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Updated November 2019

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Nomenclature

Short Name:
CK1d
Full Name:
Casein kinase I, delta isoform
Alias:
  • Casein kinase 1, delta
  • CK1-delta
  • KC1D
  • Kinase CK1-delta
  • CKId
  • CSNK1D
  • EC 2.7.11.1
  • HCKID

Classification

Type:
Protein-serine/threonine kinase
Group:
CK1
Family:
CK1
SubFamily:
NA
 
 

Specific Links

BioCarta Entry: ck1 pathway
Entrez-Gene Entry: 1453
Entrez-Protein Entry: NP_001884
GeneCards Entry: HCKID
KinBASE Entry: CK1D
OMIM Entry: 600864
Pfam Entry: P48730
PhosphoNET Entry: P48730
Phosphosite Plus Entry: 683
Protein Data Bank Entry: 1CKI
ScanSite Entry: P48730
Source Entry: CSNK1D
UniProt Entry: P48730

General Links

ClustalW2
GPS-Cuckoo
Human Protein Atlas
Kinase.com
Kinase Research
Kinasource
Kinomer
Netphorest
NetworKIN
Phosida
PhosphoElm
Protein Blast
ScanSite
String

Structure

Mol. Mass (Da):
47,330
# Amino Acids:
415
# mRNA Isoforms:
2
mRNA Isoforms:
47,330 Da (415 AA; P48730); 46,832 Da (409 AA; P48730-2)
4D Structure:
Monomer. Component of the circadian core oscillator, which includes the CRY proteins, CLOCK, or NPAS2, BMAL1 or BMAL2, CSNK1D and/or CSNK1E, TIMELESS and the PER proteins. Interacts directly with PER1 and PER2 which may lead to their degradation. Interacts with DBNDD2
1D Structure:
Retrieve Gene Sequence
Retrieve Full Protein Sequence
Retrieve Catalytic Domain Sequence
 
3D Image (rendered using PV Viewer):

PDB ID
3UYS

Subfamily Alignment
subfamily domain
 
Domain Distribution:
Start End Domain
9 269 Pkinase
 

Post-translation Modifications

For detailed information on phosphorylation of this kinase go to PhosphoNET
Acetylated:
K242.
Serine phosphorylated:

S328, S331, S350, S356, S361, S370-, S382, S383, S384, S396, S398, S406, S407, S411.
Threonine phosphorylated:

T329, T344, T347, T349, T355, T387.
Ubiquitinated:
K122, K130, K140, K263.
 

Distribution

Based on gene microarray analysis from the NCBI
Human Tissue Distribution
% Max Expression:

Mean Expression:

Number of Samples:

Standard Deviation:
% Max Expression:

Mean Expression:

Number of Samples:

Standard Deviation:
  • adipose
    25

    1163

    29

    1159

  • adrenal
    6

    281

    17

    174

  • bladder
    9

    433

    10

    302

  • brain
    16

    756

    97

    1229

  • breast
    23

    1062

    25

    803

  • cervix
    2

    104

    74

    45

  • colon
    11

    513

    35

    626

  • heart
    26

    1226

    46

    2087

  • intestine
    17

    784

    17

    536

  • kidney
    5

    252

    87

    172

  • liver
    4

    198

    33

    122

  • lung
    20

    933

    194

    758

  • lymphnode
    5

    257

    32

    225

  • ovary
    5

    218

    15

    194

  • pancreas
    7

    316

    27

    254

  • pituitary
    7

    322

    16

    156

  • prostate
    8

    359

    203

    187

  • salivarygland
    5

    246

    21

    208

  • skeletalmuscle"
    4

    192

    98

    139

  • skin
    16

    736

    109

    719

  • spinalcord
    8

    356

    25

    294

  • spleen
    8

    382

    29

    295

  • stomach
    9

    419

    20

    315

  • testis
    6

    298

    21

    171

  • thymus
    8

    354

    25

    293

  • thyroid
    24

    1120

    61

    1278

  • tonsil
    5

    237

    35

    198

  • trachea
    7

    345

    21

    276

  • uterus
    7

    352

    21

    277

  • reticulocytes"
    0.6

    29

    28

    10

  • t-lymphocytes
    19

    905

    24

    690

  • b-lymphocytes
    100

    4718

    36

    8814

  • neutrophils
    7

    322

    63

    299

  • macrophages
    23

    1103

    57

    836

  • sperm
    24

    1111

    44

    1780

 

