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 HDAC2
Gene summary
Basic gene Info.Gene symbolHDAC2
Gene namehistone deacetylase 2
CytomapUCSC genome browser: 6q21
Type of geneprotein-coding
DescriptionYY1-associated factor 1transcriptional regulator homolog RPD3
Modification date20141222
dbXrefs MIM : 605164
HPRD : 05521
ProteinUniProt: Q92769
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_HDAC2
BioGPS: 3066
PathwayNCI Pathway Interaction Database: HDAC2
Pathway Commons: HDAC2
ContextiHOP: HDAC2
ligand binding site mutation search in PubMed: HDAC2
UCL Cancer Institute: HDAC2
Assigned class in mutLBSgeneDBB: This gene belongs to targetable_mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO:0043044ATP-dependent chromatin remodeling16217013

Ligand binding site mutations for HDAC2
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 HDAC2
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 HDAC2 from PDB

Differential gene expression and gene-gene network for HDAC2
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 HDAC2 and the right PPI network was created from samples without mutations in the LBS of HDAC2. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.


Phenotype information for HDAC2
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C0024117Pulmonary Disease, Chronic Obstructive10Biomarker, Therapeutic
umls:C0014175Endometriosis3Biomarker, Therapeutic
umls:C0007137Carcinoma, Squamous Cell2Biomarker
umls:C0023470Leukemia, Myeloid1Biomarker

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

Pharmacological information for HDAC2
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|investigationalDB00227LovastatinSmall molecule
ApprovedDB00277TheophyllineSmall molecule
Approved|investigationalDB00313Valproic AcidSmall molecule
ApprovedDB01223AminophyllineSmall molecule
ApprovedDB01303OxtriphyllineSmall molecule
Approved|investigationalDB02546VorinostatSmall molecule
InvestigationalDB05223SB939Small molecule
InvestigationalDB05651MGCD-0103Small molecule
Approved|investigationalDB06176RomidepsinSmall molecule
Approved|investigationalDB06603PanobinostatSmall molecule

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of HDAC2 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS

Conservation information for LBS of HDAC2
Multiple alignments for Q92769 in multiple species
LBSAA sequence# speciesSpecies
C152EASGFCYVNDI3Homo sapiens, Arabidopsis thaliana, Mus musculus
C152EASGFCYTNDI1Caenorhabditis elegans
D100FNVGEDCPVFD3Homo sapiens, Arabidopsis thaliana, Mus musculus
D100FNVGEDCPLFD1Caenorhabditis elegans
D175RVLYIDIDIHH2Homo sapiens, Mus musculus
D175RVLYIDIDVHH1Arabidopsis thaliana
D175RVLYVDIDVHH1Caenorhabditis elegans
D177LYIDIDIHHGD2Homo sapiens, Mus musculus
D177LYIDIDVHHGD1Arabidopsis thaliana
D177LYVDIDVHHGD1Caenorhabditis elegans
D265LQCGADSLSGD3Homo sapiens, Arabidopsis thaliana, Mus musculus
D265LQCGADSLNGD1Caenorhabditis elegans
F110DGLFEFCQLST2Homo sapiens, Mus musculus
F110DGLFDFCRASA1Arabidopsis thaliana
F110DGLYEFCQLSS1Caenorhabditis elegans
F151SEASGFCYVND3Homo sapiens, Arabidopsis thaliana, Mus musculus
F151SEASGFCYTND1Caenorhabditis elegans
F199VMTVSFHKYGE2Homo sapiens, Mus musculus
F199VMTVSFHKFGD1Arabidopsis thaliana
F199VMTVSFHKYGD1Caenorhabditis elegans
F206KYGEYFPGTGD2Homo sapiens, Mus musculus
F206KFGDFFPGTGH1Arabidopsis thaliana
F206KYGDFFPGTGD1Caenorhabditis elegans
G139VNWAGGLHHAK2Homo sapiens, Mus musculus
G139INWGGGLHHAK1Arabidopsis thaliana
G139INWMGGLHHAK1Caenorhabditis elegans
G150KSEASGFCYVN3Homo sapiens, Arabidopsis thaliana, Mus musculus
G150KSEASGFCYTN1Caenorhabditis elegans
G301LLMLGGGGYTI2Homo sapiens, Mus musculus
G301LMVLGGGGYTI1Arabidopsis thaliana
G301LMMVGGGGYTP1Caenorhabditis elegans
G302LMLGGGGYTIR2Homo sapiens, Mus musculus
G302MVLGGGGYTIR1Arabidopsis thaliana
G302MMVGGGGYTPR1Caenorhabditis elegans
H141WAGGLHHAKKS2Homo sapiens, Mus musculus
H141WGGGLHHAKKS1Arabidopsis thaliana
H141WMGGLHHAKKS1Caenorhabditis elegans
H142AGGLHHAKKSE2Homo sapiens, Mus musculus
H142GGGLHHAKKSE1Arabidopsis thaliana
H142MGGLHHAKKSE1Caenorhabditis elegans
H179IDIDIHHGDGV2Homo sapiens, Mus musculus
H179IDIDVHHGDGV1Arabidopsis thaliana
H179VDIDVHHGDGV1Caenorhabditis elegans
H200MTVSFHKYGEY2Homo sapiens, Mus musculus
H200MTVSFHKFGDF1Arabidopsis thaliana
H200MTVSFHKYGDF1Caenorhabditis elegans
H29YYGQGHPMKPH3Homo sapiens, Arabidopsis thaliana, Mus musculus
H29YYGQGHVMKPH1Caenorhabditis elegans
I176VLYIDIDIHHG2Homo sapiens, Mus musculus
I176VLYIDIDVHHG1Arabidopsis thaliana
I176VLYVDIDVHHG1Caenorhabditis elegans
L140NWAGGLHHAKK2Homo sapiens, Mus musculus
L140NWGGGLHHAKK1Arabidopsis thaliana
L140NWMGGLHHAKK1Caenorhabditis elegans
L272LSGDRLGCFNL3Homo sapiens, Arabidopsis thaliana, Mus musculus
L272LNGDRLGPFNL1Caenorhabditis elegans
M31GQGHPMKPHRI3Homo sapiens, Arabidopsis thaliana, Mus musculus
M31GQGHVMKPHRI1Caenorhabditis elegans
P30YGQGHPMKPHR3Homo sapiens, Arabidopsis thaliana, Mus musculus
P30YGQGHVMKPHR1Caenorhabditis elegans
R35PMKPHRIRMTH2Homo sapiens, Mus musculus
R35PMKPHRIRMAH1Arabidopsis thaliana
R35VMKPHRIRMTH1Caenorhabditis elegans
S198RVMTVSFHKYG3Homo sapiens, Mus musculus, Caenorhabditis elegans
S198RVMTVSFHKFG1Arabidopsis thaliana
Y25IGNYYYGQGHP2Homo sapiens, Mus musculus
Y25IGDYYYGQGHP1Arabidopsis thaliana
Y25IGNYYYGQGHV1Caenorhabditis elegans
Y304LGGGGYTIRNV3Homo sapiens, Arabidopsis thaliana, Mus musculus
Y304VGGGGYTPRNV1Caenorhabditis elegans

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