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 CSNK1D
Gene summary
Basic gene Info.Gene symbolCSNK1D
Gene namecasein kinase 1, delta
SynonymsASPS|CKIdelta|FASPS2|HCKID
CytomapUCSC genome browser: 17q25
Type of geneprotein-coding
RefGenesNM_001893.4,
NM_139062.2,NR_110578.1,
DescriptionCKI-deltaCKIdcasein kinase I isoform deltatau-protein kinase CSNK1D
Modification date20141207
dbXrefs MIM : 600864
HGNC : HGNC
Ensembl : ENSG00000141551
HPRD : 02920
Vega : OTTHUMG00000178601
ProteinUniProt: P48730
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_CSNK1D
BioGPS: 1453
PathwayNCI Pathway Interaction Database: CSNK1D
KEGG: CSNK1D
REACTOME: CSNK1D
Pathway Commons: CSNK1D
ContextiHOP: CSNK1D
ligand binding site mutation search in PubMed: CSNK1D
UCL Cancer Institute: CSNK1D
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:0006468protein phosphorylation16618118
GO:0051225spindle assembly10826492


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Ligand binding site mutations for CSNK1D

Cancer type specific mutLBS sorted by frequency
LBSAAchange of nsSNVCancer type# samples
F95S97PCOAD4
F95F95LCOAD1
P66T67IGBM1
E90E90DLUAD1
D149F150LLUSC1
D132N133SSTAD1
L92L92ISTAD1
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 CSNK1D
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
D149F150L0.31983684
L92L92I-1.3492357
D132N133S-0.74497385
E90E90D-0.72714433
F95S97P-0.6591148
F95F95L-0.47100034
P66T67I-0.29970518
(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 CSNK1D from PDB
PDB IDPDB titlePDB structure
3UYSCrystal structure of apo human ck1d

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Differential gene expression and gene-gene network for CSNK1D
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 CSNK1D and the right PPI network was created from samples without mutations in the LBS of CSNK1D. 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 CSNK1D
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C3808874ADVANCED SLEEP PHASE SYNDROME, FAMILIAL, 21Biomarker, GeneticVariation

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

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Pharmacological information for CSNK1D
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

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of CSNK1D go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
1QM9-[3-(4-FLUOROPHENYL)-1-METHYL-1H-PYRAZOL-4-YL]-2,3,4, 5-TETRAHYDROPYRIDO[2,3-F][1,4]OXAZEPINE4kbaBD149
PFO4-{4-(4-FLUOROPHENYL)-1-[1-(1,2-OXAZOL-3-YLMETHYL) PIPERIDIN-4-YL]-1H-IMIDAZOL-5-YL}PYRIMIDIN-2-AMINE4tn6AE90 D132
386N-(2,2-DIFLUORO-5H-[1,3]DIOXOLO[4,5-F]BENZIMIDAZOL-6- YL)-2-{[2-(TRIFLUOROMETHOXY)BENZOYL]AMINO}-1,3- THIAZOLE-4-CARBOXAMIDE4tw9AF95
HSJOCTYL BETA-L-TALOPYRANOSIDE4tw9AF95
HSJOCTYL BETA-L-TALOPYRANOSIDE4tw9BF95
386N-(2,2-DIFLUORO-5H-[1,3]DIOXOLO[4,5-F]BENZIMIDAZOL-6- YL)-2-{[2-(TRIFLUOROMETHOXY)BENZOYL]AMINO}-1,3- THIAZOLE-4-CARBOXAMIDE4tw9BL92
37J2-{[2-(TRIFLUOROMETHOXY)BENZOYL]AMINO}-N-[6- (TRIFLUOROMETHYL)-1H-BENZIMIDAZOL-2-YL]-1,3-THIAZOLE- 4-CARBOXAMIDE4twcAL92
37J2-{[2-(TRIFLUOROMETHOXY)BENZOYL]AMINO}-N-[6- (TRIFLUOROMETHYL)-1H-BENZIMIDAZOL-2-YL]-1,3-THIAZOLE- 4-CARBOXAMIDE4twcBL92
1QON-BENZYL-4-(PYRIDIN-3-YL)PYRIMIDIN-2-AMINE4kb8BP66
1QON-BENZYL-4-(PYRIDIN-3-YL)PYRIMIDIN-2-AMINE4kb8DP66
15G2-{2-[(3,4-DIFLUOROPHENOXY)METHYL]-5-METHOXYPYRIDIN-4- YL}-1,5,6,7-TETRAHYDRO-4H-PYRROLO[3,2-C]PYRIDIN-4-ONE4hgtAP66 D149
15G2-{2-[(3,4-DIFLUOROPHENOXY)METHYL]-5-METHOXYPYRIDIN-4- YL}-1,5,6,7-TETRAHYDRO-4H-PYRROLO[3,2-C]PYRIDIN-4-ONE4hgtBP66 D149