Evolution

Species Conservation
PhosphoNET % Identity:
PhosphoNET % Similarity:
Homologene %
Identity:
PhosphoNET % Identity:
PhosphoNET % Similarity:
Homologene %
Identity:
  • tableheader
    100

    100

    100
  • tableheader
    94.4

    95.3

    100
  • tableheader
    76.1

    76.4

    -
  • tableheader
    -

    -

    -
  • tableheader
    -

    -

    -
  • tableheader
    90.4

    91.6

    98.5
  • tableheader
    -

    -

    -
  • tableheader
    99.8

    100

    100
  • tableheader
    56.9

    65.3

    100
  • tableheader
    -

    -

    -
  • tableheader
    -

    -

    -
  • tableheader
    83.9

    88.9

    96
  • tableheader
    96.6

    97.8

    97
  • tableheader
    91.1

    94.7

    95
  • tableheader
    -

    -

    -
  • tableheader
    62.5

    72

    80
  • tableheader
    66.8

    77.1

    -
  • tableheader
    -

    -

    -
  • tableheader
    71

    78.8

    -
  • tableheader
    -

    -

    -
  • tableheader
    -

    -

    -
  • tableheader
    -

    -

    61
  • tableheader
    56.7

    69.6

    73
  • tableheader
    47.8

    63.8

    66
  • tableheader
    -

    -

    78
For a wider analysis go to PhosphoNET Evolution in PhosphoNET
 

Regulation

Activation:
Heparin can stimulate CK1 activity towards certain substrates.
Inhibition:
NA
Synthesis:
NA
Degradation:
NA
 

Kinections Map

Click here to download a PPT of the image below
 
Kinections GIF
 

Known Upstream Kinases

For further details on these substrates click on the Substrate Short Name or UniProt ID. Phosphosite Location is hyperlinked to PhosphoNET predictions.
Based on in vitro and/or in vivo phosphorylation data

Kinase Short Name UniProt ID (Human) Phosphosite Location Phosphosite Sequence Effect of Phosphorylation
CLK2 P49760 S370 MERERKVSMRLHRGA -
PKCa P17252 S370 MERERKVSMRLHRGA -
Akt1 P31749 S370 MERERKVSMRLHRGA -
PKACa P17612 S370 MERERKVSMRLHRGA -
 

Known Downstream Substrates

For further details on these substrates click on the Substrate Short Name or UniProt ID. Phosphosite Location is hyperlinked to PhosphoNET predictions.
Based on in vitro and/or in vivo phosphorylation data

Substrate Short Name UniProt ID (Human) Phosphosite Location Phosphosite Sequence Effect of Phosphorylation
BACE P56817 S498 DDFADDISLLK____ ?
CDH1 P12830 S844 GSGSEAASLSSLNSS -
CTNNB1 P35222 S45 GATTTAPSLSGKGNP +
FOXO1A Q12778 S322 PRTSSNASTISGRLS -
FOXO1A Q12778 S325 SSNASTISGRLSPIM -
KIR3DL1 P43629 S385 AGNRTANSEDSDEQD +
KIR3DL1 P43629 S388 RTANSEDSDEQDPEE +
MBP P02686 S244 QGKGRGLSLSRFSWG
MDM2 Q00987 S240 GDWLDQDSVSDQFSV +
MDM2 Q00987 S242 WLDQDSVSDQFSVEF +
MDM2 Q00987 S246 DSVSDQFSVEFEVES +
NCOA3 (SRC-3) Q9Y6Q9 S601 SDKESKESSVEGAEN +
p53 P04637 S20 PLSQETFSDLWKLLP +
p53 P04637 S6 __MEEPQSDPSVEPP +
p53 P04637 S9 EEPQSDPSVEPPLSQ
p53 P04637 T18 EPPLSQETFSDLWKL +
Per2 O15055 S1236 SLGLSEVSDTKEDEN
Per2 O15055 S527 GNKTKNRSHYSHESG
Per2 O15055 S530 TKNRSHYSHESGEQK
Per2 O15055 S533 RSHYSHESGEQKKKS
Per2 O15055 S540 SGEQKKKSVTEMQTN
Per2 O15055 S544 ASVAEMQSSPPAQVK
Per2 O15055 S627 DKRKATVSPGPHAGE
Per2 O15055 S696 EMVEDAASGPESLDC
Per2 O15055 S700 DAASGPESLDCLAGP
Per2 O15055 S766 HYYLQERSKGQPSER
Per2 O15055 S771 ERSKGQPSERTAPGL
Per2 O15055 S807 KRVKPRDSSESTGSG
Per2 O15055 S808 RVKPRDSSESTGSGG
Per2 O15055 S810 KPRDSSESTGSGGPV
Per2 O15055 S813 DSSESTGSGGPVSAR
Per2 O15055 S818 TGSGGPVSARPPLVG
Per2 O15055 S93 AKSEHNPSTSGCSSD
Per2 O15055 S939 PSHPTLTSEMASASQ
Per2 O15055 S945 TSEMASASQPEFPSR
Per2 O15055 S977 PSAMGRASPPLFQSR
Per2 O15055 S986 PLFQSRSSSPLQLNL
Per2 O15055 S987 LFQSRSSSPLQLNLL
Per2 O15055 T1004 EEAPEGGTGAMGTTG
Per2 O15055 T1237 PSPGLCDTSEAKEEE
Per2 O15055 T625 SSDKRKATVSPGPHA
Per2 O15055 T781 TAPGLRNTSGIDSPW
Per2 O15055 T811 PRDSSESTGSGGPVS
Per2 O15055 T864 PVFPAPGTVAAPPAP
Per2 O15055 T94 KSEHNPSTSGCSSDQ
PSEN2 P49810 S327 DPEMEEDSYDSFGEP +
PSEN2 P49810 S330 MEEDSYDSFGEPSYP +
Tau P10636 S518 SGYSSPGSPGTPGSR
Tau P10636 S712 GAEIVYKSPVVSGDT
Tau P10636 S720 PVVSGDTSPRHLSNV
Tau iso8 P10636-8 T205 SSPGSPGTPGSRSRT
 

