Structure

Physi-Chem Properties

Molecular Weight:  566.06
Volume:  445.499
LogP:  -3.287
LogD:  -2.574
LogS:  0.128
# Rotatable Bonds:  9
TPSA:  290.67
# H-Bond Aceptor:  19
# H-Bond Donor:  7
# Rings:  3
# Heavy Atoms:  21

MedChem Properties

QED Drug-Likeness Score:  0.139
Synthetic Accessibility Score:  5.716
Fsp3:  0.733
Lipinski Rule-of-5:  Rejected
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -6.747
MDCK Permeability:  0.00013390526873990893
Pgp-inhibitor:  0.0
Pgp-substrate:  0.666
Human Intestinal Absorption (HIA):  0.978
20% Bioavailability (F20%):  0.999
30% Bioavailability (F30%):  1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.389
Plasma Protein Binding (PPB):  12.9254732131958%
Volume Distribution (VD):  0.292
Pgp-substrate:  62.75857162475586%

ADMET: Metabolism

CYP1A2-inhibitor:  0.001
CYP1A2-substrate:  0.017
CYP2C19-inhibitor:  0.032
CYP2C19-substrate:  0.023
CYP2C9-inhibitor:  0.0
CYP2C9-substrate:  0.036
CYP2D6-inhibitor:  0.032
CYP2D6-substrate:  0.051
CYP3A4-inhibitor:  0.002
CYP3A4-substrate:  0.0

ADMET: Excretion

Clearance (CL):  1.658
Half-life (T1/2):  0.862

ADMET: Toxicity

hERG Blockers:  0.012
Human Hepatotoxicity (H-HT):  0.181
Drug-inuced Liver Injury (DILI):  0.982
AMES Toxicity:  0.069
Rat Oral Acute Toxicity:  0.001
Maximum Recommended Daily Dose:  0.028
Skin Sensitization:  0.25
Carcinogencity:  0.112
Eye Corrosion:  0.003
Eye Irritation:  0.01
Respiratory Toxicity:  0.111

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Similar NPs/Drugs  

  Natural Product: NPC149843

Natural Product ID:  NPC149843
Common Name*:   Galactose-Uridine-5'-Diphosphate
IUPAC Name:   [[(2R,3S,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy-hydroxyphosphoryl] [(2R,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl] hydrogen phosphate
Synonyms:  
Standard InCHIKey:  HSCJRCZFDFQWRP-ABVWGUQPSA-N
Standard InCHI:  InChI=1S/C15H24N2O17P2/c18-3-5-8(20)10(22)12(24)14(32-5)33-36(28,29)34-35(26,27)30-4-6-9(21)11(23)13(31-6)17-2-1-7(19)16-15(17)25/h1-2,5-6,8-14,18,20-24H,3-4H2,(H,26,27)(H,28,29)(H,16,19,25)/t5-,6-,8+,9-,10+,11-,12-,13-,14-/m1/s1
SMILES:  c1cn([C@H]2[C@@H]([C@@H]([C@@H](COP(=O)(O)OP(=O)(O)O[C@@H]3[C@@H]([C@H]([C@H]([C@@H](CO)O3)O)O)O)O2)O)O)c(=O)nc1O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL439009
PubChem CID:   18068
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000289] Nucleosides, nucleotides, and analogues
      • [CHEMONTID:0001509] Pyrimidine nucleotides
        • [CHEMONTID:0001296] Pyrimidine nucleotide sugars

*Note: the InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
**Note: the Chemical Classification was calculated by NPClassifier Version 1.5. Reference: PMID:34662515.

