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2'-Deoxy-5-hydroxymethylcytidine-5'-diphosphate

Table of Contents

Details
Physical and Chemical Properties
Synonyms
2D Structure
3D Structure
ADMET Properties
Targets (proven and/or predicted)
Plants that contains it
Cross-Links

Details

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Internal ID ceeb4cb4-305c-4a08-9ac4-f1ff714d1075
Taxonomy Organic oxygen compounds > Organic oxoanionic compounds > Organic pyrophosphates
IUPAC Name [(2R,3S,5R)-5-[4-amino-5-(hydroxymethyl)-2-oxopyrimidin-1-yl]-3-hydroxyoxolan-2-yl]methyl phosphono hydrogen phosphate
SMILES (Canonical) C1C(C(OC1N2C=C(C(=NC2=O)N)CO)COP(=O)(O)OP(=O)(O)O)O
SMILES (Isomeric) C1[C@@H]([C@H](O[C@H]1N2C=C(C(=NC2=O)N)CO)COP(=O)(O)OP(=O)(O)O)O
InChI InChI=1S/C10H17N3O11P2/c11-9-5(3-14)2-13(10(16)12-9)8-1-6(15)7(23-8)4-22-26(20,21)24-25(17,18)19/h2,6-8,14-15H,1,3-4H2,(H,20,21)(H2,11,12,16)(H2,17,18,19)/t6-,7+,8+/m0/s1
InChI Key RQKDPSTWKKMBPM-XLPZGREQSA-N
Popularity 1 reference in papers

Physical and Chemical Properties

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Molecular Formula C10H17N3O11P2
Molecular Weight 417.20 g/mol
Exact Mass 417.03383236 g/mol
Topological Polar Surface Area (TPSA) 222.00 Ų
XlogP -4.70
Atomic LogP (AlogP) -1.81
H-Bond Acceptor 11
H-Bond Donor 6
Rotatable Bonds 7

Synonyms

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94714-46-2
2'-deoxy-5-hydroxymethyl-CDP
2'-deoxy-5-(hydroxymethyl)cytidine 5'-(trihydrogen diphosphate)
2'-deoxy-5-hydroxymethylcytidine 5'-diphosphate
[(2R,3S,5R)-5-[4-amino-5-(hydroxymethyl)-2-oxopyrimidin-1-yl]-3-hydroxyoxolan-2-yl]methyl phosphono hydrogen phosphate
diphosphoric acid mono-(5-hydroxymethyl-2'-deoxy-cytidin-5'-yl ester)
((2R,3S,5R)-5-(4-Amino-5-(hydroxymethyl)-2-oxopyrimidin-1(2H)-yl)-3-hydroxytetrahydrofuran-2-yl)methyl trihydrogen diphosphate
CHEBI:835
SCHEMBL2926533
DTXSID90332049
There are more than 10 synonyms. If you wish to see them all click here.

2D Structure

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2D Structure of 2'-Deoxy-5-hydroxymethylcytidine-5'-diphosphate

3D Structure

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ADMET Properties (via admetSAR 2)

