NPASS Compound

Structure

NPC264114 OpenBabel06302215392D 64 71 0 0 1 0 0 0 0 0999 V2000 7.6860 1.4792 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.8320 0.9861 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 6.8320 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 5.9780 -0.4931 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 5.1240 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 5.1240 0.9861 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 5.9780 1.4792 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.2700 1.4792 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.2700 2.4653 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 5.1240 2.9583 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 5.1240 3.9444 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.2700 4.4375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4160 3.9444 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4160 2.9583 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.5620 2.4653 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7080 2.9583 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.7080 3.9444 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8540 4.4375 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0000 3.9444 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8540 4.4375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7080 3.9444 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8540 5.4236 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 2.9583 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8540 2.4653 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8540 1.4792 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.9861 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8540 1.4792 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7080 0.9861 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7080 0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.5620 0.4931 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8540 -0.4931 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8540 -1.4792 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7080 -1.9722 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5620 -1.4792 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.5620 -3.4514 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5620 -0.4931 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.4160 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2700 -0.4931 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2700 -1.4792 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1240 -1.9722 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.9780 -1.4792 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.8320 -1.9722 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.8181 -1.9722 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.3250 -1.1182 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.8320 -2.9583 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9780 -3.4514 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9780 -4.4375 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.1240 -2.9583 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.1240 -3.9444 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2700 -3.4514 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4160 -2.9583 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4160 -1.9722 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.5620 -2.4653 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.9861 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4931 -0.8540 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -1.7080 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8540 5.4236 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5620 4.4375 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.9780 4.4375 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.9780 2.4653 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.2700 -0.4931 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.9780 -1.4792 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 7.6860 -0.4931 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 1 0 0 0 2 3 1 0 0 0 0 2 7 1 0 0 0 0 3 4 1 0 0 0 0 3 64 1 6 0 0 0 4 5 1 0 0 0 0 4 63 1 1 0 0 0 5 6 1 0 0 0 0 5 62 1 1 0 0 0 6 7 1 0 0 0 0 6 8 1 6 0 0 0 9 8 1 1 0 0 0 9 10 1 0 0 0 0 9 14 1 0 0 0 0 10 11 1 0 0 0 0 10 61 1 6 0 0 0 11 12 1 0 0 0 0 11 60 1 6 0 0 0 12 13 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 6 0 0 0 16 15 1 1 0 0 0 16 17 1 0 0 0 0 16 24 1 0 0 0 0 17 18 1 0 0 0 0 17 59 1 6 0 0 0 18 19 1 0 0 0 0 18 58 1 1 0 0 0 19 20 1 6 0 0 0 19 23 1 0 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 23 24 1 0 0 0 0 24 25 1 6 0 0 0 26 25 1 6 0 0 0 26 27 1 0 0 0 0 26 54 1 0 0 0 0 27 28 1 0 0 0 0 28 29 1 0 0 0 0 29 36 1 0 0 0 0 29 30 1 6 0 0 0 29 31 1 0 0 0 0 31 32 1 6 0 0 0 31 54 1 0 0 0 0 32 33 1 0 0 0 0 33 34 1 0 0 0 0 34 52 1 0 0 0 0 34 35 1 6 0 0 0 34 36 1 0 0 0 0 36 37 1 6 0 0 0 37 38 1 0 0 0 0 38 39 2 0 0 0 0 39 52 1 0 0 0 0 39 40 1 0 0 0 0 40 41 1 1 0 0 0 40 48 1 0 0 0 0 41 42 1 0 0 0 0 42 43 1 0 0 0 0 42 44 1 0 0 0 0 42 45 1 0 0 0 0 45 46 1 0 0 0 0 46 47 2 0 0 0 0 46 48 1 0 0 0 0 48 49 1 6 0 0 0 48 50 1 0 0 0 0 50 51 1 0 0 0 0 51 52 1 0 0 0 0 52 53 1 1 0 0 0 54 55 1 1 0 0 0 54 56 1 0 0 0 0 56 57 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	910.49
Volume:	894.541
LogP:	2.556
LogD:	1.941
LogS:	-3.884
# Rotatable Bonds:	8
TPSA:	271.59
# H-Bond Aceptor:	17
# H-Bond Donor:	9
# Rings:	8
# Heavy Atoms:	17

MedChem Properties

QED Drug-Likeness Score:	0.124
Synthetic Accessibility Score:	6.348
Fsp3:	0.915
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.765
MDCK Permeability:	2.2923024516785517e-05
Pgp-inhibitor:	0.934
Pgp-substrate:	0.011
Human Intestinal Absorption (HIA):	0.923
20% Bioavailability (F20%):	0.11
30% Bioavailability (F30%):	0.988

