Target Information
Target General Information | Top | |||||
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Target ID |
T58449
(Former ID: TTDC00094)
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Target Name |
Cyclin-dependent kinase 7 (CDK7)
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Synonyms |
TFIIH basal transcription factor complex kinase subunit; Serine/threonine-protein kinase 1; P39 Mo15; MO15; Cell division protein kinase 7; CDKN7; CDK-activating kinase 1; CDK-activating kinase; CAK1; CAK; 39 kDa protein kinase
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Gene Name |
CDK7
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Target Type |
Clinical trial target
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[1] | ||||
Disease | [+] 4 Target-related Diseases | + | ||||
1 | Lung cancer [ICD-11: 2C25] | |||||
2 | Solid tumour/cancer [ICD-11: 2A00-2F9Z] | |||||
3 | Breast cancer [ICD-11: 2C60-2C6Y] | |||||
4 | Malignant haematopoietic neoplasm [ICD-11: 2B33] | |||||
Function |
Cyclin-dependent kinases (CDKs) are activated by the binding to a cyclin and mediate the progression through the cell cycle. Each different complex controls a specific transition between 2 subsequent phases in the cell cycle. Required for both activation and complex formation of CDK1/cyclin-B during G2-M transition, and for activation of CDK2/cyclins during G1-S transition (but not complex formation). CDK7 is the catalytic subunit of the CDK-activating kinase (CAK) complex. Phosphorylates SPT5/SUPT5H, SF1/NR5A1, POLR2A, p53/TP53, CDK1, CDK2, CDK4, CDK6 and CDK11B/CDK11. CAK activates the cyclin-associated kinases CDK1, CDK2, CDK4 and CDK6 by threonine phosphorylation, thus regulating cell cycle progression. CAK complexed to the core-TFIIH basal transcription factor activates RNA polymerase II by serine phosphorylation of the repetitive C-terminal domain (CTD) of its large subunit (POLR2A), allowing its escape from the promoter and elongation of the transcripts. Phosphorylation of POLR2A in complex with DNA promotes transcription initiation by triggering dissociation from DNA. Its expression and activity are constant throughout the cell cycle. Upon DNA damage, triggers p53/TP53 activation by phosphorylation, but is inactivated in turn by p53/TP53; this feedback loop may lead to an arrest of the cell cycle and of the transcription, helping in cell recovery, or to apoptosis. Required for DNA-bound peptides-mediated transcription and cellular growth inhibition. Serine/threonine kinase involved in cell cycle control and in RNA polymerase II-mediated RNA transcription.
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BioChemical Class |
Kinase
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UniProt ID | ||||||
EC Number |
EC 2.7.11.22
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Sequence |
MALDVKSRAKRYEKLDFLGEGQFATVYKARDKNTNQIVAIKKIKLGHRSEAKDGINRTAL
REIKLLQELSHPNIIGLLDAFGHKSNISLVFDFMETDLEVIIKDNSLVLTPSHIKAYMLM TLQGLEYLHQHWILHRDLKPNNLLLDENGVLKLADFGLAKSFGSPNRAYTHQVVTRWYRA PELLFGARMYGVGVDMWAVGCILAELLLRVPFLPGDSDLDQLTRIFETLGTPTEEQWPDM CSLPDYVTFKSFPGIPLHHIFSAAGDDLLDLIQGLFLFNPCARITATQALKMKYFSNRPG PTPGCQLPRPNCPVETLKEQSNPALAIKRKRTEALEQGGLPKKLIF Click to Show/Hide
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3D Structure | Click to Show 3D Structure of This Target | PDB | ||||
HIT2.0 ID | T46NT6 |
Drugs and Modes of Action | Top | |||||
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Clinical Trial Drug(s) | [+] 3 Clinical Trial Drugs | + | ||||
1 | R-roscovitine | Drug Info | Phase 2 | Non-small-cell lung cancer | [2], [3] | |
