Structure

Physi-Chem Properties

Molecular Weight:  207.08
Volume:  231.344
LogP:  4.672
LogD:  3.995
LogS:  -5.914
# Rotatable Bonds:  1
TPSA:  11.3
# H-Bond Aceptor:  1
# H-Bond Donor:  0
# Rings:  3
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.539
Synthetic Accessibility Score:  2.362
Fsp3:  0.0
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.582
MDCK Permeability:  1.5418112525367178e-05
Pgp-inhibitor:  0.46
Pgp-substrate:  0.087
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.996
30% Bioavailability (F30%):  0.896

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.104
Plasma Protein Binding (PPB):  98.64810180664062%
Volume Distribution (VD):  0.898
Pgp-substrate:  1.8835750818252563%

ADMET: Metabolism

CYP1A2-inhibitor:  0.991
CYP1A2-substrate:  0.688
CYP2C19-inhibitor:  0.821
CYP2C19-substrate:  0.236
CYP2C9-inhibitor:  0.391
CYP2C9-substrate:  0.521
CYP2D6-inhibitor:  0.807
CYP2D6-substrate:  0.415
CYP3A4-inhibitor:  0.114
CYP3A4-substrate:  0.288

ADMET: Excretion

Clearance (CL):  7.215
Half-life (T1/2):  0.213

ADMET: Toxicity

hERG Blockers:  0.1
Human Hepatotoxicity (H-HT):  0.036
Drug-inuced Liver Injury (DILI):  0.907
AMES Toxicity:  0.634
Rat Oral Acute Toxicity:  0.479
Maximum Recommended Daily Dose:  0.06
Skin Sensitization:  0.179
Carcinogencity:  0.786
Eye Corrosion:  0.058
Eye Irritation:  0.981
Respiratory Toxicity:  0.04

Download Data

Data Type Select
General Info & Identifiers & Properties  
Structure MOL file  
Source Organisms  
Biological Activities  
Similar NPs/Drugs  

  Natural Product: NPC184560

Natural Product ID:  NPC184560
Common Name*:   Anthocyanins
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  NWKFECICNXDNOQ-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C15H11O/c1-2-6-12(7-3-1)15-11-10-13-8-4-5-9-14(13)16-15/h1-11H/q+1
SMILES:  C1=CC=C(C=C1)C1=[O+]C2=CC=CC=C2C=C1
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:0000336] Anthocyanidins

*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
NPO1751 Ribes nigrum Species n.a. n.a. Fruit n.a. n.a. DOI[10.1016/S0963-9969(99)00095-2]
NPO1751 Ribes nigrum Species n.a. n.a. n.a. fruit n.a. PMID[16417304]
NPO17551 Phytolacca americana Species Phytolaccaceae Eukaryota roots n.a. n.a. PMID[18177012]
NPO15316 Hibiscus sabdariffa Species Malvaceae Eukaryota Flowers n.a. n.a. PMID[19301817]
NPO15316 Hibiscus sabdariffa Species Malvaceae Eukaryota Flowers n.a. n.a. PMID[21535810]
NPO15316 Hibiscus sabdariffa Species Malvaceae Eukaryota Flowers n.a. n.a. PMID[22178178]
NPO15316 Hibiscus sabdariffa Species Malvaceae Eukaryota Flowers n.a. n.a. PMID[22280831]
NPO15316 Hibiscus sabdariffa Species Malvaceae Eukaryota Flowers Kunming, China n.a. PMID[24621197]
NPO17551 Phytolacca americana Species Phytolaccaceae Eukaryota Seeds n.a. n.a. PMID[26595875]
NPO1751 Ribes nigrum Species n.a. n.a. Seed n.a. n.a. Database[FooDB]
NPO15316 Hibiscus sabdariffa Species Malvaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO1751 Ribes nigrum Species n.a. n.a. Seed Essent. Oil n.a. n.a. Database[FooDB]
NPO17551 Phytolacca americana Species Phytolaccaceae Eukaryota Shoot n.a. n.a. Database[FooDB]
NPO15316 Hibiscus sabdariffa Species Malvaceae Eukaryota Stem n.a. n.a. Database[FooDB]
NPO17551 Phytolacca americana Species Phytolaccaceae Eukaryota n.a. n.a. Database[FooDB]
NPO15316 Hibiscus sabdariffa Species Malvaceae Eukaryota n.a. n.a. Database[FooDB]
NPO1751 Ribes nigrum Species n.a. n.a. n.a. n.a. Database[FooDB]
NPO1751 Ribes nigrum Species n.a. n.a. Fruits n.a. Database[FooDB]
NPO1751 Ribes nigrum Species n.a. n.a. Bulb n.a. n.a. Database[FooDB]
NPO15316 Hibiscus sabdariffa Species Malvaceae Eukaryota Calyx n.a. n.a. Database[FooDB]
NPO15316 Hibiscus sabdariffa Species Malvaceae Eukaryota Flower n.a. n.a. Database[FooDB]
NPO1751 Ribes nigrum Species n.a. n.a. Fruit n.a. n.a. Database[FooDB]
NPO17551 Phytolacca americana Species Phytolaccaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO15316 Hibiscus sabdariffa Species Malvaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO1751 Ribes nigrum Species n.a. n.a. Fruit Juice n.a. n.a. Database[FooDB]
NPO1751 Ribes nigrum Species n.a. n.a. Leaf n.a. n.a. Database[FooDB]
NPO15316 Hibiscus sabdariffa Species Malvaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO17551 Phytolacca americana Species Phytolaccaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1751 Ribes nigrum Species n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO17551 Phytolacca americana Species Phytolaccaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17551 Phytolacca americana Species Phytolaccaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO17551 Phytolacca americana Species Phytolaccaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO15316 Hibiscus sabdariffa Species Malvaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17551 Phytolacca americana Species Phytolaccaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1751 Ribes nigrum Species n.a. n.a. 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
NPO15316 NPC184560 Raw Calyx 1500 1000 2000 mg/100g Database [DUKE]
NPO1751 NPC184560 Other Fruit 2500 1000 4000 mg/100g Database [DUKE]
NPO17551 NPC184560 Other Fruit 9300 9300 9300 mg/100g Database [DUKE]

☑ 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 NPC184560 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 NPC184560 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