NPASS Compound

Structure

NPC490517 OpenBabel06302216212D 33 36 0 0 1 0 0 0 0 0999 V2000 7.4282 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.5622 -2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.5622 -3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.4282 -4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.4282 -5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.5622 -5.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6962 -5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6962 -4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8301 -5.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8301 -6.5000 0.0000 O 0 3 0 0 0 0 0 0 0 0 0 0 3.9641 -7.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9641 -8.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0981 -8.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2321 -8.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2321 -7.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0981 -6.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0981 -5.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9641 -5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9641 -4.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.0981 -3.5000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 2.2321 -4.0000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 1.3660 -3.5000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 1.3660 -2.5000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 2.2321 -2.0000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 3.0981 -2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.2321 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3660 -0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.5000 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.5000 -4.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.2321 -5.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.3660 -6.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.0981 -9.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 8.2942 -3.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 1 0 0 0 0 3 8 1 0 0 0 0 3 4 2 0 0 0 0 4 5 1 0 0 0 0 4 33 1 0 0 0 0 5 6 2 0 0 0 0 6 7 1 0 0 0 0 7 8 2 0 0 0 0 7 9 1 0 0 0 0 9 18 1 0 0 0 0 9 10 2 0 0 0 0 10 11 1 0 0 0 0 11 16 1 0 0 0 0 11 12 2 0 0 0 0 12 13 1 0 0 0 0 13 14 2 0 0 0 0 13 32 1 0 0 0 0 14 15 1 0 0 0 0 15 16 2 0 0 0 0 15 31 1 0 0 0 0 16 17 1 0 0 0 0 17 18 2 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 1 0 0 0 0 20 25 1 0 0 0 0 21 22 1 0 0 0 0 21 30 1 0 0 0 0 22 23 1 0 0 0 0 22 29 1 0 0 0 0 23 24 1 0 0 0 0 23 28 1 0 0 0 0 24 25 1 0 0 0 0 24 26 1 0 0 0 0 26 27 1 0 0 0 0 M CHG 1 10 1 M END $$$$

Physi-Chem Properties

Molecular Weight:	463.12
Volume:	431.761
LogP:	0.996
LogD:	1.231
LogS:	-3.443
# Rotatable Bonds:	5
TPSA:	180.6
# H-Bond Aceptor:	11
# H-Bond Donor:	7
# Rings:	4
# Heavy Atoms:	11

MedChem Properties

QED Drug-Likeness Score:	0.264
Synthetic Accessibility Score:	4.187
Fsp3:	0.318
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Accepted
Chelating Alert:	1
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.352
MDCK Permeability:	8.685457942192443e-06
Pgp-inhibitor:	0.023
Pgp-substrate:	0.967
Human Intestinal Absorption (HIA):	0.61
20% Bioavailability (F20%):	0.012
30% Bioavailability (F30%):	0.989

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.032
Plasma Protein Binding (PPB):	89.79536437988281%
Volume Distribution (VD):	0.705
Pgp-substrate:	15.204548835754395%

ADMET: Metabolism

CYP1A2-inhibitor:	0.25
CYP1A2-substrate:	0.106
CYP2C19-inhibitor:	0.017
CYP2C19-substrate:	0.062
CYP2C9-inhibitor:	0.005
CYP2C9-substrate:	0.255
CYP2D6-inhibitor:	0.103
CYP2D6-substrate:	0.226
CYP3A4-inhibitor:	0.012
CYP3A4-substrate:	0.022

ADMET: Excretion

Clearance (CL):	9.666
Half-life (T1/2):	0.91

ADMET: Toxicity

hERG Blockers:	0.109
Human Hepatotoxicity (H-HT):	0.133
Drug-inuced Liver Injury (DILI):	0.954
AMES Toxicity:	0.764
Rat Oral Acute Toxicity:	0.032
Maximum Recommended Daily Dose:	0.014
Skin Sensitization:	0.447
Carcinogencity:	0.061
Eye Corrosion:	0.003
Eye Irritation:	0.229
Respiratory Toxicity:	0.052

