mutLBSgeneDB

mutLBSgeneDB
mutated Ligand Binding Site gene DataBase

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 PDE4D
Gene summary
Basic gene Info.Gene symbolPDE4D
Gene namephosphodiesterase 4D, cAMP-specific
SynonymsACRDYS2|DPDE3|HSPDE4D|PDE43|PDE4DN2|STRK1
CytomapUCSC genome browser: 5q12
Type of geneprotein-coding
RefGenesNM_001104631.1,
NM_001165899.1,NM_001197218.1,NM_001197219.1,NM_001197220.1,
NM_001197221.1,NM_001197222.1,NM_001197223.1,NM_006203.4,
DescriptioncAMP-specific 3',5'-cyclic phosphodiesterase 4DcAMP-specific phosphodiesterase PDE4D6phosphodiesterase 4D, cAMP-specific (phosphodiesterase E3 dunce homolog, Drosophila)
Modification date20141207
dbXrefs MIM : 600129
HGNC : HGNC
Ensembl : ENSG00000113448
HPRD : 02530
Vega : OTTHUMG00000162218
ProteinUniProt: Q08499
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PDE4D
BioGPS: 5144
PathwayNCI Pathway Interaction Database: PDE4D
KEGG: PDE4D
REACTOME: PDE4D
Pathway Commons: PDE4D
ContextiHOP: PDE4D
ligand binding site mutation search in PubMed: PDE4D
UCL Cancer Institute: PDE4D
Assigned class in mutLBSgeneDBB: This gene belongs to targetable_mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO IDGO TermPubMed ID
GO:0006198cAMP catabolic process17404263
GO:0071320cellular response to cAMP12121997
GO:0071872cellular response to epinephrine stimulus12121997


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Ligand binding site mutations for PDE4D
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
T635T635MBRCA1
T635T635MCOAD1
F332E331QHNSC1
C660C660FLUAD1
E532E532QOV1
I638I638KSKCM1
F337F337LUCEC1
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.


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Protein structure related information for PDE4D
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
I638I638K-1.7095128
C660C660F-1.0495889
F332E331Q-0.95883169
E532E532Q-0.71152805
F337F337L-0.51425174
T635T635M-0.48577584
(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 PDE4D from PDB

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Differential gene expression and gene-gene network for PDE4D
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 PDE4D and the right PPI network was created from samples without mutations in the LBS of PDE4D. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.


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Phenotype information for PDE4D
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C0038454Stroke38Biomarker, GeneticVariation
umls:C0004096Asthma9Biomarker, GeneticVariation
umls:C3553250ACRODYSOSTOSIS 2 WITH OR WITHOUT HORMONE RESISTANCE4GeneticVariation
umls:C0236733Amphetamine-Related Disorders1Biomarker
umls:C0033578Prostatic Neoplasms1Biomarker

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

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Pharmacological information for PDE4D
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|nutraceuticalDB00131Adenosine monophosphateSmall molecule
ApprovedDB00651DyphyllineSmall molecule
ApprovedDB00920KetotifenSmall molecule
Approved|investigationalDB01088IloprostSmall molecule
ApprovedDB01656RoflumilastSmall molecule
ExperimentalDB01791PiclamilastSmall molecule
ExperimentalDB01954RolipramSmall molecule
ExperimentalDB019593,5-Dimethyl-1-(3-Nitrophenyl)-1h-Pyrazole-4-Carboxylic Acid Ethyl EsterSmall molecule
ExperimentalDB026762-[3-(2-Hydroxy-1,1-Dihydroxymethyl-Ethylamino)-Propylamino]-2-Hydroxymethyl-Propane-1,3-DiolSmall molecule
ExperimentalDB029186-(4-Difluoromethoxy-3-Methoxy-Phenyl)-2h-Pyridazin-3-OneSmall molecule
ExperimentalDB031831-(4-Aminophenyl)-3,5-Dimethyl-1h-Pyrazole-4-Carboxylic Acid Ethyl EsterSmall molecule
ExperimentalDB03606(S)-RolipramSmall molecule
InvestigationalDB03849CilomilastSmall molecule
ExperimentalDB04149(R)-RolipramSmall molecule
ExperimentalDB042713,5-Dimethyl-1h-Pyrazole-4-Carboxylic Acid Ethyl EsterSmall molecule
ExperimentalDB044691-(4-Methoxyphenyl)-3,5-Dimethyl-1h-Pyrazole-4-Carboxylic Acid Ethyl EsterSmall molecule
InvestigationalDB05219AN2728Small molecule
Approved|investigationalDB05266IbudilastSmall molecule
InvestigationalDB05298OPC-6535Small molecule
Approved|investigationalDB05676ApremilastSmall molecule
ExperimentalDB06842(4R)-4-(3-butoxy-4-methoxybenzyl)imidazolidin-2-oneSmall molecule
ExperimentalDB070513,5-DIMETHYL-1-PHENYL-1H-PYRAZOLE-4-CARBOXYLIC ACID ETHYL ESTERSmall molecule
ExperimentalDB079543-isobutyl-1-methyl-7H-xanthineSmall molecule
ExperimentalDB082994-[8-(3-nitrophenyl)-1,7-naphthyridin-6-yl]benzoic acidSmall molecule