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Conservation information for LBS of CSNK1D
Multiple alignments for P48730 in multiple species
LBSAA sequence# speciesSpecies
A36AGEEVAIKLEC3Homo sapiens, Mus musculus, Rattus norvegicus
A36SGEEVAIKLES2Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Schizosaccharomyces pombe (strain 972 / ATCC 24843)
A36TNEEVAVKLEC1Caenorhabditis elegans
A36VGEEVAIKLEC1Danio rerio
A36AAEEVAIKLEC1Xenopus tropicalis
D132RDVKPDNFLMG5Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus, Rattus norvegicus
D132RDIKPDNFLMG3Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Schizosaccharomyces pombe (strain 972 / ATCC 24843), Caenorhabditis elegans
D149LVYIIDFGLAK6Homo sapiens, Caenorhabditis elegans, Danio rerio, Xenopus tropicalis, Mus musculus, Rattus norvegicus
D149TVHVIDFGLSK1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
D149QVNIIDFGLAK1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
D91GPSLEDLFNFC7Homo sapiens, Schizosaccharomyces pombe (strain 972 / ATCC 24843), Caenorhabditis elegans, Danio rerio, Xenopus tropicalis, Mus musculus, Rattus norvegicus
D91GPSLEDLFNYC1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
E52PQLHIESKIYK5Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus, Rattus norvegicus
E52PQLDYESRVYR1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
E52PQLEYEYRVYR1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
E52PQLHIESRLYR1Caenorhabditis elegans
E83NVMVMELLGPS6Homo sapiens, Caenorhabditis elegans, Danio rerio, Xenopus tropicalis, Mus musculus, Rattus norvegicus
E83NAMVIDLLGPS1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
E83NAMVMDLLGPS1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
E90LGPSLEDLFNF7Homo sapiens, Schizosaccharomyces pombe (strain 972 / ATCC 24843), Caenorhabditis elegans, Danio rerio, Xenopus tropicalis, Mus musculus, Rattus norvegicus
E90LGPSLEDLFNY1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
F95EDLFNFCSRKF5Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus, Rattus norvegicus
F95EDLFNYCHRRF1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
F95EDLFNFCNRKF1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
F95EDLFNFCQRKF1Caenorhabditis elegans
G16LGRKIGSGSFG6Homo sapiens, Caenorhabditis elegans, Danio rerio, Xenopus tropicalis, Mus musculus, Rattus norvegicus
G16IGRKIGSGSFG2Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Schizosaccharomyces pombe (strain 972 / ATCC 24843)
G18RKIGSGSFGDI8Homo sapiens, Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Schizosaccharomyces pombe (strain 972 / ATCC 24843), Caenorhabditis elegans, Danio rerio, Xenopus tropicalis, Mus musculus, Rattus norvegicus
G86VMELLGPSLED6Homo sapiens, Caenorhabditis elegans, Danio rerio, Xenopus tropicalis, Mus musculus, Rattus norvegicus
G86VIDLLGPSLED1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
G86VMDLLGPSLED1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
I148NLVYIIDFGLA6Homo sapiens, Caenorhabditis elegans, Danio rerio, Xenopus tropicalis, Mus musculus, Rattus norvegicus
I148STVHVIDFGLS1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
I148NQVNIIDFGLA1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
I15RLGRKIGSGSF6Homo sapiens, Caenorhabditis elegans, Danio rerio, Xenopus tropicalis, Mus musculus, Rattus norvegicus
I15RIGRKIGSGSF2Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Schizosaccharomyces pombe (strain 972 / ATCC 24843)
I23GSFGDIYLGTD5Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus, Rattus norvegicus
I23GSFGDIYHGTN1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
I23GSFGDIYLGTN1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
I23GSFGDIYLGQN1Caenorhabditis elegans
I37GEEVAIKLECV4Homo sapiens, Danio rerio, Mus musculus, Rattus norvegicus
I37GEEVAIKLESI1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
I37GEEVAIKLEST1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
I37NEEVAVKLECV1Caenorhabditis elegans
I37AEEVAIKLECV1Xenopus tropicalis
K14YRLGRKIGSGS5Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus, Rattus norvegicus
