mutLBSgeneDB

mutLBSgeneDB
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 PDE6D
Gene summary
Basic gene Info.Gene symbolPDE6D
Gene namephosphodiesterase 6D, cGMP-specific, rod, delta
SynonymsJBTS22|PDED
CytomapUCSC genome browser: 2q35-q36
Type of geneprotein-coding
RefGenesNM_001291018.1,
NM_002601.3,NR_110994.1,
DescriptionGMP-PDE deltaprotein p17retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
Modification date20141207
dbXrefs MIM : 602676
HGNC : HGNC
Ensembl : ENSG00000156973
HPRD : 04056
Vega : OTTHUMG00000153785
ProteinUniProt: O43924
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PDE6D
BioGPS: 5147
PathwayNCI Pathway Interaction Database: PDE6D
KEGG: PDE6D
REACTOME: PDE6D
Pathway Commons: PDE6D
ContextiHOP: PDE6D
ligand binding site mutation search in PubMed: PDE6D
UCL Cancer Institute: PDE6D
Assigned class in mutLBSgeneDBC: This gene just belongs to mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO IDGO TermPubMed ID


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Ligand binding site mutations for PDE6D
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
V49,A47R48HUCEC2
V49,A47R48SLUAD1
S39P41SSKCM1
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 PDE6D
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
A47R48H-1.2192805
V49R48H-1.2192805
A47R48S-1.1799509
V49R48S-1.1799509
S39P41S-0.99068922
(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 PDE6D from PDB
PDB IDPDB titlePDB structure
4JV6The crystal structure of PDE6D in complex to inhibitor-1

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Differential gene expression and gene-gene network for PDE6D
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 PDE6D and the right PPI network was created from samples without mutations in the LBS of PDE6D. 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 PDE6D
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type

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

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Pharmacological information for PDE6D
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.
Drug information targeting mutLBSgene (Approved drugs only)
Drug statusDrugBank IDNameTypeDrug structure

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of PDE6D go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
FAR2-TRANS,6-TRANS-FARNESYL GROUP3t5iDA47
18F1-BENZYL-2-PHENYL-1H-BENZIMIDAZOLE4jv6BA47
17X(2S)-2-(2-PHENYL-1H-BENZIMIDAZOL-1-YL)-2-(PIPERIDIN-4- YL)ETHYL 1-(1-BENZYL-1H-BENZIMIDAZOL-2-YL)PIPERIDINE- 4-CARBOXYLATE4jvfBA47
1M1(6R)-6-(PYRIDIN-2-YL)-5,6-DIHYDROBENZIMIDAZO[1,2- C]QUINAZOLINE4jv8BA47 V49
1M01-BENZYL-2-(4-{[(2R)-2-(2-PHENYL-1H-BENZIMIDAZOL-1-YL) PENT-4-EN-1-YL]OXY}PHENYL)-1H-BENZIMIDAZOLE4jvbBA47 V49
GERGERAN-8-YL GERAN5e8fAS39
GERGERAN-8-YL GERAN5e8fCS39 A47


