NPASS Compound

Structure

NPC490401 OpenBabel06302216222D 33 36 0 0 1 0 0 0 0 0999 V2000 -0.8660 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -0.5000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -1.7321 -0.0000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -2.5981 -0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 1.0000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -2.5981 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 4.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 5.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 6.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 7.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 5.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 4.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 1.0000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 C 0 0 3 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 0.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 29 1 0 0 0 0 2 3 1 0 0 0 0 3 4 1 0 0 0 0 3 5 1 0 0 0 0 5 6 1 0 0 0 0 5 27 1 0 0 0 0 6 7 1 0 0 0 0 7 18 1 0 0 0 0 7 8 2 0 0 0 0 8 9 1 0 0 0 0 8 20 1 0 0 0 0 9 10 1 0 0 0 0 10 17 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 12 14 2 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 15 17 2 0 0 0 0 17 18 1 0 0 0 0 18 19 2 0 0 0 0 20 26 1 0 0 0 0 20 21 2 0 0 0 0 21 22 1 0 0 0 0 22 23 2 0 0 0 0 23 24 1 0 0 0 0 23 25 1 0 0 0 0 25 26 2 0 0 0 0 27 28 1 0 0 0 0 28 29 1 0 0 0 0 28 31 1 0 0 0 0 29 30 1 0 0 0 0 31 32 1 0 0 0 0 31 33 2 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	462.08
Volume:	419.301
LogP:	0.659
LogD:	0.986
LogS:	-4.081
# Rotatable Bonds:	4
TPSA:	207.35
# H-Bond Aceptor:	12
# H-Bond Donor:	7
# Rings:	4
# Heavy Atoms:	12

MedChem Properties

QED Drug-Likeness Score:	0.27
Synthetic Accessibility Score:	3.952
Fsp3:	0.238
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.361
MDCK Permeability:	1.3244236470200121e-05
Pgp-inhibitor:	0.0
Pgp-substrate:	0.195
Human Intestinal Absorption (HIA):	0.469
20% Bioavailability (F20%):	0.223
30% Bioavailability (F30%):	0.997

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.03
Plasma Protein Binding (PPB):	88.59703826904297%
Volume Distribution (VD):	0.69
Pgp-substrate:	11.039514541625977%

ADMET: Metabolism

CYP1A2-inhibitor:	0.05
CYP1A2-substrate:	0.023
CYP2C19-inhibitor:	0.024
CYP2C19-substrate:	0.042
CYP2C9-inhibitor:	0.012
CYP2C9-substrate:	0.597
CYP2D6-inhibitor:	0.018
CYP2D6-substrate:	0.133
CYP3A4-inhibitor:	0.042
CYP3A4-substrate:	0.003

ADMET: Excretion

Clearance (CL):	1.405
Half-life (T1/2):	0.89

ADMET: Toxicity

hERG Blockers:	0.011
Human Hepatotoxicity (H-HT):	0.197
Drug-inuced Liver Injury (DILI):	0.988
AMES Toxicity:	0.318
Rat Oral Acute Toxicity:	0.102
Maximum Recommended Daily Dose:	0.005
Skin Sensitization:	0.032
Carcinogencity:	0.064
Eye Corrosion:	0.003
Eye Irritation:	0.01
Respiratory Toxicity:	0.024

Download Data

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

Natural Product: NPC490401

Natural Product ID:	NPC490401
*Common Name:**	Kaempferol 3-glucuronide
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	FNTJVYCFNVUBOL-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C21H18O12/c22-8-3-1-7(2-4-8)17-18(13(25)12-10(24)5-9(23)6-11(12)31-17)32-21-16(28)14(26)15(27)19(33-21)20(29)30/h1-6,14-16,19,21-24,26-28H,(H,29,30)
SMILES:	OC1C(O)C(OC2=C(OC3=CC(O)=CC(O)=C3C2=O)C2=CC=C(O)C=C2)OC(C1O)C(O)=O
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:0002934] Flavonoid O-glucuronides [CHEMONTID:0003532] Flavonoid-3-O-glucuronides

