Natural Product: NPC229249

Natural Product ID:  NPC229249
Common Name:   Deoxycytidine
IUPAC Name:   4-amino-1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one
Synonyms:   2'-Deoxycytidine; Deoxycytidine
Molecular Formula:   C9H13N3O4
Standard InCHIKey:  CKTSBUTUHBMZGZ-SHYZEUOFSA-N
Standard InCHI:  InChI=1S/C9H13N3O4/c10-7-1-2-12(9(15)11-7)8-3-5(14)6(4-13)16-8/h1-2,5-6,8,13-14H,3-4H2,(H2,10,11,15)/t5-,6+,8+/m0/s1
Canonical SMILES:  OC[C@H]1O[C@H](C[C@@H]1O)n1ccc(=N)nc1O
First Find Year:  
Max Developmental Stage:  
Synthetic Gene Cluster:   ;

  Species Source

Organism ID Organism Name Taxonomy Level Family SuperKingdom Isolation Part Collection Location Collection Time Reference
NPO1797 Homo sapiens Species Hominidae Eukaryota DOI[10.1038/nbt.2488]
NPO1797 Homo sapiens Species Hominidae Eukaryota urine PMID[15116424]
NPO1797 Homo sapiens Species Hominidae Eukaryota blood PMID[3243806]
NPO20338 Mus musculus Species Muridae Eukaryota PMID[19425150]
NPO21658 Saccharomyces cerevisiae Species Saccharomycetaceae Eukaryota PMID[24678285]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria PMID[21988831]
NPO2438 Euryale ferox Species Nymphaeaceae Eukaryota TM-MC*
NPO25269 Ganoderma lucidum Species Ganodermataceae Eukaryota TM-MC*
NPO16609 Ganoderma sinense Species Ganodermataceae Eukaryota TM-MC*
NPO26293 Ginkgo biloba Species Ginkgoaceae Eukaryota TM-MC*

  Biological Activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT2868 Individual Protein Thymidine kinase 2 Rattus norvegicus Inhibition = 58 % 7097717
NPT2869 Individual Protein Thymidine kinase Rattus norvegicus Inhibition = 7 % 7097717
NPT2868 Individual Protein Thymidine kinase 2 Rattus norvegicus Ki = 320000 nM 7097717
NPT3794 Cell Line ATH-8 cell line ED50 > 0.1 nM 3497272
NPT3794 Cell Line ATH-8 cell line ID50 > 0.1 nM 3497272
NPT3786 Cell Line LM Mus musculus Activity = 21960 6502604
NPT404 Cell Line CCRF-CEM Homo sapiens Activity = 97 % 15615538
NPT548 Tissue Ileum Cavia porcellus Activity = 0 % 10.1021/np50060a041
NPT548 Tissue Ileum Cavia porcellus Inhibition = 27 % 10.1021/np50060a041
NPT2873 Individual Protein Thymidine phosphorylase Escherichia coli K-12 Activity = 0 % 18272369
NPT5207 Organism Woodchuck hepatitis virus Woodchuck hepatitis virus Activity = 2 17606676
NPT3800 Individual Protein Deoxynucleoside kinase Drosophila melanogaster Activity = 43734 microM/min/mg 20060716
NPT197 Protein-Protein Interaction Menin/Histone-lysine N-methyltransferase MLL Homo sapiens Potency = 39810.7 nM PubChem BioAssay data set
NPT26 Individual Protein Reverse transcriptase Human immunodeficiency virus 1 Kd = 1100 nM 21700368
NPT2 Others Unspecified Kd = 3000 nM 21700368
NPT26 Individual Protein Reverse transcriptase Human immunodeficiency virus 1 Ratio = 65 /uM/min 21700368
NPT2 Others Unspecified Ratio = 26 /uM/min 21700368
NPT839 Cell Line L6 Rattus norvegicus IC50 > 250000 nM 10.1039/C3MD00159H
NPT941 Cell Line HaCaT Homo sapiens IC50 > 250000 nM 10.1039/C3MD00159H
NPT76 Cell Line C6 Rattus norvegicus IC50 > 250000 nM 10.1039/C3MD00159H
NPT90 Cell Line DU-145 Homo sapiens IC50 > 250000 nM 10.1039/C3MD00159H
NPT83 Cell Line MCF7 Homo sapiens IC50 > 250000 nM 10.1039/C3MD00159H
NPT4216 Individual Protein Thymidine kinase, cytosolic Cricetulus griseus Inhibition = 10 % 458818
NPT4216 Individual Protein Thymidine kinase, cytosolic Cricetulus griseus Inhibition = 24 % 458818
NPT2 Others Unspecified Inhibition = 0 % 395303
NPT1531 Organism Enterococcus faecium Enterococcus faecium ED50 = 0.05 nM 214555
NPT2 Others Unspecified EC50 = 100 nM 26220519
NPT2 Others Unspecified EC50 > 0 nM 26220519
NPT393 Cell Line HCT-116 Homo sapiens EC50 > 10000 nM 26220519

  Similar Natural Products in NPASS

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules. Tc lies between [0, 1] where '1' indicates the highest similarity. What is Tanimoto coefficient

●  The left chart: Distribution of similarity level between NPC229249 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.56 or Top200).

