NPASS Compound

Structure

NPC221903 OpenBabel06302216222D 23 24 0 0 1 0 0 0 0 0999 V2000 -0.5000 -0.8660 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.1088 -1.6594 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7261 -2.5833 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.5000 -0.8660 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.0000 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.8660 -0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.7321 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7321 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8660 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.5981 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.4641 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.4641 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5981 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5981 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.3301 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.1962 1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.3301 2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.5000 0.8660 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.3660 1.3660 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.5000 0.8660 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.5000 1.8660 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8660 0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 22 1 0 0 0 0 1 2 1 1 0 0 0 1 4 1 0 0 0 0 2 3 1 0 0 0 0 4 5 1 0 0 0 0 5 6 1 1 0 0 0 5 18 1 0 0 0 0 6 7 1 0 0 0 0 7 13 1 0 0 0 0 7 8 2 0 0 0 0 8 9 1 0 0 0 0 8 10 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 11 15 1 0 0 0 0 12 13 2 0 0 0 0 13 14 1 0 0 0 0 15 16 1 0 0 0 0 15 17 2 0 0 0 0 18 19 1 6 0 0 0 18 20 1 0 0 0 0 20 21 1 1 0 0 0 20 22 1 0 0 0 0 22 23 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	154.14
Volume:	173.194
LogP:	2.326
LogD:	2.708
LogS:	-2.271
# Rotatable Bonds:	1
TPSA:	20.23
# H-Bond Aceptor:	1
# H-Bond Donor:	1
# Rings:	2
# Heavy Atoms:	1

MedChem Properties

QED Drug-Likeness Score:	0.613
Synthetic Accessibility Score:	4.448
Fsp3:	1.0
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.376
MDCK Permeability:	3.861001459881663e-05
Pgp-inhibitor:	0.0
Pgp-substrate:	0.038
Human Intestinal Absorption (HIA):	0.006
20% Bioavailability (F20%):	0.013
30% Bioavailability (F30%):	0.233

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.958
Plasma Protein Binding (PPB):	67.19975280761719%
Volume Distribution (VD):	1.112
Pgp-substrate:	34.48479461669922%

ADMET: Metabolism

CYP1A2-inhibitor:	0.08
CYP1A2-substrate:	0.569
CYP2C19-inhibitor:	0.027
CYP2C19-substrate:	0.919
CYP2C9-inhibitor:	0.044
CYP2C9-substrate:	0.511
CYP2D6-inhibitor:	0.007
CYP2D6-substrate:	0.477
CYP3A4-inhibitor:	0.066
CYP3A4-substrate:	0.29

ADMET: Excretion

Clearance (CL):	16.098
Half-life (T1/2):	0.317

ADMET: Toxicity

hERG Blockers:	0.016
Human Hepatotoxicity (H-HT):	0.141
Drug-inuced Liver Injury (DILI):	0.11
AMES Toxicity:	0.025
Rat Oral Acute Toxicity:	0.09
Maximum Recommended Daily Dose:	0.031
Skin Sensitization:	0.12
Carcinogencity:	0.113
Eye Corrosion:	0.03
Eye Irritation:	0.791
Respiratory Toxicity:	0.077

Download Data

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

Natural Product: NPC221903

Natural Product ID:	NPC221903
*Common Name:**	YPSNWSNUXIIKHO-YANYRWCTSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	YPSNWSNUXIIKHO-YANYRWCTSA-N
Standard InCHI:	InChI=1S/C13H16O10/c14-3-7-8(17)9(18)10(19)13(22-7)23-11-5(15)1-4(12(20)21)2-6(11)16/h1-2,7-10,13-19H,3H2,(H,20,21)/t7-,8-,9+,10-,13+/m1/s1
SMILES:	c1c(cc(c(c1O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)O)C(=O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	10088114
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0004603] Organic oxygen compounds [CHEMONTID:0000323] Organooxygen compounds [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates [CHEMONTID:0002105] Glycosyl compounds [CHEMONTID:0004165] Phenolic 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
NPO3347	Vaccinium corymbosum	Species	Ericaceae	Eukaryota	Fruit	n.a.	n.a.	DOI[10.1016/S0963-9969(99)00095-2]
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]
NPO3347	Vaccinium corymbosum	Species	Ericaceae	Eukaryota	n.a.	fruit	n.a.	PMID[21648406]
NPO1751	Ribes nigrum	Species	n.a.	n.a.	Fruit	n.a.	n.a.	Database[FooDB]
NPO3347	Vaccinium corymbosum	Species	Ericaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO1751	Ribes nigrum	Species	n.a.	n.a.	Fruit Juice	n.a.	n.a.	Database[FooDB]
NPO3347	Vaccinium corymbosum	Species	Ericaceae	Eukaryota	Fruit Juice	n.a.	n.a.	Database[FooDB]
NPO1751	Ribes nigrum	Species	n.a.	n.a.	Leaf	n.a.	n.a.	Database[FooDB]
NPO1751	Ribes nigrum	Species	n.a.	n.a.	Seed	n.a.	n.a.	Database[FooDB]
NPO1751	Ribes nigrum	Species	n.a.	n.a.	Seed Essent. Oil	n.a.	n.a.	Database[FooDB]
NPO3347	Vaccinium corymbosum	Species	Ericaceae	Eukaryota		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.		n.a.	n.a.	Database[FooDB]
NPO1751	Ribes nigrum	Species	n.a.	n.a.	Bulb	n.a.	n.a.	Database[FooDB]
NPO3347	Vaccinium corymbosum	Species	Ericaceae	Eukaryota	Fruits	n.a.		Database[Phenol-Explorer]
NPO1751	Ribes nigrum	Species	n.a.	n.a.	n.a.	n.a.	n.a.	Database[TCMID]
NPO1751	Ribes nigrum	Species	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO21977	Psora corallina	Species	Psoraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20026	Senecio callosus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22543	Cleome chrysantha	Species	Cleomaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3347	Vaccinium corymbosum	Species	Ericaceae	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
NPO1751	NPC221903	Raw	n.a.	0.100000004	n.a.	n.a.	mg/100g	Database [PHENOL EXPLORER]
NPO3347	NPC221903	Raw	n.a.	0.5	n.a.	n.a.	mg/100g	Database [PHENOL EXPLORER]
NPO3347	NPC221903	n.a.	Fruits	0.5	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 NPC221903 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	367
0.1-0.2	1723
0.2-0.3	4490
0.3-0.4	9367
0.4-0.5	8536
0.5-0.6	4058
0.6-0.7	5561
0.7-0.8	6797
0.8-0.85	1423
0.85-0.9	325
0.9-0.95	43
0.95-1	7

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 NPC221903 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	329
0.1-0.2	934
0.2-0.3	2120
0.3-0.4	2605
0.4-0.5	1732
0.5-0.6	923
0.6-0.7	385
0.7-0.8	101
0.8-0.85	18
0.85-0.9	3
0.9-0.95	0
0.95-1	0

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