Structure

Physi-Chem Properties

Molecular Weight:  419.1
Volume:  388.379
LogP:  1.613
LogD:  1.064
LogS:  -3.157
# Rotatable Bonds:  4
TPSA:  171.37
# H-Bond Aceptor:  10
# H-Bond Donor:  7
# Rings:  4
# Heavy Atoms:  10

MedChem Properties

QED Drug-Likeness Score:  0.239
Synthetic Accessibility Score:  4.095
Fsp3:  0.25
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  1
PAINS Alert:  1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -6.356
MDCK Permeability:  5.528788733499823e-06
Pgp-inhibitor:  0.006
Pgp-substrate:  0.974
Human Intestinal Absorption (HIA):  0.751
20% Bioavailability (F20%):  0.997
30% Bioavailability (F30%):  0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.013
Plasma Protein Binding (PPB):  91.566162109375%
Volume Distribution (VD):  0.684
Pgp-substrate:  12.68354606628418%

ADMET: Metabolism

CYP1A2-inhibitor:  0.427
CYP1A2-substrate:  0.064
CYP2C19-inhibitor:  0.021
CYP2C19-substrate:  0.052
CYP2C9-inhibitor:  0.013
CYP2C9-substrate:  0.285
CYP2D6-inhibitor:  0.098
CYP2D6-substrate:  0.206
CYP3A4-inhibitor:  0.041
CYP3A4-substrate:  0.017

ADMET: Excretion

Clearance (CL):  12.043
Half-life (T1/2):  0.881

ADMET: Toxicity

hERG Blockers:  0.029
Human Hepatotoxicity (H-HT):  0.148
Drug-inuced Liver Injury (DILI):  0.969
AMES Toxicity:  0.814
Rat Oral Acute Toxicity:  0.108
Maximum Recommended Daily Dose:  0.081
Skin Sensitization:  0.934
Carcinogencity:  0.142
Eye Corrosion:  0.003
Eye Irritation:  0.842
Respiratory Toxicity:  0.062

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  Natural Product: NPC490359

Natural Product ID:  NPC490359
Common Name*:   Cyanidin 3-arabinoside
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  SBBFXSBQYRSIPP-GNBUJSLZSA-O
Standard InCHI:  InChI=1S/C20H18O10/c21-7-16-17(26)18(27)20(30-16)29-15-6-10-12(24)4-9(22)5-14(10)28-19(15)8-1-2-11(23)13(25)3-8/h1-6,16-18,20-21,26-27H,7H2,(H3-,22,23,24,25)/p+1/t16-,17-,18+,20-/m0/s1
SMILES:  OC[C@@H]1O[C@H](OC2=CC3=C(C=C(O)C=C3O)[O+]=C2C2=CC(O)=C(O)C=C2)[C@H](O)[C@H]1O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   n.a.
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000334] Flavonoids
        • [CHEMONTID:0001111] Flavonoid glycosides
          • [CHEMONTID:0001583] Flavonoid O-glycosides
            • [CHEMONTID:0001361] Anthocyanins
              • [CHEMONTID:0002996] Anthocyanidin-3-O-glycosides

