NPASS Compound

Structure

NPC64957 OpenBabel06302216092D 25 27 0 0 1 0 0 0 0 0999 V2000 -0.8653 -4.3828 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2985 -3.6026 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6907 -2.7217 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.6497 -2.6209 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1239 -1.9416 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5161 -1.0607 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8351 -2.0424 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.4019 -1.2623 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.3190 -1.5602 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2361 -1.2623 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8029 -0.4821 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7200 -0.7801 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8029 0.4821 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2361 1.2623 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3190 1.5602 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.3190 2.5245 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0991 3.0913 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4019 2.8225 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1039 3.7396 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8351 2.0424 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.4019 1.2623 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8351 0.4821 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8351 -0.4821 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.5555 -2.2711 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 2 1 0 0 0 0 2 3 1 0 0 0 0 3 4 1 1 0 0 0 3 5 1 0 0 0 0 5 6 2 0 0 0 0 5 7 1 0 0 0 0 8 7 1 6 0 0 0 8 9 1 0 0 0 0 8 23 1 0 0 0 0 9 10 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 15 14 1 6 0 0 0 15 16 1 0 0 0 0 15 21 1 0 0 0 0 16 17 2 0 0 0 0 16 18 1 0 0 0 0 18 19 2 0 0 0 0 18 20 1 0 0 0 0 21 20 1 1 0 0 0 21 22 1 0 0 0 0 22 23 1 0 0 0 0 22 25 1 1 0 0 0 23 24 1 6 0 0 0 23 25 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	348.19
Volume:	362.212
LogP:	3.858
LogD:	3.323
LogS:	-4.318
# Rotatable Bonds:	4
TPSA:	65.13
# H-Bond Aceptor:	5
# H-Bond Donor:	0
# Rings:	3
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.339
Synthetic Accessibility Score:	4.989
Fsp3:	0.7
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Accepted
BMS Rule:	2
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.655
MDCK Permeability:	2.4715322069823742e-05
Pgp-inhibitor:	0.165
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.011
20% Bioavailability (F20%):	0.21
30% Bioavailability (F30%):	0.972

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.62
Plasma Protein Binding (PPB):	85.9678726196289%
Volume Distribution (VD):	1.151
Pgp-substrate:	19.524234771728516%

ADMET: Metabolism

CYP1A2-inhibitor:	0.419
CYP1A2-substrate:	0.101
CYP2C19-inhibitor:	0.152
CYP2C19-substrate:	0.245
CYP2C9-inhibitor:	0.262
CYP2C9-substrate:	0.056
CYP2D6-inhibitor:	0.095
CYP2D6-substrate:	0.12
CYP3A4-inhibitor:	0.677
CYP3A4-substrate:	0.27

ADMET: Excretion

Clearance (CL):	10.239
Half-life (T1/2):	0.139

ADMET: Toxicity

hERG Blockers:	0.062
Human Hepatotoxicity (H-HT):	0.804
Drug-inuced Liver Injury (DILI):	0.494
AMES Toxicity:	0.066
Rat Oral Acute Toxicity:	0.825
Maximum Recommended Daily Dose:	0.826
Skin Sensitization:	0.862
Carcinogencity:	0.271
Eye Corrosion:	0.773
Eye Irritation:	0.282
Respiratory Toxicity:	0.981

Download Data

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

Natural Product: NPC64957

Natural Product ID:	NPC64957
*Common Name:**	QPBIVEZQZLZRFV-SMAIBGKXSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	QPBIVEZQZLZRFV-SMAIBGKXSA-N
Standard InCHI:	InChI=1S/C20H28O5/c1-6-12(3)18(21)23-15-10-8-11(2)7-9-14-13(4)19(22)24-16(14)17-20(15,5)25-17/h8,12,14-17H,4,6-7,9-10H2,1-3,5H3/b11-8+/t12-,14+,15+,16+,17+,20-/m1/s1
SMILES:	CC[C@@H](C)C(=O)O[C@H]1C/C=C(C)/CC[C@H]2C(=C)C(=O)O[C@@H]2[C@H]2[C@]1(C)O2
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001283] Terpene lactones [CHEMONTID:0001543] Sesquiterpene lactones [CHEMONTID:0001771] Germacranolides and derivatives

*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
NPO20112	Syncephalastrum racemosum	Species	Syncephalastraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18558746]
NPO13906	Ficus mucuso	Species	Moraceae	Eukaryota	figs	Tongolo-Yaound, in the Central Region of Cameroon	2008-JUN	PMID[21619045]
NPO13906	Ficus mucuso	Species	Moraceae	Eukaryota	n.a.	fruit	n.a.	PMID[21619045]
NPO17503	Conospermum incurvum	Species	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[7853001]
NPO12730	Heracleum maximum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO18782.1	Pulsatilla cernua var. koreana	Varieties	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO19749	Carpolobia glabrescens	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18782.1	Pulsatilla cernua var. koreana	Varieties	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17503	Conospermum incurvum	Species	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO20469	Acer caesium	Species	Aceraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3030	Chaenorhinum villosum	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21134	Thaumetopoea pityocampa	Species	0todontidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12730	Heracleum maximum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18806	Neodilsea yendoana	Species	Dumontiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20044	Schistostephium crataegifolium	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21224	Rubus pinfaensis	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16895	Croton sarcopetalus	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19608	Aconitum likiangense	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20925	Fusarium culmorum	Species	Nectriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19874	Polygonatum glaberrimum	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21000	Elysia halimedae	Species	Placobranchidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21419	Biscogniauxia mediterranea	Species	Xylariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13906	Ficus mucuso	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21612	Anthelia glauca	Species	Xeniidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1550	Talaromyces purpureogenus	Species	Trichocomaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17763	Lobularia elongata	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7765	Quercus spicata	Species	Fagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20662	Epinephelus drummondhayi	Species	Serranidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20112	Syncephalastrum racemosum	Species	Syncephalastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21673	Lupinus caudatus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21540	Naucleopsis stipularis	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13003	Sogatella furcifera	Species	Delphacidae	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 NPC64957 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	239
0.1-0.2	1556
0.2-0.3	5706
0.3-0.4	12471
0.4-0.5	11920
0.5-0.6	6971
0.6-0.7	2817
0.7-0.8	841
0.8-0.85	84
0.85-0.9	55
0.9-0.95	20
0.95-1	17

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 NPC64957 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	218
0.1-0.2	2163
0.2-0.3	3920
0.3-0.4	1958
0.4-0.5	591
0.5-0.6	250
0.6-0.7	44
0.7-0.8	4
0.8-0.85	1
0.85-0.9	0
0.9-0.95	0
0.95-1	1

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