NPASS Compound

Structure

NPC490360 OpenBabel06302216222D 40 44 0 0 1 0 0 0 0 0999 V2000 -9.0461 -0.8183 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.6394 -1.7319 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.6449 -1.8364 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.9757 -1.0933 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 -1.5000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -6.1667 -2.4945 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.4236 -3.1637 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.1449 -2.7024 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -7.5516 -3.6160 0.0000 O 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 -5.1962 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 1.5000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -5.1962 2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 3.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.0622 3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 4.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 3.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.3301 4.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 3.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.5981 3.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 2.0000 0.0000 C 0 0 1 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 -3.4641 -0.0000 0.0000 C 0 0 0 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 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -1.0000 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 -4.3301 -2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 0.5000 0.0000 C 0 0 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 -0.0000 2.0000 0.0000 C 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 2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 3 2 1 6 0 0 0 3 4 1 0 0 0 0 3 8 1 0 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 5 10 1 0 0 0 0 6 7 1 6 0 0 0 6 8 1 0 0 0 0 8 9 1 1 0 0 0 10 32 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 11 13 1 0 0 0 0 13 14 1 0 0 0 0 13 25 2 0 0 0 0 14 23 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 6 0 0 0 16 19 1 0 0 0 0 17 18 1 0 0 0 0 19 20 1 1 0 0 0 19 21 1 0 0 0 0 21 22 1 6 0 0 0 21 23 1 0 0 0 0 23 24 1 1 0 0 0 25 31 1 0 0 0 0 25 26 1 0 0 0 0 26 27 1 0 0 0 0 27 28 2 0 0 0 0 27 34 1 0 0 0 0 28 29 1 0 0 0 0 29 30 2 0 0 0 0 29 31 1 0 0 0 0 31 32 2 0 0 0 0 32 33 1 0 0 0 0 34 40 1 0 0 0 0 34 35 2 0 0 0 0 35 36 1 0 0 0 0 36 37 2 0 0 0 0 37 38 1 0 0 0 0 37 39 1 0 0 0 0 39 40 2 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	564.15
Volume:	517.441
LogP:	-0.319
LogD:	-0.426
LogS:	-1.829
# Rotatable Bonds:	5
TPSA:	250.97
# H-Bond Aceptor:	14
# H-Bond Donor:	10
# Rings:	5
# Heavy Atoms:	14

MedChem Properties

QED Drug-Likeness Score:	0.165
Synthetic Accessibility Score:	4.703
Fsp3:	0.423
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.376
MDCK Permeability:	1.3864245374861639e-05
Pgp-inhibitor:	0.005
Pgp-substrate:	0.994
Human Intestinal Absorption (HIA):	0.973
20% Bioavailability (F20%):	0.95
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.08
Plasma Protein Binding (PPB):	79.99497985839844%
Volume Distribution (VD):	0.83
Pgp-substrate:	14.516514778137207%

ADMET: Metabolism

CYP1A2-inhibitor:	0.02
CYP1A2-substrate:	0.012
CYP2C19-inhibitor:	0.008
CYP2C19-substrate:	0.059
CYP2C9-inhibitor:	0.001
CYP2C9-substrate:	0.316
CYP2D6-inhibitor:	0.002
CYP2D6-substrate:	0.12
CYP3A4-inhibitor:	0.008
CYP3A4-substrate:	0.003

ADMET: Excretion

Clearance (CL):	1.3
Half-life (T1/2):	0.557

ADMET: Toxicity

hERG Blockers:	0.116
Human Hepatotoxicity (H-HT):	0.203
Drug-inuced Liver Injury (DILI):	0.982
AMES Toxicity:	0.796
Rat Oral Acute Toxicity:	0.142
Maximum Recommended Daily Dose:	0.002
Skin Sensitization:	0.634
Carcinogencity:	0.034
Eye Corrosion:	0.003
Eye Irritation:	0.015
Respiratory Toxicity:	0.016

Download Data

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

Natural Product: NPC490360

Natural Product ID:	NPC490360
*Common Name:**	Apigenin 6-C-arabinoside 8-C-glucoside
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	DRLZZQRQMWQRLZ-FBMRRHFKSA-N
Standard InCHI:	InChI=1S/C26H28O14/c27-6-12-17(31)21(35)23(37)26(40-12)16-20(34)15(25-22(36)18(32)13(7-28)39-25)19(33)14-10(30)5-11(38-24(14)16)8-1-3-9(29)4-2-8/h1-5,12-13,17-18,21-23,25-29,31-37H,6-7H2/t12-,13+,17-,18+,21+,22-,23-,25?,26?/m1/s1
SMILES:	OC[C@@H]1OC([C@H](O)[C@H]1O)C1=C(O)C(C2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)=C2OC(=CC(=O)C2=C1O)C1=CC=C(O)C=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:0001111] Flavonoid glycosides [CHEMONTID:0001737] Flavonoid C-glycosides [CHEMONTID:0003535] Flavonoid 8-C-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
NPO8589	Triticum aestivum	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[10993146]
NPO8589	Triticum aestivum	Species	Poaceae	Eukaryota	n.a.	Tsukuba, Japan	1998-JUN	PMID[12381108]
NPO8589	Triticum aestivum	Species	Poaceae	Eukaryota	n.a.	leaf	n.a.	PMID[24197199]
NPO8589	Triticum aestivum	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24254087]
NPO8589	Triticum aestivum	Species	Poaceae	Eukaryota	n.a.	n.a.		PMID[31861466]
NPO8589	Triticum aestivum	Species	Poaceae	Eukaryota	Oil	n.a.	n.a.	Database[FooDB]
NPO8589	Triticum aestivum	Species	Poaceae	Eukaryota	Plant	n.a.	n.a.	Database[FooDB]
NPO8589	Triticum aestivum	Species	Poaceae	Eukaryota	Root	n.a.	n.a.	Database[FooDB]
NPO8589	Triticum aestivum	Species	Poaceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO8589	Triticum aestivum	Species	Poaceae	Eukaryota	Shoot	n.a.	n.a.	Database[FooDB]
NPO8589	Triticum aestivum	Species	Poaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO8589	Triticum aestivum	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO8589	Triticum aestivum	Species	Poaceae	Eukaryota	n.a.	n.a.		Database[Phenol-Explorer]
NPO8589	Triticum aestivum	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8589	Triticum aestivum	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO8589	Triticum aestivum	Species	Poaceae	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
NPO8589	NPC490360	Dried Or Powder	n.a.	7.350000143	n.a.	n.a.	mg/100g	Database [PHENOL EXPLORER]
NPO8589	NPC490360	Dried Or Powder	n.a.	30.46666718	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 NPC490360 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 NPC490360 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