2 | SNS-032 | Drug Info | Phase 1 | Solid tumour/cancer | [8], [9] | |
3 | SY-1365 | Drug Info | Phase 1 | Solid tumour/cancer | [10] | |
Discontinued Drug(s) | [+] 2 Discontinued Drugs | + | ||||
1 | R547 | Drug Info | Discontinued in Phase 1 | Advanced solid tumour | [11], [12] | |
2 | ZK 304709 | Drug Info | Discontinued in Phase 1 | Advanced solid tumour | [13] | |
Mode of Action | [+] 1 Modes of Action | + | ||||
Inhibitor | [+] 17 Inhibitor drugs | + | ||||
1 | R-roscovitine | Drug Info | [1] | |||
2 | SNS-032 | Drug Info | [9], [14] | |||
3 | SY-1365 | Drug Info | [10] | |||
4 | Oxazolyl methylthiothiazole derivative 1 | Drug Info | [15] | |||
5 | PMID26161698-Compound-34 | Drug Info | [15] | |||
6 | Pyrazolo-triazine derivative 1 | Drug Info | [15] | |||
7 | Pyrazolo-triazine derivative 2 | Drug Info | [15] | |||
8 | Roscovitine derivative 1 | Drug Info | [15] | |||
9 | Tricyclic benzimidazole derivative 1 | Drug Info | [15] | |||
10 | R547 | Drug Info | [1] | |||
11 | ZK 304709 | Drug Info | [1] | |||
12 | 2,5-dichloro-N-p-tolylthiophene-3-sulfonamide | Drug Info | [16] | |||
13 | NU6140 | Drug Info | [17] | |||
14 | PF-228 | Drug Info | [18] | |||
15 | Phosphonothreonine | Drug Info | [19] | |||
16 | RGB-286147 | Drug Info | [20] | |||
17 | THZ1 | Drug Info | [21] |
Cell-based Target Expression Variations | Top | |||||
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Cell-based Target Expression Variations |
Drug Binding Sites of Target | Top | |||||
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Ligand Name: Adenosine triphosphate | Ligand Info | |||||
Structure Description | Crystal Structure of Human CDK7 | PDB:1UA2 | ||||
Method | X-ray diffraction | Resolution | 3.02 Å | Mutation | Yes | [22] |
PDB Sequence |
EKLDFLGEGQ
22 FATVYKARDK32 NTNQIVAIKK42 INRTALREIK64 LLQELSHPNI74 IGLLDAFGHK 84 SNISLVFDFM94 ETDLEVIIKD104 NSLVLTPSHI114 KAYMLMTLQG124 LEYLHQHWIL 134 HRDLKPNNLL144 LDENGVLKLA154 DFGLAKSFGS164 PNRAYHQVVT175 RWYRAPELLF 185 GARMYGVGVD195 MWAVGCILAE205 LLLRVPFLPG215 DSDLDQLTRI225 FETLGTPTEE 235 QWPDMCSLPD245 YVTFKSFPGI255 PLHHIFSAAG265 DDLLDLIQGL275 FLFNPCARIT 285 ATQALKMKYF295 SNRPGPTPGC305 QLPRPN
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LEU18
3.026
GLY19
3.922
GLU20
3.388
GLY21
3.214
GLN22
3.090
PHE23
3.193
ALA24
2.962
VAL26
3.278
ALA39
3.607
LYS41
2.937
ILE75
4.627
PHE91
3.944
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Ligand Name: Phosphonothreonine | Ligand Info | |||||
Structure Description | Crystal Structure of Human CDK7 | PDB:1UA2 | ||||
Method | X-ray diffraction | Resolution | 3.02 Å | Mutation | Yes | [22] |
PDB Sequence |
EKLDFLGEGQ
22 FATVYKARDK32 NTNQIVAIKK42 INRTALREIK64 LLQELSHPNI74 IGLLDAFGHK 84 SNISLVFDFM94 ETDLEVIIKD104 NSLVLTPSHI114 KAYMLMTLQG124 LEYLHQHWIL 134 HRDLKPNNLL144 LDENGVLKLA154 DFGLAKSFGS164 PNRAYHQVVT175 RWYRAPELLF 185 GARMYGVGVD195 MWAVGCILAE205 LLLRVPFLPG215 DSDLDQLTRI225 FETLGTPTEE 235 QWPDMCSLPD245 YVTFKSFPGI255 PLHHIFSAAG265 DDLLDLIQGL275 FLFNPCARIT 285 ATQALKMKYF295 SNRPGPTPGC305 QLPRPN
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Click to View More Binding Site Information of This Target with Different Ligands |
Different Human System Profiles of Target | Top |
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Human Similarity Proteins
of target is determined by comparing the sequence similarity of all human proteins with the target based on BLAST. The similarity proteins for a target are defined as the proteins with E-value < 0.005 and outside the protein families of the target.