Similarity Score Similarity Level Natural Product ID
0.9625 High Similarity NPC190334
0.9625 High Similarity NPC62927
0.8953 High Similarity NPC329384
0.8851 High Similarity NPC6166
0.8851 High Similarity NPC226769
0.8851 High Similarity NPC280946
0.875 High Similarity NPC120887
0.875 High Similarity NPC90240
0.8652 High Similarity NPC328779
0.8588 High Similarity NPC328806
0.8462 Intermediate Similarity NPC328914
0.8 Intermediate Similarity NPC106780
0.7727 Intermediate Similarity NPC43246
0.7727 Intermediate Similarity NPC89051
0.7473 Intermediate Similarity NPC315063
0.7391 Intermediate Similarity NPC324390
0.7349 Intermediate Similarity NPC315806
0.7312 Intermediate Similarity NPC322594
0.7312 Intermediate Similarity NPC320249
0.7176 Intermediate Similarity NPC469972
0.7158 Intermediate Similarity NPC17892
0.7158 Intermediate Similarity NPC36985
0.7111 Intermediate Similarity NPC112842
0.7111 Intermediate Similarity NPC71339
0.7083 Intermediate Similarity NPC73765
0.7083 Intermediate Similarity NPC283698
0.6944 Remote Similarity NPC313813
0.6882 Remote Similarity NPC163352
0.6882 Remote Similarity NPC210456
0.6737 Remote Similarity NPC171116
0.6705 Remote Similarity NPC329077
0.6629 Remote Similarity NPC325902
0.6598 Remote Similarity NPC327344
0.6465 Remote Similarity NPC324516
0.6465 Remote Similarity NPC318166
0.6415 Remote Similarity NPC329277
0.64 Remote Similarity NPC317639
0.6311 Remote Similarity NPC318142
0.6296 Remote Similarity NPC149843
0.6296 Remote Similarity NPC155087
0.617 Remote Similarity NPC319753
0.6146 Remote Similarity NPC325723
0.6068 Remote Similarity NPC245534
0.5738 Remote Similarity NPC315058
0.5673 Remote Similarity NPC216278
0.5636 Remote Similarity NPC314398
0.5636 Remote Similarity NPC314413
0.5636 Remote Similarity NPC239705
0.5618 Remote Similarity NPC316445
0.56 Remote Similarity NPC313962

  Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

●  The left chart: Distribution of similarity level between NPC229249 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