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Conservation information for LBS of PDE6D
Multiple alignments for O43924 in multiple species
LBSAA sequence# speciesSpecies
A111QSLIEAAPESQ4Homo sapiens, Mus musculus, Canis lupus familiaris, Bos taurus
A111QSTIEAAPESQ2Drosophila melanogaster, Anopheles gambiae
A111QNMIEAAPESQ1Caenorhabditis elegans
A112SLIEAAPESQM4Homo sapiens, Mus musculus, Canis lupus familiaris, Bos taurus
A112STIEAAPESQM2Drosophila melanogaster, Anopheles gambiae
A112NMIEAAPESQM1Caenorhabditis elegans
A47GVEHEARVPKK4Homo sapiens, Mus musculus, Canis lupus familiaris, Bos taurus
A47DQEHEARVPVK1Drosophila melanogaster
A47DVEHEAKVPVK1Anopheles gambiae
A47KREHKAHVPKN1Caenorhabditis elegans
C56KKILKCKAVSR4Homo sapiens, Mus musculus, Canis lupus familiaris, Bos taurus
C56VKILDMRAVSR1Drosophila melanogaster
C56VKILSLRAVSR1Anopheles gambiae
C56KNLLKCRTVSR1Caenorhabditis elegans
E110WQSLIEAAPES4Homo sapiens, Mus musculus, Canis lupus familiaris, Bos taurus
E110WQSTIEAAPES2Drosophila melanogaster, Anopheles gambiae
E110WQNMIEAAPES1Caenorhabditis elegans
E114IEAAPESQMMP6Homo sapiens, Drosophila melanogaster, Anopheles gambiae, Mus musculus, Canis lupus familiaris, Bos taurus
E114IEAAPESQMFP1Caenorhabditis elegans
E88KGQCLEEWFFE4Homo sapiens, Mus musculus, Canis lupus familiaris, Bos taurus
E88KGRIMEEWFFE2Drosophila melanogaster, Anopheles gambiae
E88KGTIIEEWYFD1Caenorhabditis elegans
F133IIETKFFDDDL4Homo sapiens, Mus musculus, Canis lupus familiaris, Bos taurus
F133TIQTSFYDNET1Drosophila melanogaster
F133TIETSFYDGDT1Anopheles gambiae
F133VVETLFYDGDL1Caenorhabditis elegans
I109TWQSLIEAAPE4Homo sapiens, Mus musculus, Canis lupus familiaris, Bos taurus
I109TWQSTIEAAPE2Drosophila melanogaster, Anopheles gambiae
I109TWQNMIEAAPE1Caenorhabditis elegans
I129TGNVIIETKFF4Homo sapiens, Mus musculus, Canis lupus familiaris, Bos taurus
I129NGNVTIQTSFY1Drosophila melanogaster
I129NGNVTIETSFY1Anopheles gambiae
I129SGNVVVETLFY1Caenorhabditis elegans
I53RVPKKILKCKA4Homo sapiens, Mus musculus, Canis lupus familiaris, Bos taurus
I53RVPVKILDMRA1Drosophila melanogaster
I53KVPVKILSLRA1Anopheles gambiae
I53HVPKNLLKCRT1Caenorhabditis elegans
K57KILKCKAVSRE4Homo sapiens, Mus musculus, Canis lupus familiaris, Bos taurus
K57KILDMRAVSRE1Drosophila melanogaster
K57KILSLRAVSRE1Anopheles gambiae
K57NLLKCRTVSRE1Caenorhabditis elegans
L147TSRVRLFYV3Homo sapiens, Canis lupus familiaris, Bos taurus
L147KSVVRLYYI2Drosophila melanogaster, Anopheles gambiae
L147TSRVRLYYD1Caenorhabditis elegans
L147TSKVRLFYV1Mus musculus
L17LRGFKLNWMNL3Homo sapiens, Mus musculus, Bos taurus
L17QKGFQINYMIL1Drosophila melanogaster
L17LNGFQINWMIL1Anopheles gambiae
L17LAGFKLNWMNL1Caenorhabditis elegans
L17LKGFKLNWMNL1Canis lupus familiaris
L22LNWMNLRDAET5Homo sapiens, Caenorhabditis elegans, Mus musculus, Canis lupus familiaris, Bos taurus
L22INYMILRDADS1Drosophila melanogaster
L22INWMILRDADT1Anopheles gambiae
L38QGTEDLSVPGV4Homo sapiens, Mus musculus, Canis lupus familiaris, Bos taurus
L38QENKDFSAPDQ1Drosophila melanogaster
L38QENKDFSCPDV1Anopheles gambiae
L38QSTEDMADPKR1Caenorhabditis elegans
L54VPKKILKCKAV4Homo sapiens, Mus musculus, Canis lupus familiaris, Bos taurus
L54VPVKILDMRAV1Drosophila melanogaster
L54VPVKILSLRAV1Anopheles gambiae
L54VPKNLLKCRTV1Caenorhabditis elegans
L63AVSRELNFSSA3Mus musculus, Canis lupus familiaris, Bos taurus