  Species Source

Organism ID Organism Name Taxonomy Level Family SuperKingdom Isolation Part Collection Location Collection Time Reference
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. DOI[10.1172/JCI16309]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. DOI[10.1371/journal.pone.0115359]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[10557354]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[11034610]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[11419736]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[11530998]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[1175644]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[12391014]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[12812989]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[12840027]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[12878451]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[15084647]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[1521032]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[15230696]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[15314235]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[16112079]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[16770722]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[1687010]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[17116739]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[17190852]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[17875433]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[18311922]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[18544912]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[18799520]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[19425150]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[19961175]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[20506249]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[20601097]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. faeces n.a. PMID[20708442]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. bile n.a. PMID[20708442]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. urine n.a. PMID[20708442]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[20876113]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[21798258]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[2268561]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[22711758]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[23315938]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[23717534]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[23752203]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[23810710]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[23811455]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[23868375]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[23919613]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[24101735]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[24399466]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[24494566]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[24558969]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[24816727]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[25114169]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[25181601]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[25293588]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[25644343]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[26236990]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[27471436]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[3179836]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[347637]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[4696527]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[5432584]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[6121420]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[6780563]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[8600370]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[8987136]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[9192820]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[9800648]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. Database[MetaboLights]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. Database[UNPD]

☑ Note for Reference:
In addition to directly collecting NP source organism data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated them from below databases:
☉ UNPD: Universal Natural Products Database [PMID: 23638153].
☉ StreptomeDB: a database of streptomycetes natural products [PMID: 33051671].
☉ TM-MC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine [PMID: 26156871].
☉ TCM@Taiwan: a Traditional Chinese Medicine database [PMID: 21253603].
☉ TCMID: a Traditional Chinese Medicine database [PMID: 29106634].
☉ TCMSP: The traditional Chinese medicine systems pharmacology database and analysis platform [PMID: 24735618].
☉ HerDing: a herb recommendation system to treat diseases using genes and chemicals [PMID: 26980517].
☉ MetaboLights: a metabolomics database [PMID: 27010336].
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

  NP Quantity Composition/Concentration

Organism ID NP ID Organism Material Preparation Organism Part NP Quantity (Standard) NP Quantity (Minimum) NP Quantity (Maximum) Quantity Unit Reference

☑ Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP quantitative records for specific NP domains (e.g., NPS from foods or herbs) from domain-specific databases. These databases include:
☉ DUKE: Dr. Duke's Phytochemical and Ethnobotanical Databases.
☉ PHENOL EXPLORER: is the first comprehensive database on polyphenol content in foods [PMID: 24103452], its homepage can be accessed at here.
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

  Biological Activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT4712 Individual Protein Purinergic receptor P2Y14 Homo sapiens EC50 = 670.0 nM PMID[527739]
NPT4712 Individual Protein Purinergic receptor P2Y14 Homo sapiens EC50 = 670.0 nM PMID[527740]
NPT2881 Individual Protein Beta-1,4-galactosyltransferase 1 Bos taurus Km = 46000.0 nM PMID[527741]
NPT2881 Individual Protein Beta-1,4-galactosyltransferase 1 Bos taurus Kcat = 0.65 /s PMID[527741]
NPT2 Others Unspecified IC50 = 17000.0 nM PMID[527741]
NPT27269 SINGLE PROTEIN N-acetyllactosaminide alpha-1,3-galactosyltransferase Bos taurus Kcat = 0.98 /s PMID[527741]
NPT27269 SINGLE PROTEIN N-acetyllactosaminide alpha-1,3-galactosyltransferase Bos taurus Km = 118000.0 nM PMID[527741]

☑ Note for Activity Records:
☉ The quantitative biological activities were primarily integrated from ChEMBL (Version-30) database and were also directly collected from PubMed literature. PubMed PMID was provided as the reference link for each activity record.