A target that has fewer human similarity proteins outside its family is commonly regarded to possess a greater capacity to avoid undesired interactions and thus increase the possibility of finding successful drugs
(Brief Bioinform, 21: 649-662, 2020).
Human Tissue Distribution
of target is determined from a proteomics study that quantified more than 12,000 genes across 32 normal human tissues. Tissue Specificity (TS) score was used to define the enrichment of target across tissues.
The distribution of targets among different tissues or organs need to be taken into consideration when assessing the target druggability, as it is generally accepted that the wider the target distribution, the greater the concern over potential adverse effects
(Nat Rev Drug Discov, 20: 64-81, 2021).
Human Pathway Affiliation
of target is determined by the life-essential pathways provided on KEGG database. The target-affiliated pathways were defined based on the following two criteria (a) the pathways of the studied target should be life-essential for both healthy individuals and patients, and (b) the studied target should occupy an upstream position in the pathways and therefore had the ability to regulate biological function.
Targets involved in a fewer pathways have greater likelihood to be successfully developed, while those associated with more human pathways increase the chance of undesirable interferences with other human processes
(Pharmacol Rev, 58: 259-279, 2006).
Biological Network Descriptors
of target is determined based on a human protein-protein interactions (PPI) network consisting of 9,309 proteins and 52,713 PPIs, which were with a high confidence score of ≥ 0.95 collected from STRING database.
The network properties of targets based on protein-protein interactions (PPIs) have been widely adopted for the assessment of target’s druggability. Proteins with high node degree tend to have a high impact on network function through multiple interactions, while proteins with high betweenness centrality are regarded to be central for communication in interaction networks and regulate the flow of signaling information
(Front Pharmacol, 9, 1245, 2018;
Curr Opin Struct Biol. 44:134-142, 2017).
Human Similarity Proteins
Human Tissue Distribution
Human Pathway Affiliation
Biological Network Descriptors
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Note:
If a protein has TS (tissue specficity) scores at least in one tissue >= 2.5, this protein is called tissue-enriched (including tissue-enriched-but-not-specific and tissue-specific). In the plots, the vertical lines are at thresholds 2.5 and 4.
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KEGG Pathway | Pathway ID | Affiliated Target | Pathway Map |
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Basal transcription factors | hsa03022 | Affiliated Target |
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Class: Genetic Information Processing => Transcription | Pathway Hierarchy | ||
Nucleotide excision repair | hsa03420 | Affiliated Target |
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Class: Genetic Information Processing => Replication and repair | Pathway Hierarchy | ||
Cell cycle | hsa04110 | Affiliated Target |
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Class: Cellular Processes => Cell growth and death | Pathway Hierarchy |
Degree | 38 | Degree centrality | 4.08E-03 | Betweenness centrality | 6.75E-04 |
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Closeness centrality | 2.27E-01 | Radiality | 1.40E+01 | Clustering coefficient | 3.50E-01 |
Neighborhood connectivity | 4.08E+01 | Topological coefficient | 1.07E-01 | Eccentricity | 12 |
Download | Click to Download the Full PPI Network of This Target | ||||
Chemical Structure based Activity Landscape of Target | Top |
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Drug Property Profile of Target | Top | |
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(1) Molecular Weight (mw) based Drug Clustering | (2) Octanol/Water Partition Coefficient (xlogp) based Drug Clustering | |
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(3) Hydrogen Bond Donor Count (hbonddonor) based Drug Clustering | (4) Hydrogen Bond Acceptor Count (hbondacc) based Drug Clustering | |
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(5) Rotatable Bond Count (rotbonds) based Drug Clustering | (6) Topological Polar Surface Area (polararea) based Drug Clustering | |
