NPASS Compound

Structure

NPC293680 OpenBabel06302215502D 21 23 0 0 1 0 0 0 0 0999 V2000 -0.1972 -3.2704 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7971 -2.4703 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7782 -2.6635 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5410 -2.0169 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.5111 -1.0174 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.3288 -0.4417 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.2752 -0.7650 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0341 0.5138 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6339 1.3140 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.0342 0.5288 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7110 -0.4175 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.7431 -0.6691 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.3364 -1.5827 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.6581 -1.4781 0.0000 C 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 0.0000 0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.4067 0.9135 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4013 1.0181 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.5878 0.8090 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7796 -0.0933 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4546 -2.4237 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 0 0 0 2 13 1 0 0 0 0 2 3 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 4 21 1 6 0 0 0 5 6 1 0 0 0 0 5 11 1 0 0 0 0 6 7 1 0 0 0 0 6 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 12 1 0 0 0 0 12 13 1 0 0 0 0 12 16 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 15 20 1 0 0 0 0 16 17 1 0 0 0 0 16 19 1 0 0 0 0 17 18 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	298.14
Volume:	289.795
LogP:	0.282
LogD:	0.547
LogS:	-1.734
# Rotatable Bonds:	1
TPSA:	107.22
# H-Bond Aceptor:	6
# H-Bond Donor:	4
# Rings:	3
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.373
Synthetic Accessibility Score:	4.996
Fsp3:	0.8
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.43
MDCK Permeability:	0.00013078174379188567
Pgp-inhibitor:	0.0
Pgp-substrate:	0.428
Human Intestinal Absorption (HIA):	0.299
20% Bioavailability (F20%):	0.068
30% Bioavailability (F30%):	0.623

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.339
Plasma Protein Binding (PPB):	38.446685791015625%
Volume Distribution (VD):	0.424
Pgp-substrate:	63.45872116088867%

ADMET: Metabolism

CYP1A2-inhibitor:	0.027
CYP1A2-substrate:	0.087
CYP2C19-inhibitor:	0.008
CYP2C19-substrate:	0.229
CYP2C9-inhibitor:	0.002
CYP2C9-substrate:	0.054
CYP2D6-inhibitor:	0.002
CYP2D6-substrate:	0.113
CYP3A4-inhibitor:	0.013
CYP3A4-substrate:	0.121

ADMET: Excretion

Clearance (CL):	4.281
Half-life (T1/2):	0.811

ADMET: Toxicity

hERG Blockers:	0.064
Human Hepatotoxicity (H-HT):	0.584
Drug-inuced Liver Injury (DILI):	0.117
AMES Toxicity:	0.021
Rat Oral Acute Toxicity:	0.794
Maximum Recommended Daily Dose:	0.343
Skin Sensitization:	0.17
Carcinogencity:	0.07
Eye Corrosion:	0.009
Eye Irritation:	0.06
Respiratory Toxicity:	0.875

Download Data

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

Natural Product: NPC293680

Natural Product ID:	NPC293680
*Common Name:**	QHLGSXMDHZRASG-KMPCWKQASA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	QHLGSXMDHZRASG-KMPCWKQASA-N
Standard InCHI:	InChI=1S/C15H22O6/c1-6-3-9(17)11-7(2)14(19)21-13(11)12-8(6)4-10(18)15(12,20)5-16/h7-13,16-18,20H,1,3-5H2,2H3/t7-,8+,9+,10+,11-,12+,13+,15-/m1/s1
SMILES:	C=C1C[C@@H]([C@H]2[C@@H](C)C(=O)O[C@@H]2[C@@H]2[C@H]1C[C@@H]([C@@]2(CO)O)O)O
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:0001770] Guaianolides 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
NPO10471	Scorzonera radiata	Species	Asteraceae	Eukaryota	n.a.	Mongolian	n.a.	PMID[19271716]
NPO9427	Lemna minor	Species	Araceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO21021	Hemisteptia lyrata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9427	Lemna minor	Species	Araceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4480	Phlojodicarpus villosus	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9427	Lemna minor	Species	Araceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11433	Candelaria concolor	Species	Candelariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10193	Agave tequilana	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11001	Ceanothus papillosus	Species	Rhamnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5142	Garcinia pedunculata	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6394	Shorea robusta	Species	Dipterocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21021	Hemisteptia lyrata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO750	Emericellopsis salmosynnemata	Species	n.a.	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10471	Scorzonera radiata	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 NPC293680 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	250
0.1-0.2	1960
0.2-0.3	7219
0.3-0.4	15990
0.4-0.5	7850
0.5-0.6	6967
0.6-0.7	2089
0.7-0.8	274
0.8-0.85	66
0.85-0.9	25
0.9-0.95	6
0.95-1	1

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 NPC293680 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	293
0.1-0.2	2791
0.2-0.3	3856
0.3-0.4	1462
0.4-0.5	450
0.5-0.6	248
0.6-0.7	44
0.7-0.8	6
0.8-0.85	0
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