  Chemically structural similarity: I. Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes 4,3285 NPs with experimentally-derived bioactivity available 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 NPC149843 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
1.0 High Similarity NPC155087
0.8788 High Similarity NPC283698
0.8788 High Similarity NPC73765
0.8687 High Similarity NPC17892
0.8687 High Similarity NPC36985
0.8684 High Similarity NPC284651
0.8491 Intermediate Similarity NPC329277
0.8485 Intermediate Similarity NPC320249
0.8485 Intermediate Similarity NPC322594
0.8384 Intermediate Similarity NPC324390
0.8058 Intermediate Similarity NPC317639
0.798 Intermediate Similarity NPC89051
0.798 Intermediate Similarity NPC43246
0.7788 Intermediate Similarity NPC324516
0.7788 Intermediate Similarity NPC318166
0.7677 Intermediate Similarity NPC106780
0.7596 Intermediate Similarity NPC327344
0.7407 Intermediate Similarity NPC328779
0.7404 Intermediate Similarity NPC315063
0.7315 Intermediate Similarity NPC120887
0.7315 Intermediate Similarity NPC90240
0.7273 Intermediate Similarity NPC328914
0.7258 Intermediate Similarity NPC315058
0.7222 Intermediate Similarity NPC226769
0.7222 Intermediate Similarity NPC280946
0.7222 Intermediate Similarity NPC6166
0.7212 Intermediate Similarity NPC163352
0.7212 Intermediate Similarity NPC210456
0.713 Intermediate Similarity NPC329384
0.7087 Intermediate Similarity NPC313962
0.7019 Intermediate Similarity NPC325723
0.6923 Remote Similarity NPC112842
0.6923 Remote Similarity NPC71339
0.6916 Remote Similarity NPC171116
0.6742 Remote Similarity NPC318142
0.6733 Remote Similarity NPC329077
0.6574 Remote Similarity NPC190334
0.6574 Remote Similarity NPC62927
0.6532 Remote Similarity NPC313813
0.6434 Remote Similarity NPC325750
0.6346 Remote Similarity NPC325902
0.6296 Remote Similarity NPC229249
0.6133 Remote Similarity NPC316244
0.6032 Remote Similarity NPC478024
0.5929 Remote Similarity NPC328806
0.5877 Remote Similarity NPC109188
0.5833 Remote Similarity NPC316807
0.5818 Remote Similarity NPC319753
0.581 Remote Similarity NPC315806
0.5673 Remote Similarity NPC223174
0.5673 Remote Similarity NPC327753
0.5673 Remote Similarity NPC327486
0.5645 Remote Similarity NPC314398
0.5645 Remote Similarity NPC314413
0.5645 Remote Similarity NPC239705
0.56 Remote Similarity NPC322449
0.56 Remote Similarity NPC92874
0.56 Remote Similarity NPC62845
0.56 Remote Similarity NPC189854
0.56 Remote Similarity NPC166242

