NPASS Compound

Structure

NPC222418 OpenBabel06302215392D 28 30 0 0 1 0 0 0 0 0999 V2000 -4.8656 -3.1012 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1225 -2.4321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1714 -2.7411 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9635 -3.7193 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4283 -2.0720 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4772 -2.3810 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.6362 -1.0938 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.8930 -0.4247 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.3578 -0.7337 0.0000 C 0 0 0 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 -0.1878 -1.5008 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6092 -0.1691 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.4013 0.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4067 0.9135 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.9420 1.2226 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5566 1.1580 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0159 0.7444 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.1444 0.1399 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.7591 0.0753 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2591 -0.7907 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0104 0.6399 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9886 0.8478 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5511 1.0534 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.7341 2.2007 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2170 2.5097 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.4388 1.4474 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 -2.5227 -0.5759 0.0000 O 0 0 0 0 0 0 0 0 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 5 1 0 0 0 0 5 6 2 0 0 0 0 5 7 1 0 0 0 0 8 7 1 1 0 0 0 8 9 1 0 0 0 0 8 18 1 0 0 0 0 9 10 1 0 0 0 0 10 27 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 28 1 1 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 14 26 1 1 0 0 0 14 27 1 0 0 0 0 15 16 2 0 0 0 0 15 24 1 0 0 0 0 17 16 1 1 0 0 0 17 18 1 0 0 0 0 17 23 1 0 0 0 0 18 19 1 1 0 0 0 19 20 2 0 0 0 0 19 21 1 0 0 0 0 21 22 2 0 0 0 0 21 23 1 0 0 0 0 24 25 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	394.16
Volume:	385.946
LogP:	0.809
LogD:	0.718
LogS:	-2.201
# Rotatable Bonds:	4
TPSA:	122.52
# H-Bond Aceptor:	8
# H-Bond Donor:	3
# Rings:	3
# Heavy Atoms:	8

MedChem Properties

QED Drug-Likeness Score:	0.36
Synthetic Accessibility Score:	6.238
Fsp3:	0.6
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
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:	-5.026
MDCK Permeability:	4.488365084398538e-05
Pgp-inhibitor:	0.08
Pgp-substrate:	0.002
Human Intestinal Absorption (HIA):	0.795
20% Bioavailability (F20%):	0.302
30% Bioavailability (F30%):	0.991

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.531
Plasma Protein Binding (PPB):	28.434040069580078%
Volume Distribution (VD):	1.004
Pgp-substrate:	45.83579635620117%

ADMET: Metabolism

CYP1A2-inhibitor:	0.034
CYP1A2-substrate:	0.274
CYP2C19-inhibitor:	0.095
CYP2C19-substrate:	0.716
CYP2C9-inhibitor:	0.106
CYP2C9-substrate:	0.041
CYP2D6-inhibitor:	0.006
CYP2D6-substrate:	0.068
CYP3A4-inhibitor:	0.518
CYP3A4-substrate:	0.612

ADMET: Excretion

Clearance (CL):	5.975
Half-life (T1/2):	0.871

ADMET: Toxicity

hERG Blockers:	0.022
Human Hepatotoxicity (H-HT):	0.457
Drug-inuced Liver Injury (DILI):	0.941
AMES Toxicity:	0.678
Rat Oral Acute Toxicity:	0.966
Maximum Recommended Daily Dose:	0.945
Skin Sensitization:	0.741
Carcinogencity:	0.663
Eye Corrosion:	0.018
Eye Irritation:	0.178
Respiratory Toxicity:	0.951

Download Data

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

Natural Product: NPC222418

Natural Product ID:	NPC222418
*Common Name:**	LJFIVFJQZWRSAJ-WHFCBKTFSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	LJFIVFJQZWRSAJ-WHFCBKTFSA-N
Standard InCHI:	InChI=1S/C20H26O8/c1-5-10(2)17(23)27-14-7-19(4)15(22)8-20(25,28-19)12(9-21)6-13-16(14)11(3)18(24)26-13/h5-6,13-16,21-22,25H,3,7-9H2,1-2,4H3/b10-5-,12-6-/t13-,14+,15-,16-,19+,20+/m0/s1
SMILES:	C/C=C(/C)C(=O)O[C@@H]1C[C@]2(C)[C@H](C[C@@](/C(=C[C@H]3[C@@H]1C(=C)C(=O)O3)/CO)(O)O2)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

*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
NPO19629	Laurencia scoparia	Species	Rhodomelaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11754610]
NPO11074	Mycale izuensis	Species	Mycalidae	Eukaryota	n.a.	n.a.	n.a.	PMID[12088446]
NPO18159	Crypteronia paniculata	Species	Crypteroniaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12502343]
NPO18159	Crypteronia paniculata	Species	Crypteroniaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15787463]
NPO19629	Laurencia scoparia	Species	Rhodomelaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16872159]
NPO15112	Premna oligotricha	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8450316]
NPO17110	Barleria prionitis	Species	Acanthaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9784173]
NPO17989	Astragalus falcatus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO17989	Astragalus falcatus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO19629	Laurencia scoparia	Species	Rhodomelaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17110	Barleria prionitis	Species	Acanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11074	Mycale izuensis	Species	Mycalidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19081	Iris halophila	Species	Iridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18159	Crypteronia paniculata	Species	Crypteroniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19007	Lycopodium fastigiatum	Species	Lycopodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17486	Alpinia javanica	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18837	Ulva rigida	Species	Ulvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23391	Nidula niveotomentosa	Species	Nidulariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17989	Astragalus falcatus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15112	Premna oligotricha	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19433	Trichocline caulescens	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9841	Picramnia hirsuta	Species	Picramniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16972	Penicillium spiculisporum	Species	Aspergillaceae	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 NPC222418 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	231
0.1-0.2	1213
0.2-0.3	4643
0.3-0.4	9267
0.4-0.5	13993
0.5-0.6	7773
0.6-0.7	4284
0.7-0.8	1077
0.8-0.85	192
0.85-0.9	19
0.9-0.95	3
0.95-1	2

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 NPC222418 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	213
0.1-0.2	1871
0.2-0.3	3710
0.3-0.4	2259
0.4-0.5	724
0.5-0.6	281
0.6-0.7	76
0.7-0.8	15
0.8-0.85	1
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