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.13
Plasma Protein Binding (PPB):	78.44422149658203%
Volume Distribution (VD):	0.27
Pgp-substrate:	15.29810619354248%

ADMET: Metabolism

CYP1A2-inhibitor:	0.0
CYP1A2-substrate:	0.928
CYP2C19-inhibitor:	0.002
CYP2C19-substrate:	0.336
CYP2C9-inhibitor:	0.002
CYP2C9-substrate:	0.017
CYP2D6-inhibitor:	0.008
CYP2D6-substrate:	0.064
CYP3A4-inhibitor:	0.068
CYP3A4-substrate:	0.013

ADMET: Excretion

Clearance (CL):	0.551
Half-life (T1/2):	0.83

ADMET: Toxicity

hERG Blockers:	0.035
Human Hepatotoxicity (H-HT):	0.233
Drug-inuced Liver Injury (DILI):	0.06
AMES Toxicity:	0.092
Rat Oral Acute Toxicity:	0.142
Maximum Recommended Daily Dose:	0.635
Skin Sensitization:	0.046
Carcinogencity:	0.088
Eye Corrosion:	0.003
Eye Irritation:	0.007
Respiratory Toxicity:	0.96

Download Data

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

Natural Product: NPC264114

Natural Product ID:	NPC264114
*Common Name:**	ZNWGBWWXJAYIOM-KEUNTRLLSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	ZNWGBWWXJAYIOM-KEUNTRLLSA-N
Standard InCHI:	InChI=1S/C47H74O17/c1-21-29(51)31(53)34(56)39(60-21)63-36-30(52)24(49)19-59-40(36)64-37-33(55)32(54)35(38(57)58)62-41(37)61-28-12-13-44(5)25(45(28,6)20-48)11-14-47(8)26(44)10-9-22-23-17-42(2,3)18-27(50)43(23,4)15-16-46(22,47)7/h9,21,23-26,28-37,39-41,48-49,51-56H,10-20H2,1-8H3,(H,57,58)/t21-,23-,24-,25+,26+,28-,29-,30-,31+,32-,33-,34+,35-,36+,37+,39-,40-,41+,43+,44-,45+,46+,47+/m0/s1
SMILES:	C[C@H]1[C@@H]([C@H]([C@H]([C@@H](O1)O[C@@H]1[C@H]([C@H](CO[C@H]1O[C@@H]1[C@H]([C@@H]([C@@H](C(=O)O)O[C@H]1O[C@H]1CC[C@@]2(C)[C@@H](CC[C@]3(C)[C@@H]2CC=C2[C@@H]4CC(C)(C)CC(=O)[C@]4(C)CC[C@@]32C)[C@@]1(C)CO)O)O)O)O)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: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
NPO20620	Eucalyptus cypellocarpa	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11000030]
NPO17542	Aconitum orientale	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO17315	Ceanothus integerrimus	Species	Rhamnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO17542	Aconitum orientale	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO17315	Ceanothus integerrimus	Species	Rhamnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO20620	Eucalyptus cypellocarpa	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO19033	Sargassum lacerifolium	Species	Sargassaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12227	Xylopia acutiflora	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24375	Micrococcus luteus	Species	Micrococcaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO23977	Helichrysum moeserianum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15338	Lampranthus aurantiacus	Species	Aizoaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18125	Suillus variegatus	Species	Suillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20277	Pentzia eenii	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25819.1	Gueldenstaedtia verna subsp. multiflora	Subspecies	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19504	Solanum canense	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20346	Acacia retinoides	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18462	Calliactis parasitica	Species	Hormathiidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20620	Eucalyptus cypellocarpa	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17315	Ceanothus integerrimus	Species	Rhamnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17542	Aconitum orientale	Species	Ranunculaceae	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 NPC264114 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	286
0.1-0.2	1982
0.2-0.3	5452
0.3-0.4	10073
0.4-0.5	11325
0.5-0.6	6975
0.6-0.7	3745
0.7-0.8	1919
0.8-0.85	355
0.85-0.9	130
0.9-0.95	331
0.95-1	124

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 NPC264114 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	275
0.1-0.2	2295
0.2-0.3	3858
0.3-0.4	1732
0.4-0.5	563
0.5-0.6	253
0.6-0.7	128
0.7-0.8	42
0.8-0.85	2
0.85-0.9	0
0.9-0.95	1
0.95-1	1

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