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of PDE4D go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS


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Conservation information for LBS of PDE4D
Multiple alignments for Q08499 in multiple species
LBSAA sequence# speciesSpecies
C660EISPMCDKHNA2Homo sapiens, Rattus norvegicus
C660DISPMCDRHNA1Drosophila melanogaster
C660EISPMCDRGNV1Caenorhabditis elegans
D503ASAIHDVDHPG2Homo sapiens, Rattus norvegicus
D503AACIHDVDHPG1Drosophila melanogaster
D503AGAVHDVDHPG1Caenorhabditis elegans
D620MVHCADLSNPT2Homo sapiens, Rattus norvegicus
D620LVHCADLSNPT1Drosophila melanogaster
D620MIHLADLSNPT1Caenorhabditis elegans
E532DSSVLENHHLA2Homo sapiens, Rattus norvegicus
E532DESVLENHHLA1Drosophila melanogaster
E532DESVLEQHHLA1Caenorhabditis elegans
F332NQVSEFISNTF1Homo sapiens
F332NQISEYICSTF1Drosophila melanogaster
F332TQVSKFLITTY1Caenorhabditis elegans
F332NQVSEYISNTF1Rattus norvegicus
F337FISNTFLDKQH1Homo sapiens
F337YICSTFLDKQQ1Drosophila melanogaster
F337FLITTYMDKEE1Caenorhabditis elegans
F337YISNTFLDKQH1Rattus norvegicus
F409WGLHVFRIAEL2Homo sapiens, Rattus norvegicus
F409WGIQIFSIGEF1Drosophila melanogaster
F409WGPDVFKIDEL1Caenorhabditis elegans
F642RIMEEFFRQGD2Homo sapiens, Rattus norvegicus
F642LLMEEFFLQGD1Drosophila melanogaster
F642RIMEEYWRQGD1Caenorhabditis elegans
F674KSQVGFIDYIV4Homo sapiens, Drosophila melanogaster, Caenorhabditis elegans, Rattus norvegicus
F734GQTEKFQFELT2Homo sapiens, Rattus norvegicus
F734-QEDRIRFQVT1Drosophila melanogaster
F734-----------1Caenorhabditis elegans
H407NKWGLHVFRIA2Homo sapiens, Rattus norvegicus
H407DTWGIQIFSIG1Drosophila melanogaster
H407DDWGPDVFKID1Caenorhabditis elegans
H462ADVAYHNNIHA2Homo sapiens, Rattus norvegicus
H462KDNPFHNSLHA1Drosophila melanogaster
H462-NNHYHNFIHA1Caenorhabditis elegans
H466YHNNIHAADVV2Homo sapiens, Rattus norvegicus
H466FHNSLHAADVT1Drosophila melanogaster
H466YHNFIHAADVA1Caenorhabditis elegans
H502FASAIHDVDHP2Homo sapiens, Rattus norvegicus
H502FAACIHDVDHP1Drosophila melanogaster
H502FAGAVHDVDHP1Caenorhabditis elegans
H506IHDVDHPGVSN2Homo sapiens, Rattus norvegicus
H506IHDVDHPGLTN1Drosophila melanogaster
H506VHDVDHPGFTN1Caenorhabditis elegans
H578TDMSKHMNLLA2Homo sapiens, Rattus norvegicus
H578TDMSKHMSLLA2Drosophila melanogaster, Caenorhabditis elegans
I333QVSEFISNTFL1Homo sapiens
I333QISEYICSTFL1Drosophila melanogaster
I333QVSKFLITTYM1Caenorhabditis elegans
I333QVSEYISNTFL1Rattus norvegicus
I638QWTDRIMEEFF2Homo sapiens, Rattus norvegicus
I638RWVALLMEEFF1Drosophila melanogaster
I638QWNQRIMEEYW1Caenorhabditis elegans
I678GFIDYIVHPLW3Homo sapiens, Drosophila melanogaster, Rattus norvegicus
I678GFIDYIVHPLY1Caenorhabditis elegans
L26AGGATLKAPKH1Homo sapiens
L26DGGGEAINGGN1Drosophila melanogaster
L26AGGSG------1Caenorhabditis elegans
L26SGGAALKAPKH1Rattus norvegicus
