NPASS Compound

Structure

NPC24413 OpenBabel06302215342D 37 41 0 0 1 0 0 0 0 0999 V2000 5.5053 -1.4220 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7034 -0.9012 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5554 -0.4671 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1826 -1.7031 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.2277 -1.6531 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.7936 -0.8011 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3144 0.0008 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.4863 0.4789 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.4858 1.4351 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6573 1.9134 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8290 0.4786 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8636 1.4558 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6574 0.0003 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.6574 -0.9569 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8284 -1.4355 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.9572 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8290 -1.4358 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0173 -1.9244 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8287 -2.3925 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6574 -2.8706 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4863 -2.3920 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.4866 -1.4353 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.3329 -0.9467 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3152 -1.9135 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1436 -1.4349 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.6579 -0.9572 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.6579 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8289 0.4786 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0000 0.9762 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3316 -2.8802 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.9354 0.7279 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8756 0.5537 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.6162 1.6293 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.2693 -0.0492 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.7070 -2.4550 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.6167 -2.5551 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 35 1 0 0 0 0 2 3 1 0 0 0 0 2 4 1 0 0 0 0 4 5 1 0 0 0 0 4 37 1 1 0 0 0 5 6 1 0 0 0 0 5 36 1 1 0 0 0 6 7 1 0 0 0 0 7 8 1 0 0 0 0 7 32 1 6 0 0 0 7 35 1 0 0 0 0 8 9 1 6 0 0 0 8 13 1 0 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 11 29 1 0 0 0 0 11 12 1 1 0 0 0 11 13 1 0 0 0 0 13 14 1 1 0 0 0 14 15 1 0 0 0 0 16 15 1 6 0 0 0 16 17 1 0 0 0 0 16 29 1 0 0 0 0 17 26 1 0 0 0 0 17 18 1 6 0 0 0 17 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 1 0 0 0 0 21 22 1 0 0 0 0 21 31 1 6 0 0 0 22 23 1 1 0 0 0 22 24 1 0 0 0 0 22 26 1 0 0 0 0 24 25 1 0 0 0 0 26 27 1 6 0 0 0 27 28 1 0 0 0 0 28 29 1 0 0 0 0 29 30 1 6 0 0 0 32 33 2 0 0 0 0 32 34 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	522.36
Volume:	543.549
LogP:	2.918
LogD:	3.513
LogS:	-3.522
# Rotatable Bonds:	3
TPSA:	127.45
# H-Bond Aceptor:	7
# H-Bond Donor:	5
# Rings:	5
# Heavy Atoms:	7

MedChem Properties

QED Drug-Likeness Score:	0.382
Synthetic Accessibility Score:	5.252
Fsp3:	0.967
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.478
MDCK Permeability:	2.1489498976734467e-05
Pgp-inhibitor:	0.254
Pgp-substrate:	0.008
Human Intestinal Absorption (HIA):	0.011
20% Bioavailability (F20%):	0.022
30% Bioavailability (F30%):	0.07

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.236
Plasma Protein Binding (PPB):	85.43230438232422%
Volume Distribution (VD):	0.571
Pgp-substrate:	4.475344181060791%

ADMET: Metabolism

CYP1A2-inhibitor:	0.005
CYP1A2-substrate:	0.491
CYP2C19-inhibitor:	0.003
CYP2C19-substrate:	0.826
CYP2C9-inhibitor:	0.036
CYP2C9-substrate:	0.107
CYP2D6-inhibitor:	0.002
CYP2D6-substrate:	0.136
CYP3A4-inhibitor:	0.104
CYP3A4-substrate:	0.175

ADMET: Excretion

Clearance (CL):	2.489
Half-life (T1/2):	0.454

ADMET: Toxicity

hERG Blockers:	0.046
Human Hepatotoxicity (H-HT):	0.544
Drug-inuced Liver Injury (DILI):	0.018
AMES Toxicity:	0.022
Rat Oral Acute Toxicity:	0.489
Maximum Recommended Daily Dose:	0.161
Skin Sensitization:	0.391
Carcinogencity:	0.105
Eye Corrosion:	0.024
Eye Irritation:	0.042
Respiratory Toxicity:	0.977

