Natural Product: NPC120887

Natural Product ID:  NPC120887
Common Name:   Cytidine Diphosphate
IUPAC Name:   [(2R,3S,4R,5R)-5-(4-amino-2-oxopyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methyl phosphono hydrogen phosphate
Synonyms:  
Molecular Formula:   C9H15N3O11P2
Standard InCHIKey:  ZWIADYZPOWUWEW-XVFCMESISA-N
Standard InCHI:  InChI=1S/C9H15N3O11P2/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(22-8)3-21-25(19,20)23-24(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H2,10,11,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
Canonical SMILES:  O[C@@H]1[C@@H](COP(=O)(OP(=O)(O)O)O)O[C@H]([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 blood Geigy Scientific Tables, 8th Rev edition. Edited by C. Lentner, West Cadwell, N.J.: Medical education Div., Ciba-Geigy Corp., Basel, Switzerland c1981-1992.
NPO20338 Mus musculus Species Muridae Eukaryota PMID[19425150]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria PMID[21988831]
NPO24062 Radix pseudostellariae Species Lymnaeidae Eukaryota TCMID*

  Biological Activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT2 Others Unspecified IC50 = 100000 nM 8709123
NPT2 Others Unspecified IC50 = 5000 nM 8709123
NPT1391 Individual Protein Pyrimidinergic receptor P2Y6 Homo sapiens Ratio EC50 = 1000 16942026
NPT3826 Individual Protein Purinergic receptor P2Y2 Homo sapiens Ratio EC50 = 110 16942026
NPT1391 Individual Protein Pyrimidinergic receptor P2Y6 Homo sapiens EC50 = 88000 nM 16942026
NPT4375 Individual Protein 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase Burkholderia pseudomallei (strain K96243) Kd = 75000 nM 24157367
NPT4376 Individual Protein 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase Escherichia coli (strain K12) Inhibition = 46 % 23509611
NPT4376 Individual Protein 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase Escherichia coli (strain K12) IC50 = 768000 nM 23509611

  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 NPC120887 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
0.9888 High Similarity NPC328779
0.9886 High Similarity NPC6166
0.9886 High Similarity NPC226769
0.9886 High Similarity NPC280946
0.967 High Similarity NPC328914
0.9556 High Similarity NPC90240
0.9551 High Similarity NPC329384
0.9091 High Similarity NPC62927
0.9091 High Similarity NPC190334
0.875 High Similarity NPC229249
0.8229 Intermediate Similarity NPC283698
0.8229 Intermediate Similarity NPC73765
0.8172 Intermediate Similarity NPC328806
0.8125 Intermediate Similarity NPC17892
0.8125 Intermediate Similarity NPC36985
0.7917 Intermediate Similarity NPC322594
0.7917 Intermediate Similarity NPC320249
0.7812 Intermediate Similarity NPC324390
0.75 Intermediate Similarity NPC317639
0.7453 Intermediate Similarity NPC329277
0.7396 Intermediate Similarity NPC89051
0.7396 Intermediate Similarity NPC43246
0.7315 Intermediate Similarity NPC155087
0.7315 Intermediate Similarity NPC149843
0.7172 Intermediate Similarity NPC315063
0.7083 Intermediate Similarity NPC106780
0.7073 Intermediate Similarity NPC318142
0.7059 Intermediate Similarity NPC324516
0.7059 Intermediate Similarity NPC318166
0.7033 Intermediate Similarity NPC315806
0.703 Intermediate Similarity NPC327344
0.687 Remote Similarity NPC313813
0.6634 Remote Similarity NPC163352
0.6634 Remote Similarity NPC210456
0.66 Remote Similarity NPC325723
0.6458 Remote Similarity NPC329077
0.6423 Remote Similarity NPC284651
0.6354 Remote Similarity NPC469972
0.6337 Remote Similarity NPC71339
0.6337 Remote Similarity NPC112842
0.6038 Remote Similarity NPC171116
0.59 Remote Similarity NPC325902
0.5827 Remote Similarity NPC177169
0.5786 Remote Similarity NPC232408
0.5786 Remote Similarity NPC64705
0.5755 Remote Similarity NPC211820
0.5755 Remote Similarity NPC251233
0.5755 Remote Similarity NPC318590
0.5736 Remote Similarity NPC315058
0.5714 Remote Similarity NPC317746
0.5669 Remote Similarity NPC245534
0.5641 Remote Similarity NPC314398
0.5641 Remote Similarity NPC314413
0.5641 Remote Similarity NPC239705
0.5612 Remote Similarity NPC186619
0.5606 Remote Similarity NPC313962
0.5603 Remote Similarity NPC274384
0.5603 Remote Similarity NPC89147

  Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC120887 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
0.967 High Similarity NPD1454 Phase 3
0.967 High Similarity NPD1455 Phase 3
0.9091 High Similarity NPD9604 Approved
0.9091 High Similarity NPD9602 Phase 3
0.9091 High Similarity NPD9603 Phase 3
0.8969 High Similarity NPD6946 Approved
0.875 High Similarity NPD9601 Approved
0.8696 High Similarity NPD9585 Discontinued
0.8409 Intermediate Similarity NPD9600 Approved
0.8381 Intermediate Similarity NPD3138 Phase 3
0.837 Intermediate Similarity NPD9553 Approved
0.837 Intermediate Similarity NPD301 Discontinued
0.837 Intermediate Similarity NPD9554 Approved
0.8333 Intermediate Similarity NPD514 Clinical (unspecified phase)
0.8302 Intermediate Similarity NPD3139 Phase 3
0.8229 Intermediate Similarity NPD9639 Clinical (unspecified phase)
0.8222 Intermediate Similarity NPD9572 Clinical (unspecified phase)
0.8191 Intermediate Similarity NPD267 Discontinued
0.8111 Intermediate Similarity NPD9573 Phase 2
0.8105 Intermediate Similarity NPD6943 Clinical (unspecified phase)
0.7938 Intermediate Similarity NPD215 Discontinued
0.7849 Intermediate Similarity NPD9555 Phase 2
0.7778 Intermediate Similarity NPD9427 Approved
0.7677 Intermediate Similarity NPD6948 Phase 3
0.7624 Intermediate Similarity NPD192 Phase 2
0.7524 Intermediate Similarity NPD3128 Phase 3
0.7453 Intermediate Similarity NPD3129 Phase 3
0.7444 Intermediate Similarity NPD9407 Approved
0.7429 Intermediate Similarity NPD4743 Phase 2
0.7404 Intermediate Similarity NPD7651 Approved
0.7396 Intermediate Similarity NPD9581 Clinical (unspecified phase)
0.7396 Intermediate Similarity NPD9580 Clinical (unspecified phase)
0.7391 Intermediate Similarity NPD9403 Discontinued
0.7339 Intermediate Similarity NPD1804 Phase 2
0.7339 Intermediate Similarity NPD1805 Phase 2
0.729 Intermediate Similarity NPD1428 Phase 2
0.72 Intermediate Similarity NPD285 Discontinued
0.7128 Intermediate Similarity NPD9429 Discontinued
0.7115 Intermediate Similarity NPD3121 Phase 2
0.7111 Intermediate Similarity NPD9405 Approved
0.7033 Intermediate Similarity NPD9653 Clinical (unspecified phase)
0.6957 Remote Similarity NPD6936 Clinical (unspecified phase)
0.6957 Remote Similarity NPD6935 Phase 3
0.6939 Remote Similarity NPD9557 Clinical (unspecified phase)
0.6923 Remote Similarity NPD762 Discontinued
0.6893 Remote Similarity NPD1706 Clinical (unspecified phase)
0.6852 Remote Similarity NPD1061 Clinical (unspecified phase)
0.6789 Remote Similarity NPD2633 Phase 1
0.6737 Remote Similarity NPD9372 Phase 2
0.6697 Remote Similarity NPD244 Clinical (unspecified phase)
0.6636 Remote Similarity NPD5789 Clinical (unspecified phase)
0.6635 Remote Similarity NPD1686 Approved
0.6634 Remote Similarity NPD1760 Approved
0.6602 Remote Similarity NPD9565 Discontinued
0.6549 Remote Similarity NPD6693 Phase 3
0.6531 Remote Similarity NPD9556 Approved
0.6505 Remote Similarity NPD755 Phase 3
0.6476 Remote Similarity NPD279 Clinical (unspecified phase)
0.6471 Remote Similarity NPD6918 Phase 1
0.6465 Remote Similarity NPD9561 Approved
0.6465 Remote Similarity NPD9560 Approved
0.6449 Remote Similarity NPD2621 Clinical (unspecified phase)
0.6422 Remote Similarity NPD223 Clinical (unspecified phase)
0.64 Remote Similarity NPD9559 Phase 1
0.64 Remote Similarity NPD9546 Phase 2
0.6389 Remote Similarity NPD502 Approved
0.6364 Remote Similarity NPD9558 Phase 3
0.6354 Remote Similarity NPD9370 Approved
0.6337 Remote Similarity NPD280 Approved
0.6337 Remote Similarity NPD9533 Phase 2
0.6327 Remote Similarity NPD9369 Clinical (unspecified phase)
0.6325 Remote Similarity NPD7914 Suspended
0.6311 Remote Similarity NPD241 Discontinued
0.63 Remote Similarity NPD2691 Clinical (unspecified phase)
0.6214 Remote Similarity NPD240 Phase 3
0.6214 Remote Similarity NPD170 Approved
0.6214 Remote Similarity NPD9562 Discovery
0.6207 Remote Similarity NPD284 Phase 1
0.6195 Remote Similarity NPD3161 Clinical (unspecified phase)
0.6111 Remote Similarity NPD501 Phase 1
0.6078 Remote Similarity NPD9529 Phase 1
0.6038 Remote Similarity NPD841 Approved
0.6019 Remote Similarity NPD239 Phase 2
0.6019 Remote Similarity NPD238 Clinical (unspecified phase)
0.6 Remote Similarity NPD7761 Suspended
0.598 Remote Similarity NPD9535 Phase 2
0.598 Remote Similarity NPD9534 Phase 2
0.5948 Remote Similarity NPD1385 Discontinued
0.5926 Remote Similarity NPD251 Approved
0.5816 Remote Similarity NPD9347 Approved
0.5816 Remote Similarity NPD9346 Approved
0.5806 Remote Similarity NPD7756 Clinical (unspecified phase)
0.5699 Remote Similarity NPD9211 Clinical (unspecified phase)
0.566 Remote Similarity NPD9654 Phase 2

Structure

External Identifiers

PubChem CID   6132
ChEMBL   CHEMBL425252
ZINC  

Physicochemical Properties

Molecular Weight:  403.02
ALogP:  -2.6039
MLogP:  0.69
XLogP:  -3.493
# Rotatable Bonds:  12
Polar Surface Area:  242.28
# H-Bond Aceptor:  14
# H-Bond Donor:  7
# Rings:  2
# Heavy Atoms:  25

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Similar NPs/Drugs