Download Data

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

Natural Product: NPC490517

Natural Product ID:	NPC490517
*Common Name:**	peonidin 3-o-glucoside
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	VDTNZDSOEFSAIZ-VXZFYHBOSA-N
Standard InCHI:	InChI=1S/C22H22O11.ClH/c1-30-15-4-9(2-3-12(15)25)21-16(7-11-13(26)5-10(24)6-14(11)31-21)32-22-20(29)19(28)18(27)17(8-23)33-22;/h2-7,17-20,22-23,27-29H,8H2,1H3,(H2-,24,25,26);1H/t17-,18-,19+,20-,22-;/m1./s1
SMILES:	COC1=C(C=CC(=C1)C2=[O+]C3=CC(=CC(=C3C=C2O[C@H]4[C@@H]([C@H]([C@@H]([C@H](O4)CO)O)O)O)O)O)O.[Cl-]
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	14311152
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
NPO15336	Prunus avium	Species	Rosaceae	Eukaryota	Fruit	n.a.	n.a.	DOI[10.1016/j.foodchem.2007.08.004]
NPO15336	Prunus avium	Species	Rosaceae	Eukaryota	n.a.	fruit	n.a.	DOI[10.1016/j.phytochem.2007.01.008]
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]
NPO21818	Vaccinium macrocarpon	Species	Ericaceae	Eukaryota	Ripe fruits	n.a.	n.a.	PMID[11000024]
NPO7546	Prunus domestica	Species	Rosaceae	Eukaryota	n.a.	kernel	n.a.	PMID[12232058]
NPO15336	Prunus avium	Species	Rosaceae	Eukaryota	n.a.	fruit	n.a.	PMID[17328933]
NPO7546	Prunus domestica	Species	Rosaceae	Eukaryota	n.a.	fruit	n.a.	PMID[21648406]
NPO3347	Vaccinium corymbosum	Species	Ericaceae	Eukaryota	n.a.	fruit	n.a.	PMID[21648406]
NPO21818	Vaccinium macrocarpon	Species	Ericaceae	Eukaryota	n.a.	fruit	n.a.	PMID[21648406]
NPO41759	Saccharomyces cerevisiae GY-1 [bAS, OAS, CPRs genes, PPDS, PPTS]	Strain	Saccharomycetaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24424342]
NPO15336	Prunus avium	Species	Rosaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO15336	Prunus avium	Species	Rosaceae	Eukaryota	Fruits	n.a.		Database[FooDB]
NPO21818	Vaccinium macrocarpon	Species	Ericaceae	Eukaryota	Fruits	n.a.		Database[FooDB]
NPO7546	Prunus domestica	Species	Rosaceae	Eukaryota	Fruits	n.a.		Database[FooDB]
NPO7546	Prunus domestica	Species	Rosaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO7546	Prunus domestica	Species	Rosaceae	Eukaryota	Fruit	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]
NPO3347	Vaccinium corymbosum	Species	Ericaceae	Eukaryota	Fruit Juice	n.a.	n.a.	Database[FooDB]
NPO7546	Prunus domestica	Species	Rosaceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO21818	Vaccinium macrocarpon	Species	Ericaceae	Eukaryota	Shoot	n.a.	n.a.	Database[FooDB]
NPO41195	Vaccinium angustifolium	Species	Ericaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO3347	Vaccinium corymbosum	Species	Ericaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO21818	Vaccinium macrocarpon	Species	Ericaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO7546	Prunus domestica	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO21818	Vaccinium macrocarpon	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO15336	Prunus avium	Species	Rosaceae	Eukaryota	Fruits	n.a.		Database[Phenol-Explorer]
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]
NPO7546	Prunus domestica	Species	Rosaceae	Eukaryota	Fruits	n.a.		Database[Phenol-Explorer]
NPO7546	Prunus domestica	Species	Rosaceae	Eukaryota	n.a.	n.a.		Database[Phenol-Explorer]
NPO7546	Prunus domestica	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]
NPO21818	Vaccinium macrocarpon	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15336	Prunus avium	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3347	Vaccinium corymbosum	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7546	Prunus domestica	Species	Rosaceae	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
NPO15336	NPC490517	n.a.	Fruits	0.74	n.a.	n.a.	mg/100g of FW	Database [Phenol-Explorer]
NPO15336	NPC490517	n.a.	Fruits	0.75687	n.a.	n.a.	mg/100g of FW	Database [Phenol-Explorer]
NPO21818	NPC490517	n.a.	Fruits	4.16	n.a.	n.a.	mg/100g of FW	Database [Phenol-Explorer]
NPO3347	NPC490517	n.a.	Fruits	0.204	n.a.	n.a.	mg/100g of FW	Database [Phenol-Explorer]
NPO41195	NPC490517	n.a.	Fruits	2.5	n.a.	n.a.	mg/100g of FW	Database [Phenol-Explorer]
NPO41195	NPC490517	n.a.	Fruits	5.526	n.a.	n.a.	mg/100g of FW	Database [Phenol-Explorer]
NPO7546	NPC490517	n.a.	Fruits	0.45757	n.a.	n.a.	mg/100g of FW	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 NPC490517 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 NPC490517 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