Protein Kinase Specificity

Matrix of observed frequency (%) of amino acids in aligned protein substrate phosphosites

Kinections GIF
Matrix Type:
Experimentally derived from alignment of 71 known protein substrate phosphosites.
Domain #:
1
 

Inhibitors

For further details on these inhibitors click on the Compound Name and enter it into DrugKiNET or click on the ID's
Based on in vitro and/or in vivo phosphorylation data
Compound Name KD, Ki or IC50 (nM) PubChem ID ChEMBL ID PubMed ID
AC1NS4N8 Kd < 10 nM 5353854 101797 19035792
CHEMBL249097 Kd < 10 nM 25138012 249097 19035792
LY364947 Kd < 10 nM 447966 261454 19035792
SureCN7018367 Kd < 10 nM 18792927 450519 19035792
Sunitinib Kd = 15 nM 5329102 535 18183025
SB220025 IC50 < 25 nM 5164 274064 22037377
Hymenialdisine IC50 = 35 nM 3035462 15261294
SB203580 Kd = 37 nM 176155 10 18183025
PP2 = 41 nM 4878 406845
1;9-Pyrazoloanthrone IC50 > 50 nM 8515 7064 22037377
Bosutinib IC50 > 50 nM 5328940 288441 22037377
PD169316 IC50 > 50 nM 4712 17331 22037377
SKF-86002 IC50 > 50 nM 5228 313417 22037377
SureCN7685369 Kd = 58 nM 9925594 526901 19035792
SB202190 Kd = 59 nM 5353940 278041 18183025
7-hydroxystaurosporine IC50 > 100 nM 72271 1236539
AT9283 IC50 > 100 nM 24905142 19143567
BML-275 IC50 = 100 nM 11524144 478629
CHEMBL1650545 IC50 > 100 nM 53316611 1650545 21128646
PP242 IC50 = 100 nM 25243800
STO609 IC50 = 100 nM 51371511
AG-E-60384 IC50 > 150 nM 6419741 413188 22037377
JNK Inhibitor; Negative Control IC50 > 150 nM 11665831 22037377
p38 MAP Kinase Inhibitor IC50 > 150 nM 4665 91730 22037377
TG003 Kd = 150 nM 1893668 408982 19837585
SB431542 Kd = 170 nM 4521392 440084 18183025
A674563 Kd = 210 nM 11314340 379218 22037378
D4476 IC50 > 250 nM 6419753 410456 22037377
Indirubin-3′-monoxime IC50 > 250 nM 5326739 22037377
ML3403 IC50 > 250 nM 6419739 111364 22037377
PKR Inhibitor IC50 > 250 nM 6490494 235641 22037377
Semaxinib IC50 > 250 nM 5329098 276711 22037377
TX010811 IC50 > 250 nM 5174 36450 22037377
Lestaurtinib Kd = 260 nM 126565 18183025
Roscovitine Kd = 260 nM 160355 14762 18183025
SU14813 Kd = 260 nM 10138259 1721885 18183025
GSK650394A IC50 < 400 nM 25022668 558642
PP1 IC50 < 400 nM 1400 306380
Compound 52 IC50 = 500 nM 2856 22037377
IDR E804 IC50 = 500 nM 6419764 1802727 22037377
PP1 Analog II; 1NM-PP1 IC50 = 500 nM 5154691 573578 22037377
PP121 IC50 < 500 nM 24905142 18849971
SU11652 IC50 = 500 nM 24906267 13485 22037377
CHEMBL590109 IC50 = 530 nM 46224684 590109 19926477
1-Naphthyl PP1 IC50 < 600 nM 4877
A 443654 IC50 > 600 nM 10172943 379300
