NPASS Compound

Structure

NPC254166 OpenBabel06302215392D 29 32 0 0 1 0 0 0 0 0999 V2000 3.2553 -2.8854 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5922 -2.0268 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5042 -1.8892 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0170 -1.3057 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0288 -1.5314 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2363 -0.8995 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2362 0.1141 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0286 0.7461 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8232 1.6454 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.0168 0.5207 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5918 1.2419 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5039 1.1045 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.2547 2.1005 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4567 -0.3925 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3790 -0.3923 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.3584 0.6209 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.3583 1.6347 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5197 2.1414 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3976 1.6344 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3975 0.6207 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3199 0.6205 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8586 -0.1782 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5195 0.1139 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.5194 -0.8997 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.3586 -1.4065 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.0001 -0.7857 0.0000 O 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 -0.9233 0.2473 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.3471 -1.3777 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 1 0 0 0 0 2 4 1 0 0 0 0 4 14 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 6 7 2 0 0 0 0 7 8 1 0 0 0 0 7 16 1 0 0 0 0 8 9 2 0 0 0 0 8 10 1 0 0 0 0 10 11 1 0 0 0 0 10 14 2 0 0 0 0 11 12 2 0 0 0 0 11 13 1 0 0 0 0 14 15 1 0 0 0 0 16 23 1 0 0 0 0 16 27 1 0 0 0 0 16 17 1 1 0 0 0 17 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 1 0 0 0 0 20 22 1 0 0 0 0 23 20 1 1 0 0 0 23 24 1 0 0 0 0 24 25 1 0 0 0 0 24 29 1 6 0 0 0 25 6 1 6 0 0 0 25 26 1 0 0 0 0 26 27 1 0 0 0 0 27 28 1 1 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	402.2
Volume:	411.697
LogP:	2.987
LogD:	1.772
LogS:	-3.89
# Rotatable Bonds:	2
TPSA:	104.06
# H-Bond Aceptor:	6
# H-Bond Donor:	3
# Rings:	5
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.657
Synthetic Accessibility Score:	5.826
Fsp3:	0.652
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.776
MDCK Permeability:	1.189995509776054e-05
Pgp-inhibitor:	0.073
Pgp-substrate:	0.308
Human Intestinal Absorption (HIA):	0.016
20% Bioavailability (F20%):	0.024
30% Bioavailability (F30%):	0.026

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.54
Plasma Protein Binding (PPB):	95.20354461669922%
Volume Distribution (VD):	1.21
Pgp-substrate:	5.169451713562012%

ADMET: Metabolism

CYP1A2-inhibitor:	0.029
CYP1A2-substrate:	0.713
CYP2C19-inhibitor:	0.04
CYP2C19-substrate:	0.851
CYP2C9-inhibitor:	0.373
CYP2C9-substrate:	0.771
CYP2D6-inhibitor:	0.027
CYP2D6-substrate:	0.234
CYP3A4-inhibitor:	0.113
CYP3A4-substrate:	0.277

ADMET: Excretion

Clearance (CL):	1.839
Half-life (T1/2):	0.08

ADMET: Toxicity

hERG Blockers:	0.01
Human Hepatotoxicity (H-HT):	0.17
Drug-inuced Liver Injury (DILI):	0.227
AMES Toxicity:	0.745
Rat Oral Acute Toxicity:	0.853
Maximum Recommended Daily Dose:	0.85
Skin Sensitization:	0.388
Carcinogencity:	0.655
Eye Corrosion:	0.003
Eye Irritation:	0.082
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: NPC254166

Natural Product ID:	NPC254166
*Common Name:**	JBKKPDPDDVIENY-FPQOSCNCSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	JBKKPDPDDVIENY-FPQOSCNCSA-N
Standard InCHI:	InChI=1S/C23H30O6/c1-10(2)12-9-13-15(17(26)14(11(3)24)16(12)25)23-8-6-7-22(4,5)20(23)18(27)19(13)29-21(23)28/h9-10,18-21,25,27-28H,6-8H2,1-5H3/t18-,19+,20-,21+,23-/m0/s1
SMILES:	CC(C)c1cc2c(c(=O)c(C(=O)C)c1O)[C@@]13CCCC(C)(C)[C@@H]1[C@H]([C@@H]2O[C@H]3O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	16090911
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0004150] Hydrocarbon derivatives [CHEMONTID:0001650] Tropones

*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
NPO25701	Amentotaxus yunnanensis	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12880325]
NPO25779	Vicia sativa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[1567426]
NPO25813	Salvia przewalskii	Species	Lamiaceae	Eukaryota	n.a.	whole plant	n.a.	PMID[17217287]
NPO25701	Amentotaxus yunnanensis	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO25813	Salvia przewalskii	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO25779	Vicia sativa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO25701	Amentotaxus yunnanensis	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO25813	Salvia przewalskii	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO24740	Uvaria klaineana	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO25779	Vicia sativa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO28257	Dioscorea communis	Species	Dioscoreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO25779	Vicia sativa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO28257	Dioscorea communis	Species	Dioscoreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25701	Amentotaxus yunnanensis	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12476	Delphinium cyphoplectrum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25813	Salvia przewalskii	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10497	Hydrolithon reinboldii	Species	Corallinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26223	Cladonia bellidiflora	Species	Cladoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23417	Rhabdia lycioides	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO6346	Phallusia fumigata	Species	Ascidiidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23960	Artemisia siversiana	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25974	Streptomyces lateritius	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO415	Deguelia hatschbachii	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27437	Camptothecium lutescens	Species	Brachytheciaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24988	Viburnum sieboldi	Species	Adoxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25212	Ritterella rubra	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO4009	Allochromatium minutissimum	Species	Chromatiaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO10155	Stauntonia obovatifoliola	Species	Lardizabalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22016	0tholaena dealbata	Species	Pteridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26054	Palmaria palmata	Species	Palmariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26316	Pleurophycus gardneri	Species	Alariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24740	Uvaria klaineana	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25779	Vicia sativa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25868	Decachaeta ovatifolia	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO26087	Euphorbia retusa	Species	Euphorbiaceae	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 NPC254166 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	360
0.1-0.2	1268
0.2-0.3	2671
0.3-0.4	5158
0.4-0.5	9629
0.5-0.6	9309
0.6-0.7	8039
0.7-0.8	6131
0.8-0.85	130
0.85-0.9	2
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 NPC254166 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	313
0.1-0.2	827
0.2-0.3	1606
0.3-0.4	2739
0.4-0.5	2106
0.5-0.6	1133
0.6-0.7	340
0.7-0.8	86
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