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"RO5" indicates the cutoff set by lipinski's rule of five; "D123AB" colored in GREEN denotes the no violation of any cutoff in lipinski's rule of five; "D123AB" colored in PURPLE refers to the violation of only one cutoff in lipinski's rule of five; "D123AB" colored in BLACK represents the violation of more than one cutoffs in lipinski's rule of five |
Co-Targets | Top | |||||
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Co-Targets |
Target Poor or Non Binders | Top | |||||
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Target Poor or Non Binders |
Target Regulators | Top | |||||
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Target-interacting Proteins |
Target-Related Models and Studies | Top | |||||
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Target Validation |
References | Top | |||||
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REF 1 | Cell cycle kinases as therapeutic targets for cancer. Nat Rev Drug Discov. 2009 Jul;8(7):547-66. | |||||
REF 2 | URL: http://www.guidetopharmacology.org Nucleic Acids Res. 2015 Oct 12. pii: gkv1037. The IUPHAR/BPS Guide to PHARMACOLOGY in 2016: towards curated quantitative interactions between 1300 protein targets and 6000 ligands. (Ligand id: 6035). | |||||
REF 3 | Trusted, scientifically sound profiles of drug programs, clinical trials, safety reports, and company deals, written by scientists. Springer. 2015. Adis Insight (drug id 800010117) | |||||
REF 4 | ClinicalTrials.gov (NCT04802759) A Phase Ib/II, Open-Label, Multicenter, Randomized Umbrella Study Evaluating the Efficacy and Safety of Multiple Treatment Combinations in Patients With Breast Cancer (MORPHEUS- BREAST CANCER). U.S.National Institutes of Health. | |||||
REF 5 | ClinicalTrials.gov (NCT04247126) A Study of SY 5609, a Selective CDK7 Inhibitor, in Advanced Solid Tumors. U.S. National Institutes of Health. | |||||
REF 6 | ClinicalTrials.gov (NCT03770494) A Study of LY3405105 in Participants With Advanced Cancer. U.S. National Institutes of Health. | |||||
REF 7 | ClinicalTrials.gov (NCT04872166) A Study of BTX-A51 in People With Advanced Solid Tumor or Non-Hodgkin Lymphoma. U.S. National Institutes of Health. | |||||
REF 8 | URL: http://www.guidetopharmacology.org Nucleic Acids Res. 2015 Oct 12. pii: gkv1037. The IUPHAR/BPS Guide to PHARMACOLOGY in 2016: towards curated quantitative interactions between 1300 protein targets and 6000 ligands. (Ligand id: 5670). | |||||
REF 9 | Mechanism of action of SNS-032, a novel cyclin-dependent kinase inhibitor, in chronic lymphocytic leukemia. Blood. 2009 May 7;113(19):4637-45. | |||||
REF 10 | Clinical pipeline report, company report or official report of the Pharmaceutical Research and Manufacturers of America (PhRMA) | |||||
REF 11 | URL: http://www.guidetopharmacology.org Nucleic Acids Res. 2015 Oct 12. pii: gkv1037. The IUPHAR/BPS Guide to PHARMACOLOGY in 2016: towards curated quantitative interactions between 1300 protein targets and 6000 ligands. (Ligand id: 5707). | |||||
REF 12 | Trusted, scientifically sound profiles of drug programs, clinical trials, safety reports, and company deals, written by scientists. Springer. 2015. Adis Insight (drug id 800018924) | |||||
REF 13 | Trusted, scientifically sound profiles of drug programs, clinical trials, safety reports, and company deals, written by scientists. Springer. 2015. Adis Insight (drug id 800022386) | |||||
REF 14 | Development of cell-cycle inhibitors for cancer therapy. Curr Oncol. 2009 Mar;16(2):36-43. | |||||
REF 15 | Cyclin-dependent kinase inhibitors for cancer therapy: a patent review (2009 - 2014).Expert Opin Ther Pat. 2015;25(9):953-70. | |||||
REF 16 | Activity of substituted thiophene sulfonamides against malarial and mammalian cyclin dependent protein kinases, Bioorg. Med. Chem. Lett. 20(13):3863-3867 (2010). | |||||
REF 17 | Potentiation of paclitaxel-induced apoptosis by the novel cyclin-dependent kinase inhibitor NU6140: a possible role for survivin down-regulation. Mol Cancer Ther. 2005 Sep;4(9):1328-37. | |||||
REF 18 | Cellular characterization of a novel focal adhesion kinase inhibitor. J Biol Chem. 2007 May 18;282(20):14845-52. | |||||
REF 19 | How many drug targets are there Nat Rev Drug Discov. 2006 Dec;5(12):993-6. | |||||
REF 20 | A systematic interaction map of validated kinase inhibitors with Ser/Thr kinases. Proc Natl Acad Sci U S A. 2007 Dec 18;104(51):20523-8. | |||||
REF 21 | Targeting transcription regulation in cancer with a covalent CDK7 inhibitor. Nature. 2014 Jul 31;511(7511):616-20. | |||||
REF 22 | The crystal structure of human CDK7 and its protein recognition properties. Structure. 2004 Nov;12(11):2067-79. |
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