Similarity Score Similarity Level Drug ID Developmental Stage
1.0 High Similarity NPD9601 Approved
0.9625 High Similarity NPD9603 Phase 3
0.9625 High Similarity NPD9602 Phase 3
0.9625 High Similarity NPD9604 Approved
0.961 High Similarity NPD9600 Approved
0.9506 High Similarity NPD9554 Approved
0.9506 High Similarity NPD9553 Approved
0.9367 High Similarity NPD9572 Clinical (unspecified phase)
0.9277 High Similarity NPD267 Discontinued
0.9268 High Similarity NPD301 Discontinued
0.9241 High Similarity NPD9573 Phase 2
0.9167 High Similarity NPD9585 Discontinued
0.8953 High Similarity NPD215 Discontinued
0.8902 High Similarity NPD9555 Phase 2
0.875 High Similarity NPD514 Clinical (unspecified phase)
0.8556 High Similarity NPD192 Phase 2
0.8506 High Similarity NPD6943 Clinical (unspecified phase)
0.8462 Intermediate Similarity NPD1455 Phase 3
0.8462 Intermediate Similarity NPD1454 Phase 3
0.8101 Intermediate Similarity NPD9405 Approved
0.8021 Intermediate Similarity NPD6946 Approved
0.7957 Intermediate Similarity NPD3121 Phase 2
0.7938 Intermediate Similarity NPD1428 Phase 2
0.7889 Intermediate Similarity NPD285 Discontinued
0.7816 Intermediate Similarity NPD9557 Clinical (unspecified phase)
0.7805 Intermediate Similarity NPD9407 Approved
0.7742 Intermediate Similarity NPD762 Discontinued
0.7727 Intermediate Similarity NPD9580 Clinical (unspecified phase)
0.7727 Intermediate Similarity NPD9581 Clinical (unspecified phase)
0.7708 Intermediate Similarity NPD7651 Approved
0.7624 Intermediate Similarity NPD1804 Phase 2
0.7624 Intermediate Similarity NPD1805 Phase 2
0.7551 Intermediate Similarity NPD2633 Phase 1
0.7551 Intermediate Similarity NPD4743 Phase 2
0.7442 Intermediate Similarity NPD9429 Discontinued
0.7356 Intermediate Similarity NPD9556 Approved
0.7349 Intermediate Similarity NPD9653 Clinical (unspecified phase)
0.734 Intermediate Similarity NPD1706 Clinical (unspecified phase)
0.7333 Intermediate Similarity NPD3138 Phase 3
0.7326 Intermediate Similarity NPD9427 Approved
0.7273 Intermediate Similarity NPD9560 Approved
0.7273 Intermediate Similarity NPD9561 Approved
0.7264 Intermediate Similarity NPD3139 Phase 3
0.7255 Intermediate Similarity NPD6693 Phase 3
0.7209 Intermediate Similarity NPD9372 Phase 2
0.7204 Intermediate Similarity NPD9565 Discontinued
0.7196 Intermediate Similarity NPD6935 Phase 3
0.7196 Intermediate Similarity NPD6936 Clinical (unspecified phase)
0.7191 Intermediate Similarity NPD9546 Phase 2
0.7191 Intermediate Similarity NPD9559 Phase 1
0.7176 Intermediate Similarity NPD9370 Approved
0.713 Intermediate Similarity NPD6918 Phase 1
0.7111 Intermediate Similarity NPD280 Approved
0.7111 Intermediate Similarity NPD9533 Phase 2
0.71 Intermediate Similarity NPD1061 Clinical (unspecified phase)
0.7083 Intermediate Similarity NPD6948 Phase 3
0.7083 Intermediate Similarity NPD9639 Clinical (unspecified phase)
0.7079 Intermediate Similarity NPD2691 Clinical (unspecified phase)
0.7065 Intermediate Similarity NPD1760 Approved
0.701 Intermediate Similarity NPD2621 Clinical (unspecified phase)
0.6957 Remote Similarity NPD170 Approved
0.6957 Remote Similarity NPD240 Phase 3
0.6957 Remote Similarity NPD9562 Discovery
0.6931 Remote Similarity NPD244 Clinical (unspecified phase)
0.6813 Remote Similarity NPD9529 Phase 1
0.6804 Remote Similarity NPD501 Phase 1
0.6778 Remote Similarity NPD9558 Phase 3
0.6742 Remote Similarity NPD9403 Discontinued
0.6742 Remote Similarity NPD9369 Clinical (unspecified phase)
0.6739 Remote Similarity NPD238 Clinical (unspecified phase)
0.6739 Remote Similarity NPD239 Phase 2
0.6737 Remote Similarity NPD755 Phase 3
0.6737 Remote Similarity NPD841 Approved
0.6703 Remote Similarity NPD9535 Phase 2
0.6703 Remote Similarity NPD9534 Phase 2
0.6701 Remote Similarity NPD279 Clinical (unspecified phase)
0.6701 Remote Similarity NPD1686 Approved
0.6634 Remote Similarity NPD223 Clinical (unspecified phase)
0.66 Remote Similarity NPD502 Approved
0.6552 Remote Similarity NPD9346 Approved
0.6552 Remote Similarity NPD9347 Approved
0.6538 Remote Similarity NPD3161 Clinical (unspecified phase)
0.6526 Remote Similarity NPD241 Discontinued
0.6476 Remote Similarity NPD3128 Phase 3
0.6429 Remote Similarity NPD251 Approved
0.6415 Remote Similarity NPD3129 Phase 3
0.6214 Remote Similarity NPD5789 Clinical (unspecified phase)
0.6111 Remote Similarity NPD1385 Discontinued
0.6071 Remote Similarity NPD9211 Clinical (unspecified phase)
0.5979 Remote Similarity NPD9654 Phase 2
0.5686 Remote Similarity NPD500 Discontinued
0.5673 Remote Similarity NPD6427 Approved
0.5673 Remote Similarity NPD6423 Approved
0.5673 Remote Similarity NPD6426 Approved
0.5673 Remote Similarity NPD6425 Approved
0.5648 Remote Similarity NPD2663 Approved
0.5647 Remote Similarity NPD9642 Approved
0.5619 Remote Similarity NPD6424 Approved

Structure

External Identifiers

PubChem CID   13711
ChEMBL   CHEMBL66115
ZINC  

Physicochemical Properties

Molecular Weight:  227.09
ALogP:  -2.1656
MLogP:  1.68
XLogP:  -0.005
# Rotatable Bonds:  5
Polar Surface Area:  109.37
# H-Bond Aceptor:  7
# H-Bond Donor:  4
# Rings:  2
# Heavy Atoms:  16

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