NPASS Compound

Structure

NPC490270 OpenBabel06302216222D 53 56 0 0 1 0 0 0 0 0999 V2000 1.7321 1.0000 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 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 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 -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 -5.1962 1.0000 0.0000 O 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 -5.1962 3.0000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -5.1962 4.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 4.5000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -6.0622 5.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 6.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 7.0000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -4.3301 7.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 8.5000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -3.4641 9.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 10.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 9.0000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -5.1962 10.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 8.5000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -6.9282 9.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 7.5000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -6.9282 7.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 4.0000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -7.7942 4.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 3.0000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -7.7942 2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 2.5000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -6.0622 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.7942 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.6603 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.5263 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.5263 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -10.3923 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -10.3923 4.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -11.2583 4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -11.2583 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -12.1244 3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -11.2583 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -12.1244 1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -12.9904 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -10.3923 1.0000 0.0000 C 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 -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 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -2.0000 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 0.8660 -0.5000 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 52 1 0 0 0 0 3 4 2 0 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 5 48 2 0 0 0 0 6 7 2 0 0 0 0 7 8 1 0 0 0 0 8 9 2 0 0 0 0 8 10 1 0 0 0 0 10 11 1 0 0 0 0 11 31 1 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 14 1 0 0 0 0 13 27 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 25 1 0 0 0 0 16 17 1 0 0 0 0 17 18 1 0 0 0 0 18 19 1 0 0 0 0 18 21 1 0 0 0 0 19 20 1 0 0 0 0 21 22 1 0 0 0 0 21 23 1 0 0 0 0 23 24 1 0 0 0 0 23 25 1 0 0 0 0 25 26 1 0 0 0 0 27 28 1 0 0 0 0 27 29 1 0 0 0 0 29 30 1 0 0 0 0 29 31 1 0 0 0 0 31 32 1 0 0 0 0 32 33 1 0 0 0 0 33 34 2 0 0 0 0 33 35 1 0 0 0 0 35 36 2 0 0 0 0 36 37 1 0 0 0 0 37 47 1 0 0 0 0 37 38 2 0 0 0 0 38 39 1 0 0 0 0 39 40 1 0 0 0 0 39 42 2 0 0 0 0 40 41 1 0 0 0 0 42 43 1 0 0 0 0 42 44 1 0 0 0 0 44 45 1 0 0 0 0 44 47 2 0 0 0 0 45 46 1 0 0 0 0 48 49 1 0 0 0 0 49 50 1 0 0 0 0 49 52 2 0 0 0 0 50 51 1 0 0 0 0 52 53 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	754.23
Volume:	703.044
LogP:	-0.033
LogD:	1.305
LogS:	-2.57
# Rotatable Bonds:	16
TPSA:	279.05
# H-Bond Aceptor:	19
# H-Bond Donor:	8
# Rings:	4
# Heavy Atoms:	19

MedChem Properties

QED Drug-Likeness Score:	0.081
Synthetic Accessibility Score:	4.94
Fsp3:	0.471
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	1
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.543
MDCK Permeability:	0.00011591874499572441
Pgp-inhibitor:	0.012
Pgp-substrate:	0.997
Human Intestinal Absorption (HIA):	0.997
20% Bioavailability (F20%):	0.998
30% Bioavailability (F30%):	0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.475
Plasma Protein Binding (PPB):	63.416748046875%
Volume Distribution (VD):	0.374
Pgp-substrate:	24.670682907104492%

ADMET: Metabolism

CYP1A2-inhibitor:	0.003
CYP1A2-substrate:	0.074
CYP2C19-inhibitor:	0.006
CYP2C19-substrate:	0.415
CYP2C9-inhibitor:	0.0
CYP2C9-substrate:	0.304
CYP2D6-inhibitor:	0.001
CYP2D6-substrate:	0.215
CYP3A4-inhibitor:	0.013
CYP3A4-substrate:	0.036

ADMET: Excretion

Clearance (CL):	1.336
Half-life (T1/2):	0.783

ADMET: Toxicity

hERG Blockers:	0.106
Human Hepatotoxicity (H-HT):	0.169
Drug-inuced Liver Injury (DILI):	0.028
AMES Toxicity:	0.105
Rat Oral Acute Toxicity:	0.042
Maximum Recommended Daily Dose:	0.196
Skin Sensitization:	0.517
Carcinogencity:	0.044
Eye Corrosion:	0.003
Eye Irritation:	0.004
Respiratory Toxicity:	0.023

Download Data

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

Natural Product: NPC490270

Natural Product ID:	NPC490270
*Common Name:**	1,2-Disinapoylgentiobiose
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	MBGNTECDWBKCKH-KQQUZDAGSA-N
Standard InCHI:	InChI=1S/C34H42O19/c1-45-17-9-15(10-18(46-2)25(17)38)5-7-23(36)52-32-30(43)28(41)22(14-49-33-31(44)29(42)27(40)21(13-35)50-33)51-34(32)53-24(37)8-6-16-11-19(47-3)26(39)20(12-16)48-4/h5-12,21-22,27-35,38-44H,13-14H2,1-4H3/b7-5+,8-6+
SMILES:	COC1=CC(C=CC(=O)OC2OC(COC3OC(CO)C(O)C(O)C3O)C(O)C(O)C2OC(=O)C=CC2=CC(OC)=C(O)C(OC)=C2)=CC(OC)=C1O
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:0000476] Cinnamic acids and derivatives [CHEMONTID:0001391] Hydroxycinnamic acids and derivatives [CHEMONTID:0003002] Hydroxycinnamic acid esters [CHEMONTID:0003003] Hydroxycinnamic acid 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
NPO7576	Brassica oleracea	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24014097]
NPO7576	Brassica oleracea	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24128451]
NPO7576	Brassica oleracea	Species	Brassicaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO7576	Brassica oleracea	Species	Brassicaceae	Eukaryota	Leaf	n.a.	n.a.	Database[FooDB]
NPO7576	Brassica oleracea	Species	Brassicaceae	Eukaryota	Shoot	n.a.	n.a.	Database[FooDB]
NPO7576	Brassica oleracea	Species	Brassicaceae	Eukaryota	Sprout Seedling	n.a.	n.a.	Database[FooDB]
NPO7576	Brassica oleracea	Species	Brassicaceae	Eukaryota	Stem	n.a.	n.a.	Database[FooDB]
NPO7576	Brassica oleracea	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO7576	Brassica oleracea	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO7576	Brassica oleracea	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO7576	Brassica oleracea	Species	Brassicaceae	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
NPO7576	NPC490270	Raw	n.a.	1.267600005	n.a.	n.a.	mg/100g	Database [PHENOL EXPLORER]
NPO7576	NPC490270	Raw	Leaf	6.4	n.a.	n.a.	ug/g of FW	PMID[FooDB]

☑ 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 NPC490270 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 NPC490270 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