NPASS Compound

Structure

NPC58843 OpenBabel06302215142D 30 33 0 0 1 0 0 0 0 0999 V2000 6.4562 -2.2601 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.1472 -1.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 -1.0000 0.0000 C 0 0 2 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 3.4641 -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 2.5981 0.5000 0.0000 C 0 0 1 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 3.4641 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 5.1962 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 0.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 5.1962 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 6.1472 0.3090 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.7350 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7350 -0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 0.5000 0.0000 C 0 0 2 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 0.0000 2.0000 0.0000 C 0 0 2 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 -0.8660 0.5000 0.0000 C 0 0 1 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 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 -1.7321 2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 3.0000 0.0000 O 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 1 2 2 0 0 0 0 2 17 1 0 0 0 0 2 3 1 0 0 0 0 3 4 1 0 0 0 0 3 15 1 0 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 6 14 1 0 0 0 0 6 7 1 0 0 0 0 6 8 1 0 0 0 0 8 9 1 0 0 0 0 8 19 1 6 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 11 12 1 0 0 0 0 11 14 1 0 0 0 0 12 13 2 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 17 18 2 0 0 0 0 19 20 1 0 0 0 0 20 21 1 0 0 0 0 20 27 1 0 0 0 0 21 22 1 0 0 0 0 21 30 1 0 0 0 0 22 23 1 0 0 0 0 22 29 1 0 0 0 0 23 24 1 0 0 0 0 23 28 1 0 0 0 0 24 25 1 0 0 0 0 24 27 1 0 0 0 0 25 26 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	426.19
Volume:	408.749
LogP:	0.393
LogD:	0.608
LogS:	-2.208
# Rotatable Bonds:	4
TPSA:	142.75
# H-Bond Aceptor:	9
# H-Bond Donor:	4
# Rings:	4
# Heavy Atoms:	9

MedChem Properties

QED Drug-Likeness Score:	0.26
Synthetic Accessibility Score:	4.983
Fsp3:	0.81
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	3
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.58
MDCK Permeability:	8.532289211871102e-05
Pgp-inhibitor:	0.001
Pgp-substrate:	0.002
Human Intestinal Absorption (HIA):	0.89
20% Bioavailability (F20%):	0.011
30% Bioavailability (F30%):	0.958

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.266
Plasma Protein Binding (PPB):	38.031394958496094%
Volume Distribution (VD):	0.609
Pgp-substrate:	63.14097595214844%

ADMET: Metabolism

CYP1A2-inhibitor:	0.017
CYP1A2-substrate:	0.076
CYP2C19-inhibitor:	0.011
CYP2C19-substrate:	0.174
CYP2C9-inhibitor:	0.003
CYP2C9-substrate:	0.043
CYP2D6-inhibitor:	0.007
CYP2D6-substrate:	0.1
CYP3A4-inhibitor:	0.032
CYP3A4-substrate:	0.167

ADMET: Excretion

Clearance (CL):	2.07
Half-life (T1/2):	0.88

ADMET: Toxicity

hERG Blockers:	0.036
Human Hepatotoxicity (H-HT):	0.088
Drug-inuced Liver Injury (DILI):	0.307
AMES Toxicity:	0.056
Rat Oral Acute Toxicity:	0.114
Maximum Recommended Daily Dose:	0.027
Skin Sensitization:	0.813
Carcinogencity:	0.199
Eye Corrosion:	0.019
Eye Irritation:	0.17
Respiratory Toxicity:	0.86

Download Data

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

Natural Product: NPC58843

Natural Product ID:	NPC58843
*Common Name:**	KNNCRAFUQKPIRD-QSRMXYNLSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	KNNCRAFUQKPIRD-QSRMXYNLSA-N
Standard InCHI:	InChI=1S/C21H30O9/c1-9-11-5-6-21(2)13(4-3-10(7-22)14(21)18(11)30-19(9)27)29-20-17(26)16(25)15(24)12(8-23)28-20/h7,10-18,20,23-26H,1,3-6,8H2,2H3/t10-,11-,12+,13+,14+,15+,16-,17+,18-,20+,21-/m0/s1
SMILES:	C=C1[C@@H]2CC[C@@]3(C)[C@@H](CC[C@@H](C=O)[C@@H]3[C@H]2OC1=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:	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:0001772] Eudesmanolides, secoeudesmanolides, 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
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]
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]
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]
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]

☑ 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 NPC58843 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	262
0.1-0.2	1657
0.2-0.3	5088
0.3-0.4	8913
0.4-0.5	11289
0.5-0.6	6550
0.6-0.7	5595
0.7-0.8	2932
0.8-0.85	387
0.85-0.9	24
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 NPC58843 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	260
0.1-0.2	2044
0.2-0.3	3856
0.3-0.4	1913
0.4-0.5	578
0.5-0.6	284
0.6-0.7	174
0.7-0.8	37
0.8-0.85	4
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