*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
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Seeds n.a. DOI[10.1002/(SICI)1097-0010(199909)79:12<1620::AID-JSFA410>3.0.CO;2-G]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Fruits n.a. DOI[10.1007/s00217-002-0656-1]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Fruits n.a. DOI[10.1007/s00217-015-2561-4]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota n.a. n.a. DOI[10.1016/j.foodchem.2007.07.014]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Fruits n.a. DOI[10.1016/j.foodchem.2010.05.061]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota n.a. n.a. DOI[10.1016/j.foodchem.2010.05.061]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Fruits n.a. DOI[10.1016/j.indcrop.2013.08.051]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota n.a. n.a. DOI[10.1016/j.ssnmr.2006.05.001]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Fruits n.a. DOI[10.1016/j.yclnex.2017.01.002; 10.31989/ffhd.v6i3.245]DOI[10.1016/j.yclnex.2017.01.002; 10.31989/ffhd.v6i3.245]
NPO3347 Vaccinium corymbosum Species Ericaceae Eukaryota Fruit n.a. n.a. DOI[10.1016/S0963-9969(99)00095-2]
NPO21818 Vaccinium macrocarpon Species Ericaceae Eukaryota Fruit n.a. n.a. DOI[10.1016/S0963-9969(99)00095-2]
NPO16230 Malus pumila Species Rosaceae Eukaryota Fruit n.a. n.a. DOI[10.1021/jf970571j]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Fruits n.a. DOI[10.1080/09064710.2011.598543]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Fruits n.a. DOI[10.1111/j.1365-2621.1989.tb04709.x]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Fruits n.a. DOI[10.1111/j.1745-4530.2009.00507.x]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Fruits n.a. DOI[10.15835/NBHA4017181]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Fruits n.a. DOI[10.17221/540/2012-CJFS]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Fruits n.a. DOI[10.2137/145960607781635822]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Fruits n.a. DOI[10.2478/aoas-2014-0072]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Fruits n.a. DOI[10.3136/NSKKK.48.606]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Fruits n.a. DOI[10.3390/agriculture2030244]
NPO21818 Vaccinium macrocarpon Species Ericaceae Eukaryota Ripe fruits n.a. n.a. PMID[11000024]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Fruits n.a. PMID[15563205]
NPO25870 Vaccinium vitis-idaea Species Ericaceae Eukaryota n.a. fruit n.a. PMID[16417304]
NPO7156 Vaccinium myrtillus Species Ericaceae Eukaryota n.a. fruit n.a. PMID[16417304]
NPO21818 Vaccinium macrocarpon Species Ericaceae Eukaryota n.a. fruit n.a. PMID[21648406]
NPO3347 Vaccinium corymbosum Species Ericaceae Eukaryota n.a. fruit n.a. PMID[21648406]
NPO16230 Malus pumila Species Rosaceae Eukaryota n.a. fruit n.a. PMID[240326]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Fruits n.a. PMID[25026919]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Fruits n.a. PMID[25977015]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Fruits n.a. PMID[26351516]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Fruits n.a. PMID[27556441]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Fruits Schirgiswalde, Germany 2008-Sep PMID[31206724]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Fruits Schirgiswalde, Germany 2008-Oct PMID[31206724]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Fruits Schirgiswalde, Germany 2008-Aug PMID[31206724]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Fruits Cracow, Poland 2008-Sep PMID[31206724]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Fruits n.a. PMID[31619015]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Flowers n.a. PMID[9301422]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Fruits n.a. PMID[9301422]
NPO7156 Vaccinium myrtillus Species Ericaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO16230 Malus pumila Species Rosaceae Eukaryota Fruits n.a. Database[FooDB]
NPO3347 Vaccinium corymbosum Species Ericaceae Eukaryota Fruit Juice n.a. n.a. Database[FooDB]
NPO21818 Vaccinium macrocarpon Species Ericaceae Eukaryota Fruits n.a. Database[FooDB]
NPO7156 Vaccinium myrtillus Species Ericaceae Eukaryota Fruit Juice n.a. n.a. Database[FooDB]
NPO25870 Vaccinium vitis-idaea Species Ericaceae Eukaryota Fruits n.a. Database[FooDB]
NPO7156 Vaccinium myrtillus Species Ericaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO7156 Vaccinium myrtillus Species Ericaceae Eukaryota Fruits n.a. Database[FooDB]
NPO16230 Malus pumila Species Rosaceae Eukaryota Pericarp n.a. n.a. Database[FooDB]
NPO16230 Malus pumila Species Rosaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO7156 Vaccinium myrtillus Species Ericaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO16230 Malus pumila Species Rosaceae Eukaryota Pollen Or Spore n.a. n.a. Database[FooDB]
NPO16230 Malus pumila Species Rosaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO21818 Vaccinium macrocarpon Species Ericaceae Eukaryota Shoot n.a. n.a. Database[FooDB]
NPO7156 Vaccinium myrtillus Species Ericaceae Eukaryota Shoot n.a. n.a. Database[FooDB]
NPO16230 Malus pumila Species Rosaceae Eukaryota n.a. n.a. Database[FooDB]
NPO41195 Vaccinium angustifolium Species Ericaceae Eukaryota n.a. n.a. Database[FooDB]
NPO7156 Vaccinium myrtillus Species Ericaceae Eukaryota n.a. n.a. Database[FooDB]
NPO3347 Vaccinium corymbosum Species Ericaceae Eukaryota n.a. n.a. Database[FooDB]
NPO25870 Vaccinium vitis-idaea Species Ericaceae Eukaryota n.a. n.a. Database[FooDB]
NPO21818 Vaccinium macrocarpon Species Ericaceae Eukaryota n.a. n.a. Database[FooDB]
NPO16230 Malus pumila Species Rosaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota n.a. n.a. Database[FooDB]
NPO3347 Vaccinium corymbosum Species Ericaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO21818 Vaccinium macrocarpon Species Ericaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO21818 Vaccinium macrocarpon Species Ericaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16230 Malus pumila Species Rosaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25870 Vaccinium vitis-idaea Species Ericaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21818 Vaccinium macrocarpon Species Ericaceae Eukaryota Fruits n.a. Database[Phenol-Explorer]
NPO3347 Vaccinium corymbosum Species Ericaceae Eukaryota Fruits n.a. Database[Phenol-Explorer]
NPO41195 Vaccinium angustifolium Species Ericaceae Eukaryota Fruits n.a. Database[Phenol-Explorer]
NPO7156 Vaccinium myrtillus Species Ericaceae Eukaryota Fruits n.a. Database[Phenol-Explorer]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Fruits n.a. Database[Phenol-Explorer]
NPO25870 Vaccinium vitis-idaea Species Ericaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16230 Malus pumila Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21818 Vaccinium macrocarpon Species Ericaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21818 Vaccinium macrocarpon Species Ericaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO3347 Vaccinium corymbosum Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16230 Malus pumila Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25870 Vaccinium vitis-idaea Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21818 Vaccinium macrocarpon Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7156 Vaccinium myrtillus Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16230 Malus pumila Species Rosaceae Eukaryota Fruit n.a. n.a. Database[USDA]

☑ 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
NPO7156 NPC490359 Raw Leaf 32.85 21.9 43.8 mg/100g Database [DUKE]
NPO41195 NPC490359 Other n.a. 4.032291746 n.a. n.a. mg/100g Database [PHENOL EXPLORER]
NPO21818 NPC490359 Raw n.a. 4.479287624 n.a. n.a. mg/100g Database [PHENOL EXPLORER]
NPO7269 NPC490359 Raw n.a. 252.7671127 n.a. n.a. mg/100g Database [PHENOL EXPLORER]
NPO25870 NPC490359 Raw n.a. 5.851068974 n.a. n.a. mg/100g Database [PHENOL EXPLORER]
NPO3347 NPC490359 Raw n.a. 2.16148777 n.a. n.a. mg/100g Database [PHENOL EXPLORER]
NPO16230 NPC490359 n.a. n.a. 0.066005758 n.a. n.a. mg/100g Database [PHENOL EXPLORER]
NPO41195 NPC490359 n.a. n.a. 0.67749998 n.a. n.a. mg/100g Database [PHENOL EXPLORER]

☑ 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

☑ 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 NPC490359 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

  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 NPC490359 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

  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