ovarian serous cystadenocarcinoma, PAAD: Pancreatic adenocarcinoma, PRAD: Prostate adenocarcinoma, SKCM: Skin cutaneous melanoma, STAD: Stomach adenocarcinoma, THCA: Thyroid carcinoma, UCEC: Uterine corpus endometrial carcinoma.

Protein structure related information for HDAC3
Relative protein structure stability change (ΔΔE) using Mupro 1.1
Mupro score denotes assessment of the effect of mutations on thermodynamic stability.
  (ΔΔE<0: mutation decreases stability, ΔΔE>0: mutation increases stability)
: nsSNV at non-LBS: nsSNV at LBS

nsSNVs sorted by the relative stability change of protein structure by each mutation
Blue: mutations of positive stability change. and red : the most recurrent mutation for this gene.
LBSAAchange of nsSNVRelative stability change
(MuPro1.1: Jianlin Cheng et al., Prediction of Protein Stability Changes for Single-Site Mutations Using Support Vector Machines, PROTEINS: Structure, Function, and Bioinformatics. 2006, 62:1125-1132)

Structure image for HDAC3 from PDB

Differential gene expression and gene-gene network for HDAC3
Differential gene expression between mutated and non-mutated LBS samples in all 16 major cancer types

Differential co-expressed gene network based on protein-protein interaction data (CePIN)
* Left PPI network was created from samples with mutations in the LBS of HDAC3 and the right PPI network was created from samples without mutations in the LBS of HDAC3. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.


Phenotype information for HDAC3
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C0018799Heart Diseases1Biomarker

Mutation level pathogenic information (ClinVar annotation)
Allele IDAA changeClinical significanceOriginPhenotype IDs

Pharmacological information for HDAC3
Gene expression profile of anticancer drug treated cell-lines (CCLE)
Heatmap showing the correlation between gene expression and drug response across all the cell-lines. We chose the top 20 among 138 drugs.We used Pearson's correlation coefficient.

Gene-centered drug-gene interaction network
Drug information targeting mutLBSgene (Approved drugs only)
Drug statusDrugBank IDNameTypeDrug structure
Approved|investigationalDB02546VorinostatSmall molecule
InvestigationalDB05223SB939Small molecule
InvestigationalDB05651MGCD-0103Small molecule
Approved|investigationalDB06603PanobinostatSmall molecule

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of HDAC3 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS

Conservation information for LBS of HDAC3
Multiple alignments for O15379 in multiple species
LBSAA sequence# speciesSpecies
D170LYIDIDIHHGD4Homo sapiens, Danio rerio, Gallus gallus, Rattus norvegicus
D170LYIDIDVHHGD1Arabidopsis thaliana
D170LYVDIDIHHGD1Xenopus tropicalis
D259LQCGADSLGCD4Homo sapiens, Danio rerio, Xenopus tropicalis, Rattus norvegicus
D259LQCGADSLARD1Arabidopsis thaliana
D259LQCGADSLGRD1Gallus gallus
G21FHYGAGHPMKP4Homo sapiens, Danio rerio, Gallus gallus, Rattus norvegicus
G21VYFGPNHPMKP1Arabidopsis thaliana
G21FHYGTGHPMKP1Xenopus tropicalis
H17DVGNFHYGAGH4Homo sapiens, Danio rerio, Gallus gallus, Rattus norvegicus
H17DVGSVYFGPNH1Arabidopsis thaliana
H17DVGNFHYGTGH1Xenopus tropicalis
H172IDIDIHHGDGV4Homo sapiens, Danio rerio, Gallus gallus, Rattus norvegicus
H172IDIDVHHGDGV1Arabidopsis thaliana
H172VDIDIHHGDGV1Xenopus tropicalis
K25AGHPMKPHRLA3Homo sapiens, Gallus gallus, Rattus norvegicus
K25PNHPMKPHRLC1Arabidopsis thaliana
K25AGHPMKPHRLS1Danio rerio
K25TGHPMKPHRLS1Xenopus tropicalis
R265SLGCDRLGCFN4Homo sapiens, Danio rerio, Xenopus tropicalis, Rattus norvegicus
R265SLARDRLGCFN1Arabidopsis thaliana
R265SLGRDRLGCFN1Gallus gallus
R301GGYTVRNVARC5Homo sapiens, Danio rerio, Xenopus tropicalis, Gallus gallus, Rattus norvegicus
R301GGYTKENVARC1Arabidopsis thaliana
V300GGGYTVRNVAR5Homo sapiens, Danio rerio, Xenopus tropicalis, Gallus gallus, Rattus norvegicus
V300GGGYTKENVAR1Arabidopsis thaliana
Y331SEYFEYFAPDF5Homo sapiens, Danio rerio, Xenopus tropicalis, Gallus gallus, Rattus norvegicus
Y331NDYIKYFAPDF1Arabidopsis thaliana

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