MNK1 Inhibitor IC50 < 600 nM 11644425 1240885
Kinome_714 IC50 = 740 nM 46886323 20346655
IRAK-4 kinase inhibitor b IC50 < 800 nM
JNKIN7 IC50 < 800 nM 57340685
BX517 IC50 > 900 nM 11161844 228654
Gö6976 IC50 > 900 nM 3501 302449
A-83-01 IC50 = 1 µM 16218924 1170377
Aloisine A IC50 > 1 µM 5326843 75680 22037377
AS601245 IC50 > 1 µM 11422035 191384 22037377
BMS-690514 Kd = 1 µM 11349170 21531814
FR180204 IC50 > 1 µM 11493598 259551 22037377
GSK-3 Inhibitor IX IC50 = 1 µM 5287844 409450
HG-10-102-01 IC50 = 1 µM
IC261 IC50 > 1 µM 3674 576349 22037377
IRAK-1-4 Inhibitor I IC50 = 1 µM 11983295 379787
JNKIN8 IC50 = 1 µM 57340686
Meridianin B IC50 = 1 µM 10380356 15026054
MK5108 IC50 > 1 µM 24748204 20053775
MSC 2032964A IC50 = 1 µM
Novartis 12a (PKD1) IC50 = 1 µM
Orantinib IC50 = 1 µM 5329099 274654
Purvalanol B IC50 = 1 µM 448991 23254
SB431542 IC50 = 1 µM 4521392
SB505124 IC50 > 1 µM 16079009 1835714 22037377
SB590885 IC50 = 1 µM 11465183 477989
Silmitasertib IC50 > 1 µM 24748573 21174434
SNS314 IC50 > 1 µM 16047143 514582 18678489
SU4312 IC50 > 1 µM 6450842 328710 22037377
SureCN3470757 IC50 = 1 µM 11588244 375236
TBCA IC50 > 1 µM 1095828 22037377
WZ3146 Kd > 1 µM 44607360 20033049
WZ4002 Kd > 1 µM 44607530 20033049
Pelitinib Kd = 1.1 µM 6445562 607707 18183025
Nintedanib Kd = 1.3 µM 9809715 502835 22037378
TG100115 Kd = 1.3 µM 10427712 230011 22037378
GDC0879 Kd = 1.4 µM 11717001 525191 22037378
Staurosporine IC50 = 1.4 µM 5279 12941331
BI2536 Kd = 1.5 µM 11364421 513909 22037378
AC1NS7CD Kd = 1.8 µM 5329665 295136 22037378
SNS032 Kd = 1.8 µM 3025986 296468 18183025
IRAK-4 kinase inhibitor a IC50 < 2 µM
KW2449 Kd = 2.3 µM 11427553 1908397 22037378
AST-487 Kd = 2.5 µM 11409972 574738 18183025
IKK-2 Inhibitor IV Kd < 2.5 µM 9903786 257167 19035792
SureCN373973 Kd < 2.5 µM 9818573 30678 19035792
Cdk1/2 Inhibitor III IC50 = 2.8 µM 5330812 261720 15974571
Amgen TBK 1 inhibitor (Compound II) IC50 > 3 µM
CKI-7 IC50 < 3 µM 129236 489157
Harmaline IC50 > 3 µM 5280951 340807
MRT67307 IC50 > 3 µM 44464263
CHEMBL191336 IC50 = 3.05 µM 9863538 191336 15999992
Gefitinib Kd = 3.2 µM 123631 939 22037378
Erlotinib Kd = 3.5 µM 176870 553 18183025
GSK1838705A Kd = 3.5 µM 25182616 464552 22037378
FMK IC50 > 4 µM 5737
JNJ-28871063 IC50 > 4 µM 17747413 17975007
PP3 IC50 < 4 µM 4879 65063
PHA-665752 Kd = 4.2 µM 10461815 450786 22037378
GW441756 hydrochloride IC50 > 4.5 µM 16219400
HG-9-91-01 IC50 > 4.5 µM
Purvalanol A IC50 > 4.5 µM 456214 23327
R406 IC50 > 4.5 µM 11984591
Ruxolitinib IC50 > 4.5 µM 25126798 1789941
Canertinib Kd = 4.6 µM 156414 31965 22037378
 