L63AVSRELNFSST1Homo sapiens
L63AVSREINFSTI1Drosophila melanogaster
L63AVSREINFSTV1Anopheles gambiae
L63TVSREINFTSS1Caenorhabditis elegans
L87FKGQCLEEWFF4Homo sapiens, Mus musculus, Canis lupus familiaris, Bos taurus
L87FKGRIMEEWFF2Drosophila melanogaster, Anopheles gambiae
L87LKGTIIEEWYF1Caenorhabditis elegans
M117APESQMMPASV4Homo sapiens, Mus musculus, Canis lupus familiaris, Bos taurus
M117APESQMMPAKV2Drosophila melanogaster, Anopheles gambiae
M117APESQMFPPSV1Caenorhabditis elegans
M118PESQMMPASVL4Homo sapiens, Mus musculus, Canis lupus familiaris, Bos taurus
M118PESQMMPAKVL2Drosophila melanogaster, Anopheles gambiae
M118PESQMFPPSVL1Caenorhabditis elegans
M20FKLNWMNLRDA5Homo sapiens, Caenorhabditis elegans, Mus musculus, Canis lupus familiaris, Bos taurus
M20FQINYMILRDA1Drosophila melanogaster
M20FQINWMILRDA1Anopheles gambiae
Q116AAPESQMMPAS4Homo sapiens, Mus musculus, Canis lupus familiaris, Bos taurus
Q116AAPESQMMPAK2Drosophila melanogaster, Anopheles gambiae
Q116AAPESQMFPPS1Caenorhabditis elegans
Q78KFRLEQKVYFK4Homo sapiens, Mus musculus, Canis lupus familiaris, Bos taurus
Q78NFRLDQKVLFK2Drosophila melanogaster, Anopheles gambiae
Q78KFRLEQRVYLK1Caenorhabditis elegans
R61CKAVSRELNFS4Homo sapiens, Mus musculus, Canis lupus familiaris, Bos taurus
R61MRAVSREINFS1Drosophila melanogaster
R61LRAVSREINFS1Anopheles gambiae
R61CRTVSREINFT1Caenorhabditis elegans
S143LLVSTSRVRLF3Homo sapiens, Canis lupus familiaris, Bos taurus
S143TLITKSVVRLY1Drosophila melanogaster
S143TLISKSVVRLY1Anopheles gambiae
S143LLVSTSRVRLY1Caenorhabditis elegans
S143LLVSTSKVRLF1Mus musculus
S39GTEDLSVPGVE4Homo sapiens, Mus musculus, Canis lupus familiaris, Bos taurus
S39ENKDFSAPDQE1Drosophila melanogaster
S39ENKDFSCPDVE1Anopheles gambiae
S39STEDMADPKRE1Caenorhabditis elegans
T131NVIIETKFFDD4Homo sapiens, Mus musculus, Canis lupus familiaris, Bos taurus
T131NVTIQTSFYDN1Drosophila melanogaster
T131NVTIETSFYDG1Anopheles gambiae
T131NVVVETLFYDG1Caenorhabditis elegans
V145VSTSRVRLFYV3Homo sapiens, Canis lupus familiaris, Bos taurus
V145ITKSVVRLYYI1Drosophila melanogaster
V145ISKSVVRLYYI1Anopheles gambiae
V145VSTSRVRLYYD1Caenorhabditis elegans
V145VSTSKVRLFYV1Mus musculus
V49EHEARVPKKIL4Homo sapiens, Mus musculus, Canis lupus familiaris, Bos taurus
V49EHEARVPVKIL1Drosophila melanogaster
V49EHEAKVPVKIL1Anopheles gambiae
V49EHKAHVPKNLL1Caenorhabditis elegans
V59LKCKAVSRELN4Homo sapiens, Mus musculus, Canis lupus familiaris, Bos taurus
V59LDMRAVSREIN1Drosophila melanogaster
V59LSLRAVSREIN1Anopheles gambiae
V59LKCRTVSREIN1Caenorhabditis elegans
V80RLEQKVYFKGQ4Homo sapiens, Mus musculus, Canis lupus familiaris, Bos taurus
V80RLDQKVLFKGR2Drosophila melanogaster, Anopheles gambiae
V80RLEQRVYLKGT1Caenorhabditis elegans
W32TGKILWQGTED4Homo sapiens, Mus musculus, Canis lupus familiaris, Bos taurus
W32SGKIIWQENKD1Drosophila melanogaster
W32TGKIIWQENKD1Anopheles gambiae
W32TGKVLWQSTED1Caenorhabditis elegans
W90QCLEEWFFEFG4Homo sapiens, Mus musculus, Canis lupus familiaris, Bos taurus
W90RIMEEWFFEMG2Drosophila melanogaster, Anopheles gambiae
W90TIIEEWYFDFG1Caenorhabditis elegans
Y149RVRLFYV3Homo sapiens, Canis lupus familiaris, Bos taurus
Y149VVRLYYI2Drosophila melanogaster, Anopheles gambiae
Y149RVRLYYD1Caenorhabditis elegans
Y149KVRLFYV1Mus musculus


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