  Chemically structural similarity: II. Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC149843 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
0.8788 High Similarity NPD9639 Clinical (unspecified phase)
0.8491 Intermediate Similarity NPD3129 Phase 3
0.8396 Intermediate Similarity NPD3128 Phase 3
0.798 Intermediate Similarity NPD9581 Clinical (unspecified phase)
0.798 Intermediate Similarity NPD9580 Clinical (unspecified phase)
0.7826 Intermediate Similarity NPD3139 Phase 3
0.7739 Intermediate Similarity NPD3138 Phase 3
0.7723 Intermediate Similarity NPD241 Discontinued
0.7664 Intermediate Similarity NPD5789 Clinical (unspecified phase)
0.7525 Intermediate Similarity NPD9557 Clinical (unspecified phase)
0.7524 Intermediate Similarity NPD1686 Approved
0.7273 Intermediate Similarity NPD1454 Phase 3
0.7273 Intermediate Similarity NPD1455 Phase 3
0.7265 Intermediate Similarity NPD7914 Suspended
0.717 Intermediate Similarity NPD9565 Discontinued
0.7129 Intermediate Similarity NPD9556 Approved
0.7105 Intermediate Similarity NPD6946 Approved
0.7075 Intermediate Similarity NPD755 Phase 3
0.7059 Intermediate Similarity NPD9560 Approved
0.7059 Intermediate Similarity NPD9561 Approved
0.699 Remote Similarity NPD9546 Phase 2
0.6961 Remote Similarity NPD9558 Phase 3
0.6937 Remote Similarity NPD502 Approved
0.6923 Remote Similarity NPD9533 Phase 2
0.6923 Remote Similarity NPD280 Approved
0.6887 Remote Similarity NPD1760 Approved
0.6829 Remote Similarity NPD7756 Clinical (unspecified phase)
0.6815 Remote Similarity NPD7761 Suspended
0.6792 Remote Similarity NPD240 Phase 3
0.6792 Remote Similarity NPD9562 Discovery
0.6792 Remote Similarity NPD170 Approved
0.6759 Remote Similarity NPD841 Approved
0.6667 Remote Similarity NPD9559 Phase 1
0.6667 Remote Similarity NPD501 Phase 1
0.6667 Remote Similarity NPD9529 Phase 1
0.6638 Remote Similarity NPD1061 Clinical (unspecified phase)
0.6636 Remote Similarity NPD6943 Clinical (unspecified phase)
0.6604 Remote Similarity NPD239 Phase 2
0.6604 Remote Similarity NPD238 Clinical (unspecified phase)
0.6574 Remote Similarity NPD9603 Phase 3
0.6574 Remote Similarity NPD9602 Phase 3
0.6574 Remote Similarity NPD9604 Approved
0.6549 Remote Similarity NPD762 Discontinued
0.6486 Remote Similarity NPD251 Approved
0.6471 Remote Similarity NPD1385 Discontinued
0.641 Remote Similarity NPD7651 Approved
0.6349 Remote Similarity NPD7992 Clinical (unspecified phase)
0.6339 Remote Similarity NPD9585 Discontinued
0.6296 Remote Similarity NPD9601 Approved
0.6239 Remote Similarity NPD223 Clinical (unspecified phase)
0.6179 Remote Similarity NPD284 Phase 1
0.6121 Remote Similarity NPD514 Clinical (unspecified phase)
0.6071 Remote Similarity NPD9554 Approved
0.6071 Remote Similarity NPD9553 Approved
0.6071 Remote Similarity NPD301 Discontinued
0.6034 Remote Similarity NPD6948 Phase 3
0.6019 Remote Similarity NPD9600 Approved
0.6 Remote Similarity NPD279 Clinical (unspecified phase)
0.5965 Remote Similarity NPD267 Discontinued
0.5909 Remote Similarity NPD9572 Clinical (unspecified phase)
0.5902 Remote Similarity NPD2633 Phase 1
0.5902 Remote Similarity NPD4743 Phase 2
0.5882 Remote Similarity NPD192 Phase 2
0.5877 Remote Similarity NPD1331 Approved
0.5873 Remote Similarity NPD1805 Phase 2
0.5873 Remote Similarity NPD1804 Phase 2
0.5846 Remote Similarity NPD6935 Phase 3
0.5846 Remote Similarity NPD6936 Clinical (unspecified phase)
0.5826 Remote Similarity NPD500 Discontinued
0.5818 Remote Similarity NPD2691 Clinical (unspecified phase)
0.5818 Remote Similarity NPD9573 Phase 2
0.5812 Remote Similarity NPD215 Discontinued
0.581 Remote Similarity NPD9653 Clinical (unspecified phase)
0.5806 Remote Similarity NPD1428 Phase 2
0.5714 Remote Similarity NPD6693 Phase 3
0.5673 Remote Similarity NPD9445 Approved
0.5664 Remote Similarity NPD9555 Phase 2
0.5648 Remote Similarity NPD372 Clinical (unspecified phase)
0.5645 Remote Similarity NPD1407 Approved
0.5636 Remote Similarity NPD9429 Discontinued
0.562 Remote Similarity NPD3121 Phase 2

  Bioactivity similarity: Similar Natural Products in NPASS

Bioactivity similarity was calculated based on bioactivity descriptors of compounds. The bioactivity descriptors were calculated by a recently developed AI algorithm Chemical Checker (CC) [Nature Biotechnology, 38:1087–1096, 2020; Nature Communications, 12:3932, 2021], which evaluated bioactivity similarities at five levels:
☉ A: chemistry similarity;
☉ B: biological targets similarity;
☉ C: networks similarity;
☉ D: cell-based bioactivity similarity;
☉ E: similarity based on clinical data.

Those 5 categories of CC bioactivity descriptors were calculated and then subjected to manifold projection using UMAP algorithm, to project all NPs on a 2-Dimensional space. The current NP was highlighted with a small circle in the 2-D map. Below figures: left-to-right, A-to-E.

A: chemistry similarity
B: biological targets similarity
C: networks similarity
D: cell-based bioactivity similarity
E: similarity based on clinical data