NPASS Compound

Structure

NPC260221 OpenBabel06302216142D 42 46 0 0 1 0 0 0 0 0999 V2000 5.1962 2.0000 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 6.0622 3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 2.0000 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 6.0622 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 -0.0000 0.0000 C 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 7.7942 -1.5000 0.0000 O 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 6.0622 -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 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 5.1962 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.7321 -1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8660 -1.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8660 -2.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.7321 -3.0000 0.0000 C 0 0 1 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 2.5981 -4.5000 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 0.0000 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8660 1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0000 2.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8660 1.5000 0.0000 C 0 0 1 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 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 0.0000 3.0000 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 3.4641 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 7.7942 3.5000 0.0000 O 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 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 4 1 0 0 0 0 3 42 1 0 0 0 0 4 5 2 0 0 0 0 4 41 1 0 0 0 0 5 6 1 0 0 0 0 6 7 1 0 0 0 0 7 17 1 0 0 0 0 7 8 2 0 0 0 0 8 9 1 0 0 0 0 9 10 2 0 0 0 0 9 11 1 0 0 0 0 11 16 2 0 0 0 0 11 12 1 0 0 0 0 12 13 2 0 0 0 0 12 40 1 0 0 0 0 13 14 1 0 0 0 0 14 15 2 0 0 0 0 14 39 1 0 0 0 0 15 16 1 0 0 0 0 15 18 1 0 0 0 0 16 17 1 0 0 0 0 19 18 1 6 0 0 0 19 20 1 0 0 0 0 19 26 1 0 0 0 0 20 21 1 0 0 0 0 20 29 1 1 0 0 0 21 22 1 0 0 0 0 21 28 1 6 0 0 0 22 23 1 0 0 0 0 22 27 1 1 0 0 0 23 24 1 6 0 0 0 23 26 1 0 0 0 0 24 25 1 0 0 0 0 30 29 1 6 0 0 0 30 31 1 0 0 0 0 30 35 1 0 0 0 0 31 32 1 0 0 0 0 31 38 1 1 0 0 0 32 33 1 0 0 0 0 32 37 1 6 0 0 0 33 34 1 0 0 0 0 33 36 1 1 0 0 0 34 35 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	596.14
Volume:	535.022
LogP:	-0.28
LogD:	-0.36
LogS:	-3.679
# Rotatable Bonds:	6
TPSA:	269.43
# H-Bond Aceptor:	16
# H-Bond Donor:	10
# Rings:	5
# Heavy Atoms:	16

MedChem Properties

QED Drug-Likeness Score:	0.137
Synthetic Accessibility Score:	4.778
Fsp3:	0.423
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	2
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.543
MDCK Permeability:	1.645844167796895e-05
Pgp-inhibitor:	0.014
Pgp-substrate:	0.995
Human Intestinal Absorption (HIA):	0.932
20% Bioavailability (F20%):	0.029
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.061
Plasma Protein Binding (PPB):	84.47045135498047%
Volume Distribution (VD):	0.661
Pgp-substrate:	17.298608779907227%

ADMET: Metabolism

CYP1A2-inhibitor:	0.065
CYP1A2-substrate:	0.035
CYP2C19-inhibitor:	0.016
CYP2C19-substrate:	0.046
CYP2C9-inhibitor:	0.008
CYP2C9-substrate:	0.067
CYP2D6-inhibitor:	0.009
CYP2D6-substrate:	0.131
CYP3A4-inhibitor:	0.018
CYP3A4-substrate:	0.005

ADMET: Excretion

Clearance (CL):	1.476
Half-life (T1/2):	0.825

ADMET: Toxicity

hERG Blockers:	0.388
Human Hepatotoxicity (H-HT):	0.147
Drug-inuced Liver Injury (DILI):	0.981
AMES Toxicity:	0.843
Rat Oral Acute Toxicity:	0.019
Maximum Recommended Daily Dose:	0.003
Skin Sensitization:	0.94
Carcinogencity:	0.083
Eye Corrosion:	0.003
Eye Irritation:	0.359
Respiratory Toxicity:	0.022

Download Data

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

Natural Product: NPC260221

Natural Product ID:	NPC260221
*Common Name:**	YWBYOKPVBQBJDO-JXYLQRTFSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	YWBYOKPVBQBJDO-JXYLQRTFSA-N
Standard InCHI:	InChI=1S/C26H28O16/c27-6-16-19(35)20(36)24(42-25-21(37)18(34)14(33)7-38-25)26(40-16)41-22-13(32)4-11(30)17-12(31)5-15(39-23(17)22)8-1-2-9(28)10(29)3-8/h1-5,14,16,18-21,24-30,32-37H,6-7H2/t14-,16-,18+,19-,20+,21-,24-,25+,26+/m1/s1
SMILES:	c1cc(c(cc1c1cc(=O)c2c(cc(c(c2o1)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O[C@H]1[C@@H]([C@H]([C@@H](CO1)O)O)O)O)O)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:0003540] Flavonoid-8-O-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
NPO16297	Gentiana arisanensis	Species	Gentianaceae	Eukaryota	Whole Plant	Yu Shieh, Chiayi Hsieh, Taiwan	1994-APR	PMID[9287421]
NPO12948	Solanum dulcamara	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO12948	Solanum dulcamara	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12948	Solanum dulcamara	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO16297	Gentiana arisanensis	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15721	Derris reticulata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16918	Ballota lanata	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18413	Eucalyptus ovata	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12948	Solanum dulcamara	Species	Solanaceae	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 NPC260221 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	496
0.1-0.2	1967
0.2-0.3	4611
0.3-0.4	10220
0.4-0.5	7811
0.5-0.6	4567
0.6-0.7	5717
0.7-0.8	4788
0.8-0.85	1442
0.85-0.9	558
0.9-0.95	408
0.95-1	112

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 NPC260221 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	426
0.1-0.2	987
0.2-0.3	2104
0.3-0.4	2728
0.4-0.5	1756
0.5-0.6	776
0.6-0.7	247
0.7-0.8	94
0.8-0.85	18
0.85-0.9	6
0.9-0.95	3
0.95-1	5

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