NPASS Compound

Structure

NPC246086 OpenBabel06302215282D 27 29 0 0 1 0 0 0 0 0999 V2000 -0.8660 -3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -1.5000 0.0000 C 0 0 0 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 -1.7321 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.5981 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -0.5000 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 3.4641 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 -2.0000 0.0000 O 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 0.8660 -0.5000 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 -0.8660 2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -3.5000 0.0000 C 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 2 27 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 5 24 2 0 0 0 0 5 6 1 0 0 0 0 6 7 2 0 0 0 0 6 26 1 0 0 0 0 7 8 1 0 0 0 0 7 9 1 0 0 0 0 9 10 2 0 0 0 0 9 25 1 0 0 0 0 10 24 1 0 0 0 0 10 11 1 0 0 0 0 11 12 2 0 0 0 0 11 13 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 1 0 0 0 14 23 1 0 0 0 0 15 20 2 0 0 0 0 15 16 1 0 0 0 0 16 17 2 0 0 0 0 17 18 1 0 0 0 0 18 19 2 0 0 0 0 18 21 1 0 0 0 0 19 20 1 0 0 0 0 21 22 1 0 0 0 0 23 24 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	368.16
Volume:	386.258
LogP:	5.568
LogD:	3.265
LogS:	-3.863
# Rotatable Bonds:	4
TPSA:	75.99
# H-Bond Aceptor:	5
# H-Bond Donor:	2
# Rings:	3
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.77
Synthetic Accessibility Score:	3.168
Fsp3:	0.318
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.715
MDCK Permeability:	1.5029639143904205e-05
Pgp-inhibitor:	0.277
Pgp-substrate:	0.012
Human Intestinal Absorption (HIA):	0.007
20% Bioavailability (F20%):	0.004
30% Bioavailability (F30%):	0.004

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.044
Plasma Protein Binding (PPB):	95.97759246826172%
Volume Distribution (VD):	0.746
Pgp-substrate:	6.167635440826416%

ADMET: Metabolism

CYP1A2-inhibitor:	0.262
CYP1A2-substrate:	0.933
CYP2C19-inhibitor:	0.952
CYP2C19-substrate:	0.507
CYP2C9-inhibitor:	0.927
CYP2C9-substrate:	0.947
CYP2D6-inhibitor:	0.553
CYP2D6-substrate:	0.755
CYP3A4-inhibitor:	0.399
CYP3A4-substrate:	0.28

ADMET: Excretion

Clearance (CL):	13.581
Half-life (T1/2):	0.08

ADMET: Toxicity

hERG Blockers:	0.04
Human Hepatotoxicity (H-HT):	0.717
Drug-inuced Liver Injury (DILI):	0.84
AMES Toxicity:	0.026
Rat Oral Acute Toxicity:	0.865
Maximum Recommended Daily Dose:	0.2
Skin Sensitization:	0.919
Carcinogencity:	0.168
Eye Corrosion:	0.003
Eye Irritation:	0.388
Respiratory Toxicity:	0.903

Download Data

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

Natural Product: NPC246086

Natural Product ID:	NPC246086
*Common Name:**	LLJWVWIUMYXGDE-SFHVURJKSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	LLJWVWIUMYXGDE-SFHVURJKSA-N
Standard InCHI:	InChI=1S/C22H24O5/c1-12(2)5-10-16-20(24)13(3)21(25)19-17(23)11-18(27-22(16)19)14-6-8-15(26-4)9-7-14/h5-9,18,24-25H,10-11H2,1-4H3/t18-/m0/s1
SMILES:	CC(=CCc1c(c(C)c(c2C(=O)C[C@@H](c3ccc(cc3)OC)Oc12)O)O)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	16099396
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0000337] Flavans [CHEMONTID:0003642] 8-prenylated flavans [CHEMONTID:0003508] 8-prenylated flavanones

*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
NPO27636	Hippasteria phrygiana	Species	Goniasteridae	Eukaryota	n.a.	pacific	n.a.	PMID[16252922]
NPO27230	Eysenhardtia platycarpa	Species	Fabaceae	Eukaryota	n.a.	branch	n.a.	PMID[17190443]
NPO27230	Eysenhardtia platycarpa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[17190443]
NPO27449	Halichondria okadai	Species	Halichondriidae	Eukaryota	n.a.	n.a.	n.a.	PMID[21410164]
NPO27837	Sarracenia flava	Species	Sarraceniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO27837	Sarracenia flava	Species	Sarraceniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27837	Sarracenia flava	Species	Sarraceniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO9137	Tasmannia lanceolata	Species	Winteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27449	Halichondria okadai	Species	Halichondriidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27709	Rhododendron maximum	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27211	Adenocarpus hispanicus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27651	Cissus tricuspidata	Species	Vitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27173	Ramalina pollinaria	Species	Ramalinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27194	Conger myriaster	Species	Congridae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29258	Virola oleifera	Species	Myristicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27594	Viola odorata	Species	Violaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6740	Amycolatopsis sulphurea	Species	Pseudonocardiaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO27837	Sarracenia flava	Species	Sarraceniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27340	Campylopus clavatus	Species	Leucobryaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27636	Hippasteria phrygiana	Species	Goniasteridae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27411	Liparis nakaharai	Species	Liparidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27131	Methylosinus trichosporium	Species	Methylocystaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO27756	Lepidiota negatoria	Species	Scarabaeidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27230	Eysenhardtia platycarpa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27074	Dermocybe semisanguinea	Species	Cortinariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27794	Acritopappus longifolius	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 NPC246086 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	350
0.1-0.2	1454
0.2-0.3	3681
0.3-0.4	9820
0.4-0.5	8702
0.5-0.6	3513
0.6-0.7	5611
0.7-0.8	5283
0.8-0.85	2190
0.85-0.9	1239
0.9-0.95	596
0.95-1	258

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 NPC246086 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	311
0.1-0.2	923
0.2-0.3	1499
0.3-0.4	2541
0.4-0.5	1943
0.5-0.6	1196
0.6-0.7	504
0.7-0.8	163
0.8-0.85	45
0.85-0.9	16
0.9-0.95	6
0.95-1	3

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