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Target Value Probability (raw) Probability (%)
Human Intestinal Absorption + 0.8355 83.55%
Caco-2 - 0.9034 90.34%
Blood Brain Barrier + 0.7750 77.50%
Human oral bioavailability + 0.5714 57.14%
Subcellular localzation Nucleus 0.4807 48.07%
OATP2B1 inhibitior - 1.0000 100.00%
OATP1B1 inhibitior + 0.9344 93.44%
OATP1B3 inhibitior + 0.9405 94.05%
MATE1 inhibitior - 1.0000 100.00%
OCT2 inhibitior - 0.9250 92.50%
BSEP inhibitior - 0.9103 91.03%
P-glycoprotein inhibitior - 0.7086 70.86%
P-glycoprotein substrate - 0.8089 80.89%
CYP3A4 substrate + 0.5872 58.72%
CYP2C9 substrate - 0.7880 78.80%
CYP2D6 substrate - 0.8587 85.87%
CYP3A4 inhibition - 0.8296 82.96%
CYP2C9 inhibition - 0.8573 85.73%
CYP2C19 inhibition - 0.8541 85.41%
CYP2D6 inhibition - 0.8930 89.30%
CYP1A2 inhibition - 0.8863 88.63%
CYP2C8 inhibition - 0.8192 81.92%
CYP inhibitory promiscuity - 0.9439 94.39%
UGT catelyzed + 0.6000 60.00%
Carcinogenicity (binary) - 0.8600 86.00%
Carcinogenicity (trinary) Non-required 0.4943 49.43%
Eye corrosion - 0.9821 98.21%
Eye irritation - 0.9836 98.36%
Skin irritation - 0.7736 77.36%
Skin corrosion - 0.9272 92.72%
Ames mutagenesis - 0.6700 67.00%
Human Ether-a-go-go-Related Gene inhibition - 0.4502 45.02%
Micronuclear + 0.9800 98.00%
Hepatotoxicity - 0.5330 53.30%
skin sensitisation - 0.8522 85.22%
Respiratory toxicity + 0.8667 86.67%
Reproductive toxicity + 0.9111 91.11%
Mitochondrial toxicity + 0.9500 95.00%
Nephrotoxicity + 0.5311 53.11%
Acute Oral Toxicity (c) III 0.5378 53.78%
Estrogen receptor binding + 0.6613 66.13%
Androgen receptor binding + 0.7684 76.84%
Thyroid receptor binding + 0.7113 71.13%
Glucocorticoid receptor binding + 0.5971 59.71%
Aromatase binding + 0.6260 62.60%
PPAR gamma + 0.6459 64.59%
Honey bee toxicity - 0.7345 73.45%
Biodegradation - 0.5750 57.50%
Crustacea aquatic toxicity - 0.5700 57.00%
Fish aquatic toxicity - 0.5674 56.74%

Targets

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Proven Targets:

CHEMBL ID UniProt ID Name Min activity Assay type Source
No proven targets yet!

Predicted Targets (via Super-PRED):

CHEMBL ID UniProt ID Name Probability Model accuracy
CHEMBL3251 P19838 Nuclear factor NF-kappa-B p105 subunit 98.20% 96.09%
CHEMBL3137262 O60341 LSD1/CoREST complex 94.17% 97.09%
CHEMBL1075162 Q13304 Uracil nucleotide/cysteinyl leukotriene receptor 93.80% 80.33%
CHEMBL2635 P51452 Dual specificity protein phosphatase 3 91.87% 94.00%
CHEMBL335 P18031 Protein-tyrosine phosphatase 1B 91.31% 95.17%
CHEMBL1293249 Q13887 Kruppel-like factor 5 89.80% 86.33%
CHEMBL5619 P27695 DNA-(apurinic or apyrimidinic site) lyase 89.44% 91.11%
CHEMBL3384 Q16512 Protein kinase N1 88.23% 80.71%
CHEMBL2140 P48775 Tryptophan 2,3-dioxygenase 86.35% 98.46%
CHEMBL3401 O75469 Pregnane X receptor 86.04% 94.73%
CHEMBL3038477 P67870 Casein kinase II alpha/beta 85.38% 99.23%
CHEMBL3108638 O15164 Transcription intermediary factor 1-alpha 85.33% 95.56%
CHEMBL3230 O95977 Sphingosine 1-phosphate receptor Edg-6 84.90% 94.01%
CHEMBL2373 P21730 C5a anaphylatoxin chemotactic receptor 84.35% 92.62%
CHEMBL226 P30542 Adenosine A1 receptor 82.87% 95.93%
CHEMBL5608 Q16288 NT-3 growth factor receptor 82.68% 95.89%
CHEMBL3351 Q13085 Acetyl-CoA carboxylase 1 82.56% 93.04%
CHEMBL3137261 O14744 PRMT5/MEP50 complex 81.64% 100.00%
CHEMBL4203 Q9HAZ1 Dual specificity protein kinase CLK4 81.45% 94.45%
CHEMBL2107 P61073 C-X-C chemokine receptor type 4 80.89% 93.10%
CHEMBL4016 P42262 Glutamate receptor ionotropic, AMPA 2 80.89% 86.92%
CHEMBL2094108 P49354 Protein farnesyltransferase 80.74% 97.92%
CHEMBL3891 P07384 Calpain 1 80.56% 93.04%
CHEMBL279 P35968 Vascular endothelial growth factor receptor 2 80.56% 95.52%

Plants that contains it

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Below are displayed all the plants proven (via scientific papers) to contain this compound!
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There are no matching plants.

Cross-Links

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PubChem 443051
LOTUS LTS0124882
wikiData Q27105365