Download Data

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

Natural Product: NPC24413

Natural Product ID:	NPC24413
*Common Name:**	UVHCBPZJADNRKK-FQPCDPSRSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	UVHCBPZJADNRKK-FQPCDPSRSA-N
Standard InCHI:	InChI=1S/C30H50O7/c1-25(2)23(34)19(32)15-30(37-25,24(35)36)18-9-13-28(5)17(18)7-8-21-26(3)12-11-22(33)27(4,16-31)20(26)10-14-29(21,28)6/h17-23,31-34H,7-16H2,1-6H3,(H,35,36)/t17-,18+,19+,20-,21-,22+,23+,26+,27-,28-,29-,30+/m1/s1
SMILES:	CC1(C)[C@H]([C@H](C[C@]([C@H]2CC[C@]3(C)[C@@H]2CC[C@@H]2[C@@]4(C)CC[C@@H]([C@](C)(CO)[C@@H]4CC[C@@]32C)O)(C(=O)O)O1)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	44423055
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0002049] Terpene glycosides [CHEMONTID:0001580] Triterpene glycosides [CHEMONTID:0002358] Triterpene saponins

*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
NPO18234	Gentiana rigescens	Species	Gentianaceae	Eukaryota	roots	n.a.	n.a.	PMID[17375953]
NPO18234	Gentiana rigescens	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20813533]
NPO17493	Alstonia spatulata	Species	Apocynaceae	Eukaryota	n.a.	leaf	n.a.	PMID[21043460]
NPO17493	Alstonia spatulata	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21043460]
NPO17493	Alstonia spatulata	Species	Apocynaceae	Eukaryota	n.a.	stem	n.a.	PMID[21043460]
NPO27624	Swartzia simplex	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26654828]
NPO12009	Abies pinsapo	Species	Pinaceae	Eukaryota	Wood	n.a.	n.a.	PMID[7931362]
NPO15856	Podocarpus hallii	Species	Podocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO16646	Artemisia campestris	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO17368	Erythrina senegalensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO17493	Alstonia spatulata	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO18843	Antirrhinum majus	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO16073	Sarcomelicope megistophylla	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO19120	Strychnos aculeata	Species	Loganiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO18234	Gentiana rigescens	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO16073	Sarcomelicope megistophylla	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO16646	Artemisia campestris	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO18843	Antirrhinum majus	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO19120	Strychnos aculeata	Species	Loganiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15856	Podocarpus hallii	Species	Podocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO16817	Aglaia argentea	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO17368	Erythrina senegalensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO18234	Gentiana rigescens	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO17493	Alstonia spatulata	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15856	Podocarpus hallii	Species	Podocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO18843	Antirrhinum majus	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO16646	Artemisia campestris	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO18234	Gentiana rigescens	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO18234	Gentiana rigescens	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO12009	Abies pinsapo	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19120	Strychnos aculeata	Species	Loganiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15856	Podocarpus hallii	Species	Podocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18511	Latimeria chalumnae	Species	Coelacanthidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17368	Erythrina senegalensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17711	Sphenoclea zeylanica	Species	Sphenocleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27624	Swartzia simplex	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14721	Dentitheca habereri	Species	Plumulariidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16073	Sarcomelicope megistophylla	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16646	Artemisia campestris	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17493	Alstonia spatulata	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3046	Schisandra bicolor	Species	Schisandraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17699	Solanum glaucophyllum	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17054	Streptomyces gardneri	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO16958	Jurinea albicaulis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18234	Gentiana rigescens	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18372	Lobophytum crassospiculatum	Species	Alcyoniidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15518	Streptomyces netropsis	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO18843	Antirrhinum majus	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16817	Aglaia argentea	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13251	Iris nertchinskia	Species	Tarachodidae	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 NPC24413 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.56 or Top200).

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 NPC24413 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

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