*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
NPO4934	Phaseolus vulgaris	Species	Fabaceae	Eukaryota	n.a.	retail stores, supermarkets and market stalls in Forssa and in the Helsinki area	2003–2005	DOI[10.1016/j.jfca.2006.05.007]
NPO10339	Fragaria x ananassa	Species	Rosaceae	Eukaryota	Fruit	n.a.	n.a.	DOI[10.1016/S0963-9969(99)00095-2]
NPO19774	Rubus idaeus	Species	n.a.	n.a.	Fruit	n.a.	n.a.	DOI[10.1016/S0963-9969(99)00095-2]
NPO4934	Phaseolus vulgaris	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1021/jf980687v]
NPO10339	Fragaria x ananassa	Species	Rosaceae	Eukaryota	Leaves (mother plant)	Suwon, Korea	2011-Sep	DOI[10.7235/HORT.2013.12200]
NPO10339	Fragaria x ananassa	Species	Rosaceae	Eukaryota	Roots (runner plant)	Suwon, Korea	2011-Sep	DOI[10.7235/HORT.2013.12200]
NPO10339	Fragaria x ananassa	Species	Rosaceae	Eukaryota	Fruits	Suwon, Korea	2012-Nov	DOI[10.7235/HORT.2013.12200]
NPO10339	Fragaria x ananassa	Species	Rosaceae	Eukaryota	Leaves	Suwon, Korea		DOI[10.7235/HORT.2013.12200]
NPO10339	Fragaria x ananassa	Species	Rosaceae	Eukaryota	Runners	Suwon, Korea	2011-Sep	DOI[10.7235/HORT.2013.12200]
NPO10339	Fragaria x ananassa	Species	Rosaceae	Eukaryota	Leaves (runner plant)	Suwon, Korea	2011-Sep	DOI[10.7235/HORT.2013.12200]
NPO10339	Fragaria x ananassa	Species	Rosaceae	Eukaryota	Roots (mother plant)	Suwon, Korea	2011-Sep	DOI[10.7235/HORT.2013.12200]
NPO10339	Fragaria x ananassa	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[1453178]
NPO10339	Fragaria x ananassa	Species	Rosaceae	Eukaryota	Fruits	n.a.	n.a.	PMID[15568772]
NPO26643	Cichorium endivia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15877880]
NPO26643	Cichorium endivia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18460139]
NPO19774	Rubus idaeus	Species	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[21381697]
NPO26643	Cichorium endivia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[6821187]
NPO4934	Phaseolus vulgaris	Species	Fabaceae	Eukaryota	Leaf	n.a.	n.a.	Database[FooDB]
NPO19774	Rubus idaeus	Species	n.a.	n.a.	Fruits	n.a.		Database[FooDB]
NPO19774	Rubus idaeus	Species	n.a.	n.a.	Seed	n.a.	n.a.	Database[FooDB]
NPO26643	Cichorium endivia	Species	Asteraceae	Eukaryota	Leaves	n.a.		Database[FooDB]
NPO4934	Phaseolus vulgaris	Species	Fabaceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO4934	Phaseolus vulgaris	Species	Fabaceae	Eukaryota	n.a.	n.a.		Database[FooDB]
NPO4934	Phaseolus vulgaris	Species	Fabaceae	Eukaryota	Sprout Seedling	n.a.	n.a.	Database[FooDB]
NPO19774	Rubus idaeus	Species	n.a.	n.a.		n.a.	n.a.	Database[FooDB]
NPO2143	Rubus adenotrichos	Species	Rosaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO4934	Phaseolus vulgaris	Species	Fabaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO10339	Fragaria x ananassa	Species	Rosaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO26643	Cichorium endivia	Species	Asteraceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO19774	Rubus idaeus	Species	n.a.	n.a.	Fruit	n.a.	n.a.	Database[FooDB]
NPO4934	Phaseolus vulgaris	Species	Fabaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO26643	Cichorium endivia	Species	Asteraceae	Eukaryota	Leaf	n.a.	n.a.	Database[FooDB]
NPO19774	Rubus idaeus	Species	n.a.	n.a.	Leaf	n.a.	n.a.	Database[FooDB]
NPO10339	Fragaria x ananassa	Species	Rosaceae	Eukaryota	Fruits	n.a.		Database[FooDB]
NPO19774	Rubus idaeus	Species	n.a.	n.a.	n.a.	n.a.	n.a.	Database[HerDing]
NPO4934	Phaseolus vulgaris	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO10339	Fragaria x ananassa	Species	Rosaceae	Eukaryota	Fruits	n.a.		Database[Phenol-Explorer]
NPO19774	Rubus idaeus	Species	n.a.	n.a.	Fruits	n.a.		Database[Phenol-Explorer]
NPO19774	Rubus idaeus	Species	n.a.	n.a.	n.a.	n.a.		Database[Phenol-Explorer]
NPO26643	Cichorium endivia	Species	Asteraceae	Eukaryota	n.a.	n.a.		Database[Phenol-Explorer]
NPO10339	Fragaria x ananassa	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4934	Phaseolus vulgaris	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO19774	Rubus idaeus	Species	n.a.	n.a.	n.a.	n.a.	n.a.	Database[TCMID]
NPO4934	Phaseolus vulgaris	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO4934	Phaseolus vulgaris	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19774	Rubus idaeus	Species	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO26643	Cichorium endivia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2143	Rubus adenotrichos	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10339	Fragaria x ananassa	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
NPO2143	NPC490401	Raw, Frozen, Dried	Fruit	5.6	5.2	6	mg/100g of DW	PMID[FooDB]
NPO19774	NPC490401	Beverage (juice)	n.a.	0.206923078	n.a.	n.a.	mg/100g	Database [PHENOL EXPLORER]
NPO10339	NPC490401	Raw	n.a.	0.200880389	n.a.	n.a.	mg/100g	Database [PHENOL EXPLORER]
NPO4934	NPC490401	Raw	n.a.	0.08	n.a.	n.a.	mg/100g	Database [PHENOL EXPLORER]
NPO26643	NPC490401	Raw	n.a.	18.50423122	n.a.	n.a.	mg/100g	Database [PHENOL EXPLORER]
NPO26643	NPC490401	Raw	n.a.	14.92615318	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 NPC490401 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 NPC490401 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