NPASS Compound

Structure

NPC242834 OpenBabel06302216132D 24 27 0 0 1 0 0 0 0 0999 V2000 2.5208 -0.7486 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8879 0.1484 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8482 0.2789 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2947 0.9148 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.6833 1.6926 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3175 2.4814 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9327 3.2302 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.4727 2.6871 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7851 2.1549 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7725 1.2856 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.4443 0.7336 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0126 0.8694 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.7464 1.3076 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.5062 0.8914 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.2649 1.3296 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2523 2.1990 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.9095 2.8755 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7338 2.1770 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0374 2.5784 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0541 3.5214 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.1954 2.2127 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.5189 0.0220 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6572 -0.6765 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 0 0 0 2 3 1 0 0 0 0 4 2 1 6 0 0 0 4 5 1 0 0 0 0 4 11 1 0 0 0 0 5 6 1 0 0 0 0 6 7 2 0 0 0 0 6 8 1 0 0 0 0 8 9 2 0 0 0 0 9 19 1 0 0 0 0 9 10 1 0 0 0 0 10 11 1 1 0 0 0 10 12 1 0 0 0 0 12 13 1 0 0 0 0 12 23 1 0 0 0 0 13 14 1 0 0 0 0 13 18 1 0 0 0 0 14 15 1 0 0 0 0 14 22 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 6 0 0 0 16 18 1 0 0 0 0 16 21 1 0 0 0 0 18 19 1 0 0 0 0 19 20 2 0 0 0 0 22 23 1 0 0 0 0 23 24 2 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	330.15
Volume:	333.723
LogP:	1.733
LogD:	1.409
LogS:	-3.193
# Rotatable Bonds:	1
TPSA:	86.99
# H-Bond Aceptor:	5
# H-Bond Donor:	3
# Rings:	4
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.543
Synthetic Accessibility Score:	4.983
Fsp3:	0.526
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:	-5.732
MDCK Permeability:	7.5706343523052055e-06
Pgp-inhibitor:	0.301
Pgp-substrate:	0.997
Human Intestinal Absorption (HIA):	0.278
20% Bioavailability (F20%):	0.933
30% Bioavailability (F30%):	0.025

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.375
Plasma Protein Binding (PPB):	61.78968811035156%
Volume Distribution (VD):	1.896
Pgp-substrate:	38.33916473388672%

ADMET: Metabolism

CYP1A2-inhibitor:	0.018
CYP1A2-substrate:	0.395
CYP2C19-inhibitor:	0.019
CYP2C19-substrate:	0.807
CYP2C9-inhibitor:	0.023
CYP2C9-substrate:	0.909
CYP2D6-inhibitor:	0.003
CYP2D6-substrate:	0.213
CYP3A4-inhibitor:	0.034
CYP3A4-substrate:	0.249

ADMET: Excretion

Clearance (CL):	2.546
Half-life (T1/2):	0.729

ADMET: Toxicity

hERG Blockers:	0.016
Human Hepatotoxicity (H-HT):	0.305
Drug-inuced Liver Injury (DILI):	0.434
AMES Toxicity:	0.312
Rat Oral Acute Toxicity:	0.876
Maximum Recommended Daily Dose:	0.951
Skin Sensitization:	0.294
Carcinogencity:	0.101
Eye Corrosion:	0.003
Eye Irritation:	0.015
Respiratory Toxicity:	0.79

Download Data

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

Natural Product: NPC242834

Natural Product ID:	NPC242834
*Common Name:**	NBNQTBIRANPTTL-PWENJLEFSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	NBNQTBIRANPTTL-PWENJLEFSA-N
Standard InCHI:	InChI=1S/C19H22O5/c1-8(2)9-4-10(20)6-12-11(5-9)14-15-13(24-18(14)22)7-19(3,23)16(15)17(12)21/h6,9,11,13-16,23H,1,4-5,7H2,2-3H3/t9-,11+,13-,14+,15+,16+,19+/m0/s1
SMILES:	C=C(C)[C@H]1CC(=O)C=C2[C@@H](C1)[C@@H]1[C@H]3[C@H](C[C@](C)([C@H]3C2=O)O)OC1=O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	101222669
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001283] Terpene lactones

*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
NPO20598	Lythrum salicaria	Species	Lythraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24459770]
NPO20598	Lythrum salicaria	Species	Lythraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO12662	Torilis japonica	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO20598	Lythrum salicaria	Species	Lythraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13208	Discaria americana	Species	Rhamnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12662	Torilis japonica	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO20598	Lythrum salicaria	Species	Lythraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO12662	Torilis japonica	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO20598	Lythrum salicaria	Species	Lythraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12662	Torilis japonica	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12403	Microdesmis keayana	Species	Pandaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14537	Manfreda tigrina	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16342	Schizanthus hookeri	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16157	Chaetomium amygdalisporum	Species	Chaetomiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25180	Sargassum fluitans	Species	Sargassaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3101	Primula deorum	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15747	Ryania speciosa	Species	Salicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15633	Maasella edwardsi	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO13208	Discaria americana	Species	Rhamnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14023	Cicer judaicum	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7354	Aralia bipinnata	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16505	Angelica komarovii	Species	Apiaceae	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 NPC242834 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	215
0.1-0.2	1391
0.2-0.3	5818
0.3-0.4	10753
0.4-0.5	11150
0.5-0.6	7376
0.6-0.7	5221
0.7-0.8	757
0.8-0.85	15
0.85-0.9	1
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 NPC242834 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	179
0.1-0.2	1890
0.2-0.3	4129
0.3-0.4	1978
0.4-0.5	540
0.5-0.6	210
0.6-0.7	167
0.7-0.8	57
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