NPASS Compound

Structure

NPC200502 OpenBabel06302216112D 45 48 0 0 1 0 0 0 0 0999 V2000 -4.2198 -2.4128 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2198 -1.4332 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.0682 -0.9434 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.0682 0.0362 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.2198 0.5260 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.3715 0.0362 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.3715 -0.9434 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.6748 1.0158 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8264 0.5260 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.1776 1.2599 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4889 2.1888 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.1599 2.9227 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.0083 2.4329 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8566 2.9227 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.7050 2.4329 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.8566 1.9431 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8566 0.9635 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.2808 3.2254 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.2124 2.9227 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.2124 1.9431 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 5.0049 1.3673 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9025 0.3931 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.2808 1.6404 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.0049 3.4985 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.9781 4.1571 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.7546 3.2738 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.7033 4.2520 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.2429 4.5056 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.5939 5.4201 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0225 6.1814 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.7764 3.6840 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.4646 4.8685 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.5762 2.7402 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.5820 -0.0974 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.2226 -1.0087 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.2449 -0.9485 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.3786 -1.7041 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0359 -2.6218 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7486 -1.8351 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5305 0.1474 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.2198 1.5056 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.9165 0.5260 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.9165 -1.4332 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.0682 -2.9026 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 45 1 0 0 0 0 2 1 1 6 0 0 0 2 3 1 0 0 0 0 2 7 1 0 0 0 0 3 4 1 0 0 0 0 3 44 1 1 0 0 0 4 5 1 0 0 0 0 4 43 1 6 0 0 0 5 6 1 0 0 0 0 5 42 1 1 0 0 0 6 7 1 0 0 0 0 6 8 1 1 0 0 0 8 9 1 0 0 0 0 9 39 1 0 0 0 0 9 10 1 1 0 0 0 9 34 1 0 0 0 0 10 11 1 0 0 0 0 11 12 1 0 0 0 0 12 31 1 0 0 0 0 12 13 1 6 0 0 0 12 26 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 23 1 0 0 0 0 15 16 1 6 0 0 0 15 18 1 0 0 0 0 16 17 1 0 0 0 0 18 19 1 0 0 0 0 18 25 1 1 0 0 0 19 20 1 0 0 0 0 19 24 1 6 0 0 0 20 21 1 1 0 0 0 20 23 1 0 0 0 0 21 22 1 0 0 0 0 26 27 1 0 0 0 0 26 33 1 1 0 0 0 27 28 1 0 0 0 0 27 32 1 6 0 0 0 28 29 1 1 0 0 0 28 31 1 0 0 0 0 29 30 1 0 0 0 0 34 35 1 0 0 0 0 34 41 1 6 0 0 0 35 36 1 0 0 0 0 35 40 1 1 0 0 0 36 37 1 6 0 0 0 36 39 1 0 0 0 0 37 38 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	666.22
Volume:	574.029
LogP:	-3.71
LogD:	-3.151
LogS:	-0.137
# Rotatable Bonds:	13
TPSA:	347.83
# H-Bond Aceptor:	21
# H-Bond Donor:	14
# Rings:	4
# Heavy Atoms:	21

MedChem Properties

QED Drug-Likeness Score:	0.087
Synthetic Accessibility Score:	5.706
Fsp3:	1.0
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:	-6.643
MDCK Permeability:	0.0003754404897335917
Pgp-inhibitor:	0.001
Pgp-substrate:	0.936
Human Intestinal Absorption (HIA):	1.0
20% Bioavailability (F20%):	1.0
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.266
Plasma Protein Binding (PPB):	18.614742279052734%
Volume Distribution (VD):	0.121
Pgp-substrate:	53.31646728515625%

ADMET: Metabolism

CYP1A2-inhibitor:	0.001
CYP1A2-substrate:	0.023
CYP2C19-inhibitor:	0.001
CYP2C19-substrate:	0.045
CYP2C9-inhibitor:	0.0
CYP2C9-substrate:	0.002
CYP2D6-inhibitor:	0.0
CYP2D6-substrate:	0.036
CYP3A4-inhibitor:	0.002
CYP3A4-substrate:	0.001