Disease Linkage

General Disease Association:

Neurological disorders
Specific Diseases (Non-cancerous):

Advanced sleep phase syndrome; Advanced sleep-phase syndrome, familial, 2; Familial advanced sleep phase syndrome 1
Comments:
Several loss-of-function mutations in the CSNK1D gene have been identified in ASPS patients, including a T44A substitution mutation, and a H46R substitution mutation. The T44A mutation occurs at a highly conserved residue that is found in the casein kinase 1 protein from Drosphila through mammals. Enzymatic anaylsis revealed that the T44A mutant CSNK1D protein displays significantly reduced kinase catalytic activity compared to the wildtype protein. Similarly, the H46R residue also occurs at a highly conserved residue and has been shown to reduce the kinase catalytic activity of the H46R mutant CSNK1D protein by 53% compared to the wildtype protein. Therefore, the ASPS phenotype is associated with a loss-of-function in the catalytic activity of the CSNK1D protein. In animal studies, Drosophila carrying the T44A mutation displayed lengthened circadian cycles. In constrast, mice carrying the same mutation display shortened circadian cycles and a similar phenotype to human ASPS. In addition, overexpression of the CSNK1D gene in the forebrain and striatum of mice results in hyperactivity, decreased anxiety, increased impulsivity, and defective nesting behaviours, potential due to abnormal circadian rythyms. Furthermore, these mice showed paradoxical responses to the injection of dopamine receptor agonists into the brain. In addition, CSNK1D overexpression is associated with decreased expression of the dopamine receptors D1 and D2 in the affected brain regions, indicating a role for the protein in the modulation of dopaminergic signalling in the brain. Advanced sleep phase syndrome (ASPS) is a sleep disorder characterized by the abnormal alteration of the circadian rhythym. Symptoms include falling asleep in the early evening (6:00-8:00 pm) and waking up early in the morning (e.g. 3:00 am). ASPS is a rare disorder that appears to affect men and women equally with a strong genetic association.
 
Gene Expression in Cancers:

TranscriptoNET (www.transcriptonet.ca) analysis with mRNA expression data retrieved from the National Center for Biotechnology Information's Gene Expression Omnibus (GEO) database, which was normalized against 60 abundantly and commonly found proteins, indicated altered expression for this protein kinase as shown here as the percent change from normal tissue controls (%CFC) as supported with the Student T-test in the following types of human cancers: Bladder carcinomas (%CFC= +96, p<0.0001); Large B-cell lymphomas (%CFC= +54, p<0.018); Large B-cell lymphomas (%CFC= +54, p<0.023); Malignant pleural mesotheliomas (MPM) tumours (%CFC= +57, p<0.028); and Skin melanomas - malignant (%CFC= +61, p<0.008).
Mutagenesis Experiments:

Insertional mutagenesis studies in mice have not yet revealed a role for this protein kinase in mouse cancer oncogenesis.
Mutation Rate in All Cancers:

Percent mutation rates per 100 amino acids length in human cancers: 0.07 % in 24440 diverse cancer specimens. This rate is only -1 % lower and is very similar to the average rate of 0.075 % calculated for human protein kinases in general.
Mutation Rate in Specific Cancers:

Highest percent mutation rates per 100 amino acids length in human cancers: 0.51 % in 1270 large intestine cancers tested.
Frequency of Mutated Sites:

Most frequent mutations with the number of reports indicated in brackets: A36V (5), S97P (4).
Comments:
Only 3 deletions, no insertions or complex mutations.
 
COSMIC Entry:
CSNK1D_ENST00000314028
OMIM Entry:
600864
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