NPASS Compound

Structure

NPC16050 OpenBabel06302215272D 36 39 0 0 1 0 0 0 0 0999 V2000 4.3301 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -0.5000 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 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 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 O 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 1.7321 3.0000 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 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 0.0000 -3.0000 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 -0.8660 -0.5000 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 -2.5981 -0.5000 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 -1.7321 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -3.0000 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 -3.4641 -3.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.3301 -3.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.1962 -3.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.1962 -2.0000 0.0000 C 0 0 1 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 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 -3.5000 0.0000 O 0 0 0 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 -2.5981 -3.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 0.0000 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 1.7321 -2.0000 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 8 2 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 5 12 1 0 0 0 0 6 7 2 0 0 0 0 7 8 1 0 0 0 0 7 10 1 0 0 0 0 8 9 1 0 0 0 0 10 11 1 0 0 0 0 12 35 1 0 0 0 0 12 13 2 0 0 0 0 13 14 1 0 0 0 0 13 36 1 0 0 0 0 14 15 2 0 0 0 0 14 16 1 0 0 0 0 16 21 2 0 0 0 0 16 17 1 0 0 0 0 17 18 2 0 0 0 0 17 35 1 0 0 0 0 18 19 1 0 0 0 0 19 20 2 0 0 0 0 19 34 1 0 0 0 0 20 21 1 0 0 0 0 21 22 1 0 0 0 0 23 20 1 1 0 0 0 23 24 1 0 0 0 0 23 30 1 0 0 0 0 24 25 1 0 0 0 0 24 33 1 6 0 0 0 25 26 1 0 0 0 0 25 32 1 1 0 0 0 26 27 1 0 0 0 0 26 31 1 6 0 0 0 27 28 1 1 0 0 0 27 30 1 0 0 0 0 28 29 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	332.2
Volume:	347.502
LogP:	4.451
LogD:	3.748
LogS:	-4.65
# Rotatable Bonds:	3
TPSA:	52.6
# H-Bond Aceptor:	4
# H-Bond Donor:	0
# Rings:	4
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.74
Synthetic Accessibility Score:	5.172
Fsp3:	0.8
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
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:	-4.983
MDCK Permeability:	2.7811556719825603e-05
Pgp-inhibitor:	0.943
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.003
20% Bioavailability (F20%):	0.991
30% Bioavailability (F30%):	0.989

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.059
Plasma Protein Binding (PPB):	88.28006744384766%
Volume Distribution (VD):	0.428
Pgp-substrate:	6.86791467666626%

ADMET: Metabolism

CYP1A2-inhibitor:	0.331
CYP1A2-substrate:	0.232
CYP2C19-inhibitor:	0.406
CYP2C19-substrate:	0.55
CYP2C9-inhibitor:	0.098
CYP2C9-substrate:	0.055
CYP2D6-inhibitor:	0.325
CYP2D6-substrate:	0.164
CYP3A4-inhibitor:	0.877
CYP3A4-substrate:	0.333

ADMET: Excretion

Clearance (CL):	18.006
Half-life (T1/2):	0.341

ADMET: Toxicity

hERG Blockers:	0.396
Human Hepatotoxicity (H-HT):	0.512
Drug-inuced Liver Injury (DILI):	0.131
AMES Toxicity:	0.108
Rat Oral Acute Toxicity:	0.034
Maximum Recommended Daily Dose:	0.927
Skin Sensitization:	0.948
Carcinogencity:	0.542
Eye Corrosion:	0.12
Eye Irritation:	0.248
Respiratory Toxicity:	0.946

Download Data

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

Natural Product: NPC16050

Natural Product ID:	NPC16050
*Common Name:**	MYNFZWCOUVQEMY-WGZQPDPOSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	MYNFZWCOUVQEMY-WGZQPDPOSA-N
Standard InCHI:	InChI=1S/C23H24O13/c1-33-10-3-7(4-11(34-2)15(10)26)22-20(31)18(29)14-9(35-22)5-8(25)13(17(14)28)23-21(32)19(30)16(27)12(6-24)36-23/h3-5,12,16,19,21,23-28,30-32H,6H2,1-2H3/t12-,16-,19+,21-,23+/m1/s1
SMILES:	COc1cc(cc(c1O)OC)c1c(c(=O)c2c(cc(c(c2O)[C@H]2[C@@H]([C@H]([C@@H]([C@@H](CO)O2)O)O)O)O)o1)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	101713180
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0001111] Flavonoid glycosides [CHEMONTID:0001737] Flavonoid 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
NPO453	Teucrium marum	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15763383]
NPO12927	Astragalus bicuspis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18771242]
NPO10684	Parameria laevigata	Species	Apocynaceae	Eukaryota	n.a.	bark	n.a.	PMID[21875098]
NPO14098	Styrax agrestis	Species	Styracaceae	Eukaryota	n.a.	ripe fruit	n.a.	PMID[21939219]
NPO14098	Styrax agrestis	Species	Styracaceae	Eukaryota	fruits	Thua Thien, Hue district, Vietnam	n.a.	PMID[21939219]
NPO7255	Pterocarpus indicus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO453	Teucrium marum	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO10684	Parameria laevigata	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO10684	Parameria laevigata	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO453	Teucrium marum	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO14686	Justicia adhatoda	Species	Acanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO7255	Pterocarpus indicus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO14098	Styrax agrestis	Species	Styracaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10684	Parameria laevigata	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6748	Strongylodesma algoaensis	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO11574	Usnea canariensis	Species	Parmeliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12927	Astragalus bicuspis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10059	Hyoscyamus pusillus	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14686	Justicia adhatoda	Species	Acanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7255	Pterocarpus indicus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8380	Hibiscus schizopetalus	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7995	Tolypocladium album	Species	Ophiocordycipitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11386	Chelonaplysilla violacea	Species	Darwinellidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8612	Flemingia macrophylla	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25132	[clostridium] cellulolyticum	Species	Ruminococcaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO17134	Amietophrynus regularis	Species	Bufonidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO453	Teucrium marum	Species	Lamiaceae	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 NPC16050 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	440
0.1-0.2	1685
0.2-0.3	3842
0.3-0.4	9682
0.4-0.5	8733
0.5-0.6	4019
0.6-0.7	5017
0.7-0.8	4921
0.8-0.85	2165
0.85-0.9	1505
0.9-0.95	674
0.95-1	14

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 NPC16050 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	392
0.1-0.2	927
0.2-0.3	1859
0.3-0.4	2659
0.4-0.5	1837
0.5-0.6	936
0.6-0.7	360
0.7-0.8	129
0.8-0.85	22
0.85-0.9	22
0.9-0.95	7
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