ADMET: Excretion

Clearance (CL):	1.185
Half-life (T1/2):	0.889

ADMET: Toxicity

hERG Blockers:	0.586
Human Hepatotoxicity (H-HT):	0.123
Drug-inuced Liver Injury (DILI):	0.037
AMES Toxicity:	0.05
Rat Oral Acute Toxicity:	0.0
Maximum Recommended Daily Dose:	0.0
Skin Sensitization:	0.727
Carcinogencity:	0.007
Eye Corrosion:	0.003
Eye Irritation:	0.012
Respiratory Toxicity:	0.001

Download Data

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

Natural Product: NPC200502

Natural Product ID:	NPC200502
*Common Name:**	FLDFNEBHEXLZRX-DLQNOBSRSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	FLDFNEBHEXLZRX-DLQNOBSRSA-N
Standard InCHI:	InChI=1S/C24H42O21/c25-1-8-12(30)16(34)17(35)21(41-8)45-24(20(38)15(33)11(4-28)44-24)7-40-23(19(37)14(32)10(3-27)43-23)6-39-22(5-29)18(36)13(31)9(2-26)42-22/h8-21,25-38H,1-7H2/t8-,9-,10-,11-,12-,13-,14-,15-,16+,17-,18+,19+,20+,21-,22-,23-,24+/m1/s1
SMILES:	C([C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O[C@@]1(CO[C@@]2(CO[C@@]3(CO)[C@H]([C@@H]([C@@H](CO)O3)O)O)[C@H]([C@@H]([C@@H](CO)O2)O)O)[C@H]([C@@H]([C@@H](CO)O1)O)O)O)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	166775
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0004603] Organic oxygen compounds [CHEMONTID:0000323] Organooxygen compounds [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates [CHEMONTID:0000198] Oligosaccharides

*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
NPO7472	Litsea hypophaea	Species	Lauraceae	Eukaryota	roots	n.a.	n.a.	PMID[20384293]
NPO26622	Taraxacum officinale	Species	Asteraceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO26622	Taraxacum officinale	Species	Asteraceae	Eukaryota	Leaf	n.a.	n.a.	Database[FooDB]
NPO26622	Taraxacum officinale	Species	Asteraceae	Eukaryota	Plant	n.a.	n.a.	Database[FooDB]
NPO26622	Taraxacum officinale	Species	Asteraceae	Eukaryota	Root	n.a.	n.a.	Database[FooDB]
NPO26622	Taraxacum officinale	Species	Asteraceae	Eukaryota	n.a.	n.a.		Database[FooDB]
NPO1918	Magnolia kobus	Species	Magnoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO26785	Taraxacum mongolicum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO26622	Taraxacum officinale	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO30972	Morinda officinalis	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO26622	Taraxacum officinale	Species	Asteraceae	Eukaryota	n.a.	n.a.		Database[Phenol-Explorer]
NPO1918	Magnolia kobus	Species	Magnoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO26785	Taraxacum mongolicum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO26622	Taraxacum officinale	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO30972	Morinda officinalis	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO26785	Taraxacum mongolicum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO26622	Taraxacum officinale	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO26622	Taraxacum officinale	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO1596	Taraxacum borealisinense	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO1918	Magnolia kobus	Species	Magnoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO13668	Taraxacum platycarpum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO23327	Taraxacum coreanum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO26785	Taraxacum mongolicum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO26785	Taraxacum mongolicum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13668	Taraxacum platycarpum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1918	Magnolia kobus	Species	Magnoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23327	Taraxacum coreanum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7472	Litsea hypophaea	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26622	Taraxacum officinale	Species	Asteraceae	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

☑ 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 NPC200502 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	1103
0.1-0.2	12633
0.2-0.3	15616
0.3-0.4	9174
0.4-0.5	3304
0.5-0.6	733
0.6-0.7	87
0.7-0.8	40
0.8-0.85	5
0.85-0.9	2
0.9-0.95	0
0.95-1	0

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 NPC200502 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	1375
0.1-0.2	5578
0.2-0.3	1540
0.3-0.4	409
0.4-0.5	175
0.5-0.6	34
0.6-0.7	18
0.7-0.8	17
0.8-0.85	4
0.85-0.9	0
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