L621VHCADLSNPTK3Homo sapiens, Drosophila melanogaster, Rattus norvegicus
L621IHLADLSNPTK1Caenorhabditis elegans
L630TKPLQLYRQWT2Homo sapiens, Rattus norvegicus
L630TKPLPLYKRWV1Drosophila melanogaster
L630TKPIELYQQWN1Caenorhabditis elegans
M575VLATDMSKHMN2Homo sapiens, Rattus norvegicus
M575VLSTDMSKHMS1Drosophila melanogaster
M575VLATDMSKHMS1Caenorhabditis elegans
M639WTDRIMEEFFR2Homo sapiens, Rattus norvegicus
M639WVALLMEEFFL1Drosophila melanogaster
M639WNQRIMEEYWR1Caenorhabditis elegans
M659MEISPMCDKHN2Homo sapiens, Rattus norvegicus
M659MDISPMCDRHN1Drosophila melanogaster
M659LEISPMCDRGN1Caenorhabditis elegans
N623CADLSNPTKPL3Homo sapiens, Drosophila melanogaster, Rattus norvegicus
N623LADLSNPTKPI1Caenorhabditis elegans
P624ADLSNPTKPLQ2Homo sapiens, Rattus norvegicus
P624ADLSNPTKPLP1Drosophila melanogaster
P624ADLSNPTKPIE1Caenorhabditis elegans
Q645EEFFRQGDRER2Homo sapiens, Rattus norvegicus
Q645EEFFLQGDKER1Drosophila melanogaster
Q645EEYWRQGDKEK1Caenorhabditis elegans
Q671SVEKSQVGFID2Homo sapiens, Rattus norvegicus
Q671TIEKSQVGFID2Drosophila melanogaster, Caenorhabditis elegans
Q735QTEKFQFELTL2Homo sapiens, Rattus norvegicus
Q735QEDRIRFQVTL1Drosophila melanogaster
Q735-----------1Caenorhabditis elegans
R410GLHVFRIAELS2Homo sapiens, Rattus norvegicus
R410GIQIFSIGEFS1Drosophila melanogaster
R410GPDVFKIDELS1Caenorhabditis elegans
S510DHPGVSNQFLI2Homo sapiens, Rattus norvegicus
S510DHPGLTNQFLV1Drosophila melanogaster
S510DHPGFTNQYLI1Caenorhabditis elegans
S670ASVEKSQVGFI2Homo sapiens, Rattus norvegicus
S670ATIEKSQVGFI1Drosophila melanogaster
S670VTIEKSQVGFI1Caenorhabditis elegans
T336EFISNTFLDKQ1Homo sapiens
T336EYICSTFLDKQ1Drosophila melanogaster
T336KFLITTYMDKE1Caenorhabditis elegans
T336EYISNTFLDKQ1Rattus norvegicus
T573DIVLATDMSKH2Homo sapiens, Rattus norvegicus
T573DIVLSTDMSKH1Drosophila melanogaster
T573DMVLATDMSKH1Caenorhabditis elegans
T635LYRQWTDRIME2Homo sapiens, Rattus norvegicus
T635LYKRWVALLME1Drosophila melanogaster
T635LYQQWNQRIME1Caenorhabditis elegans
T731GRQGQTEKFQF2Homo sapiens, Rattus norvegicus
T731----QEDRIRF1Drosophila melanogaster
T731-----------1Caenorhabditis elegans
V329RSGNQVSEFIS1Homo sapiens
V329RSGNQISEYIC1Drosophila melanogaster
V329KSGTQVSKFLI1Caenorhabditis elegans
V329RSGNQVSEYIS1Rattus norvegicus
V509VDHPGVSNQFL2Homo sapiens, Rattus norvegicus
V509VDHPGLTNQFL1Drosophila melanogaster
V509VDHPGFTNQYL1Caenorhabditis elegans
W634QLYRQWTDRIM2Homo sapiens, Rattus norvegicus
W634PLYKRWVALLM1Drosophila melanogaster
W634ELYQQWNQRIM1Caenorhabditis elegans
Y461HADVAYHNNIH2Homo sapiens, Rattus norvegicus
Y461VKDNPFHNSLH1Drosophila melanogaster
Y461R-NNHYHNFIH1Caenorhabditis elegans
Y631KPLQLYRQWTD2Homo sapiens, Rattus norvegicus
Y631KPLPLYKRWVA1Drosophila melanogaster
Y631KPIELYQQWNQ1Caenorhabditis elegans


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