K14FRIGRKIGSGS1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
K14YRIGRKIGSGS1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
K14FRLGRKIGSGS1Caenorhabditis elegans
K38EEVAIKLECVK5Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus, Rattus norvegicus
K38EEVAIKLESIR1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
K38EEVAIKLESTR1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
K38EEVAVKLECVK1Caenorhabditis elegans
L135KPDNFLMGLGK6Homo sapiens, Caenorhabditis elegans, Danio rerio, Xenopus tropicalis, Mus musculus, Rattus norvegicus
L135KPDNFLMGVGR1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
L135KPDNFLMGIGK1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
L25FGDIYLGTDIA4Homo sapiens, Xenopus tropicalis, Mus musculus, Rattus norvegicus
L25FGDIYHGTNLI1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
L25FGDIYLGTNVV1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
L25FGDIYLGQNIQ1Caenorhabditis elegans
L25FGDIYLGTDIS1Danio rerio
L293FDWNMLKF---5Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus, Rattus norvegicus
L293FDWTMLRYTKA1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
L293FDWTL------1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
L293FDWNTYKF---1Caenorhabditis elegans
L84VMVMELLGPSL6Homo sapiens, Caenorhabditis elegans, Danio rerio, Xenopus tropicalis, Mus musculus, Rattus norvegicus
L84AMVIDLLGPSL1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
L84AMVMDLLGPSL1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
L85MVMELLGPSLE6Homo sapiens, Caenorhabditis elegans, Danio rerio, Xenopus tropicalis, Mus musculus, Rattus norvegicus
L85MVIDLLGPSLE1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
L85MVMDLLGPSLE1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
L92PSLEDLFNFCS5Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus, Rattus norvegicus
L92PSLEDLFNYCH1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
L92PSLEDLFNFCN1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
L92PSLEDLFNFCQ1Caenorhabditis elegans
M80GDYNVMVMELL6Homo sapiens, Caenorhabditis elegans, Danio rerio, Xenopus tropicalis, Mus musculus, Rattus norvegicus
M80GEYNAMVIDLL1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
M80CDYNAMVMDLL1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
M82YNVMVMELLGP6Homo sapiens, Caenorhabditis elegans, Danio rerio, Xenopus tropicalis, Mus musculus, Rattus norvegicus
M82YNAMVIDLLGP1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
M82YNAMVMDLLGP1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
N94LEDLFNFCSRK5Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus, Rattus norvegicus
N94LEDLFNYCHRR1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
N94LEDLFNFCNRK1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
N94LEDLFNFCQRK1Caenorhabditis elegans
P66GGVGIPTIRWC3Homo sapiens, Mus musculus, Rattus norvegicus
P66GGVGIPTIKWC2Danio rerio, Xenopus tropicalis
P66GGVGIPFIRWF1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
P66GGVGIPFVRWF1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
P66GGIGIPEIRWC1Caenorhabditis elegans
P87MELLGPSLEDL6Homo sapiens, Caenorhabditis elegans, Danio rerio, Xenopus tropicalis, Mus musculus, Rattus norvegicus
P87IDLLGPSLEDL1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
P87MDLLGPSLEDL1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
S17GRKIGSGSFGD8Homo sapiens, Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Schizosaccharomyces pombe (strain 972 / ATCC 24843), Caenorhabditis elegans, Danio rerio, Xenopus tropicalis, Mus musculus, Rattus norvegicus
S88ELLGPSLEDLF6Homo sapiens, Caenorhabditis elegans, Danio rerio, Xenopus tropicalis, Mus musculus, Rattus norvegicus
S88DLLGPSLEDLF2Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Y56IESKIYKMMQG5Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus, Rattus norvegicus
Y56YESRVYRYLSG1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Y56YEYRVYRILSG1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Y56IESRLYRIMLG1Caenorhabditis elegans


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