NPASS Compound

Structure

NPC271445 OpenBabel06302215432D 27 28 0 0 1 0 0 0 0 0999 V2000 6.0622 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 -1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 -1.0000 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 -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 2.5981 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -1.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.7321 -0.0000 0.0000 C 0 0 2 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 4.4641 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9641 0.8660 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 0.8660 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8660 -1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7321 -1.0000 0.0000 C 0 0 2 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 -0.8660 0.5000 0.0000 C 0 0 1 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 -1.7321 2.0000 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 -2.5981 0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -1.5000 0.0000 O 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 2 1 0 0 0 0 2 3 2 0 0 0 0 2 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 6 12 1 0 0 0 0 6 7 2 0 0 0 0 7 8 1 0 0 0 0 7 9 1 0 0 0 0 9 10 1 0 0 0 0 9 16 1 1 0 0 0 10 11 1 0 0 0 0 10 15 1 1 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 12 14 1 0 0 0 0 17 16 1 1 0 0 0 17 18 1 0 0 0 0 17 24 1 0 0 0 0 18 19 1 0 0 0 0 18 27 1 6 0 0 0 19 20 1 0 0 0 0 19 26 1 1 0 0 0 20 21 1 0 0 0 0 20 25 1 6 0 0 0 21 22 1 1 0 0 0 21 24 1 0 0 0 0 22 23 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	386.19
Volume:	382.48
LogP:	0.13
LogD:	0.119
LogS:	-1.421
# Rotatable Bonds:	5
TPSA:	136.68
# H-Bond Aceptor:	8
# H-Bond Donor:	5
# Rings:	2
# Heavy Atoms:	8

MedChem Properties

QED Drug-Likeness Score:	0.396
Synthetic Accessibility Score:	4.601
Fsp3:	0.737
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:	-5.257
MDCK Permeability:	2.1175901565584354e-05
Pgp-inhibitor:	0.898
Pgp-substrate:	0.977
Human Intestinal Absorption (HIA):	0.904
20% Bioavailability (F20%):	0.007
30% Bioavailability (F30%):	0.737

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.193
Plasma Protein Binding (PPB):	57.50678253173828%
Volume Distribution (VD):	1.35
Pgp-substrate:	27.843856811523438%

ADMET: Metabolism

CYP1A2-inhibitor:	0.018
CYP1A2-substrate:	0.06
CYP2C19-inhibitor:	0.011
CYP2C19-substrate:	0.53
CYP2C9-inhibitor:	0.001
CYP2C9-substrate:	0.065
CYP2D6-inhibitor:	0.008
CYP2D6-substrate:	0.13
CYP3A4-inhibitor:	0.005
CYP3A4-substrate:	0.088

ADMET: Excretion

Clearance (CL):	1.561
Half-life (T1/2):	0.813

ADMET: Toxicity

hERG Blockers:	0.029
Human Hepatotoxicity (H-HT):	0.233
Drug-inuced Liver Injury (DILI):	0.068
AMES Toxicity:	0.647
Rat Oral Acute Toxicity:	0.186
Maximum Recommended Daily Dose:	0.075
Skin Sensitization:	0.536
Carcinogencity:	0.583
Eye Corrosion:	0.003
Eye Irritation:	0.012
Respiratory Toxicity:	0.703

Download Data

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

Natural Product: NPC271445

Natural Product ID:	NPC271445
*Common Name:**	XSVHCRJRFKFCSN-MMNBODBLSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	XSVHCRJRFKFCSN-MMNBODBLSA-N
Standard InCHI:	InChI=1S/C19H30O8/c1-9(21)5-6-11-10(2)17(12(22)7-19(11,3)4)27-18-16(25)15(24)14(23)13(8-20)26-18/h5-6,12-18,20,22-25H,7-8H2,1-4H3/b6-5+/t12-,13+,14+,15-,16+,17+,18-/m0/s1
SMILES:	CC(=O)/C=C/C1=C(C)[C@H]([C@H](CC1(C)C)O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	11567211
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0002049] Terpene glycosides

*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
NPO29151	Jaborosa odonelliana	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12027740]
NPO29169	Origanum vulgare	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16249088]
NPO29169	Origanum vulgare	Species	Lamiaceae	Eukaryota	n.a.	aerial part	n.a.	PMID[20973550]
NPO29343	Phoebe porosa	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21574561]
NPO28947	Dendrobium draconis	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24844664]
NPO5973	Sonchus asper	Species	Asteraceae	Eukaryota	n.a.	Molise Region, Italy	Autumn 2018	PMID[32803719]
NPO5973	Sonchus asper	Species	Asteraceae	Eukaryota	n.a.	Molise Region, Italy	Spring 2019	PMID[32803719]
NPO5973	Sonchus asper	Species	Asteraceae	Eukaryota	n.a.	Molise Region, Italy		PMID[32803719]
NPO29239	Anopterus glandulosus	Species	Escalloniaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[3443859]
NPO5973	Sonchus asper	Species	Asteraceae	Eukaryota	n.a	The rural area of Viçosa, State of Minas Gerais (MG), Brazil	Adult stage	PMID[35282307]
NPO29169	Origanum vulgare	Species	Lamiaceae	Eukaryota	Leaf	n.a.	n.a.	Database[FooDB]
NPO29169	Origanum vulgare	Species	Lamiaceae	Eukaryota	Plant	n.a.	n.a.	Database[FooDB]
NPO29169	Origanum vulgare	Species	Lamiaceae	Eukaryota	Shoot Essent. Oil	n.a.	n.a.	Database[FooDB]
NPO29169	Origanum vulgare	Species	Lamiaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO29169	Origanum vulgare	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO9857	Saussurea medusa	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO9857	Saussurea medusa	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO29169	Origanum vulgare	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5973	Sonchus asper	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO29169	Origanum vulgare	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO9857	Saussurea medusa	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29343	Phoebe porosa	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29151	Jaborosa odonelliana	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28782	Melodinus insulae-pinorum	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29239	Anopterus glandulosus	Species	Escalloniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28983	Cladonia grayi	Species	Cladoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29412	Stenocarpus sinuatus	Species	Proteaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29169	Origanum vulgare	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29223	Cystoseira algeriensis	Species	Sargassaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28947	Dendrobium draconis	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28714	Chromolaena opadoclinia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29329	Teucrium lepicephalum	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5973	Sonchus asper	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 NPC271445 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	198
0.1-0.2	1207
0.2-0.3	4684
0.3-0.4	8790
0.4-0.5	15142
0.5-0.6	8887
0.6-0.7	3274
0.7-0.8	473
0.8-0.85	40
0.85-0.9	1
0.9-0.95	0
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 NPC271445 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	175
0.1-0.2	1422
0.2-0.3	4002
0.3-0.4	2424
0.4-0.5	798
0.5-0.6	274
0.6-0.7	50
0.7-0.8	5
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