NPASS Compound

Structure

NPC31361 OpenBabel06302215512D 24 27 0 0 1 0 0 0 0 0999 V2000 -0.2788 -1.7601 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5878 -0.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5388 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4049 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2709 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1369 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0029 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0029 0.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.8690 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.8690 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.3690 0.1340 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.8690 2.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.0029 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0029 3.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.1369 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1369 1.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.2709 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2709 0.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.4049 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5388 0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.5878 0.8090 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.7350 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 22 1 0 0 0 0 2 3 2 0 0 0 0 3 20 1 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 18 1 0 0 0 0 5 6 1 0 0 0 0 6 7 1 0 0 0 0 8 7 1 6 0 0 0 8 9 1 0 0 0 0 8 16 1 0 0 0 0 9 10 1 0 0 0 0 9 11 1 0 0 0 0 9 12 1 0 0 0 0 12 13 1 0 0 0 0 12 24 1 6 0 0 0 13 14 2 0 0 0 0 13 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 6 0 0 0 16 18 1 0 0 0 0 18 19 1 6 0 0 0 20 19 1 1 0 0 0 20 21 1 0 0 0 0 21 22 1 0 0 0 0 22 23 2 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	330.18
Volume:	344.865
LogP:	3.399
LogD:	3.101
LogS:	-2.951
# Rotatable Bonds:	0
TPSA:	70.67
# H-Bond Aceptor:	4
# H-Bond Donor:	2
# Rings:	4
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.762
Synthetic Accessibility Score:	4.805
Fsp3:	0.65
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
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:	-4.821
MDCK Permeability:	2.3212385713122785e-05
Pgp-inhibitor:	0.024
Pgp-substrate:	0.684
Human Intestinal Absorption (HIA):	0.01
20% Bioavailability (F20%):	0.002
30% Bioavailability (F30%):	0.004

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.277
Plasma Protein Binding (PPB):	96.84355926513672%
Volume Distribution (VD):	1.304
Pgp-substrate:	3.887587785720825%

ADMET: Metabolism

CYP1A2-inhibitor:	0.053
CYP1A2-substrate:	0.68
CYP2C19-inhibitor:	0.028
CYP2C19-substrate:	0.753
CYP2C9-inhibitor:	0.087
CYP2C9-substrate:	0.438
CYP2D6-inhibitor:	0.012
CYP2D6-substrate:	0.39
CYP3A4-inhibitor:	0.074
CYP3A4-substrate:	0.275

ADMET: Excretion

Clearance (CL):	16.752
Half-life (T1/2):	0.441

ADMET: Toxicity

hERG Blockers:	0.004
Human Hepatotoxicity (H-HT):	0.633
Drug-inuced Liver Injury (DILI):	0.563
AMES Toxicity:	0.128
Rat Oral Acute Toxicity:	0.949
Maximum Recommended Daily Dose:	0.913
Skin Sensitization:	0.285
Carcinogencity:	0.947
Eye Corrosion:	0.004
Eye Irritation:	0.073
Respiratory Toxicity:	0.984

Download Data

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

Natural Product: NPC31361

Natural Product ID:	NPC31361
*Common Name:**	PTWUMSGLZPRHJW-RZRATATOSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	PTWUMSGLZPRHJW-RZRATATOSA-N
Standard InCHI:	InChI=1S/C20H26O4/c1-10-12-7-11-5-6-16-19(2,3)17(22)14(21)9-20(16,4)13(11)8-15(12)24-18(10)23/h7,13,15-17,22H,5-6,8-9H2,1-4H3/t13-,15-,16-,17-,20+/m1/s1
SMILES:	CC1=C2C=C3CC[C@@H]4C(C)(C)[C@@H](C(=O)C[C@@]4(C)[C@@H]3C[C@H]2OC1=O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	101627297
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001283] Terpene lactones [CHEMONTID:0001538] Diterpene lactones

*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
NPO28245	Strychnos nux-vomica	Species	Loganiaceae	Eukaryota	n.a.	seed	n.a.	PMID[10.1016/j.tet.2012.03.006]
NPO28245	Strychnos nux-vomica	Species	Loganiaceae	Eukaryota	n.a.	seed	n.a.	DOI[10.1016/j.tet.2012.03.006]
NPO28245	Strychnos nux-vomica	Species	Loganiaceae	Eukaryota	n.a.	seed	n.a.	PMID[16317898]
NPO28245	Strychnos nux-vomica	Species	Loganiaceae	Eukaryota	n.a.	seed	n.a.	PMID[17449162]
NPO28245	Strychnos nux-vomica	Species	Loganiaceae	Eukaryota	n.a.	seed	n.a.	PMID[19235686]
NPO28245	Strychnos nux-vomica	Species	Loganiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19666019]
NPO28245	Strychnos nux-vomica	Species	Loganiaceae	Eukaryota	n.a.	seed	n.a.	PMID[22707864]
NPO28245	Strychnos nux-vomica	Species	Loganiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23088673]
NPO28245	Strychnos nux-vomica	Species	Loganiaceae	Eukaryota	n.a.	seed	n.a.	PMID[2393954]
NPO28245	Strychnos nux-vomica	Species	Loganiaceae	Eukaryota	n.a.	seed	n.a.	PMID[25594733]
NPO28245	Strychnos nux-vomica	Species	Loganiaceae	Eukaryota	n.a.	seed	n.a.	PMID[7912074]
NPO17794	Streptomyces violaceusniger	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	PMID[8557611]
NPO28245	Strychnos nux-vomica	Species	Loganiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO28245	Strychnos nux-vomica	Species	Loganiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12190	Carduus acanthoides	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO28245	Strychnos nux-vomica	Species	Loganiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO21065	Euphorbia calyptrata	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1891	Chorilaena quercifolia	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8081	Crataegus flava	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28332	Lecidea tumida	Species	Lecideaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27972	Clitocybe phosphorea	Species	Tricholomataceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28007	Cakile maritima	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6223	Ceiba insignis	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28142	Anthoceros agrestis	Species	Anthocerotaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28157	Vriesea regina	Species	Bromeliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12190	Carduus acanthoides	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28299	Leucaena diversifolia	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5402	Hypogymnia billardieri	Species	Parmeliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28245	Strychnos nux-vomica	Species	Loganiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16779.1	Amaranthus hybridus subsp. cruentus	Subspecies	Amaranthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27863	Diospyros nigra	Species	Ebenaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17794	Streptomyces violaceusniger	Species	Streptomycetaceae	Bacteria	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 NPC31361 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	1013
0.2-0.3	3410
0.3-0.4	6745
0.4-0.5	14413
0.5-0.6	7769
0.6-0.7	5939
0.7-0.8	2926
0.8-0.85	225
0.85-0.9	57
0.9-0.95	2
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 NPC31361 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	168
0.1-0.2	1220
0.2-0.3	3245
0.3-0.4	2688
0.4-0.5	1229
0.5-0.6	288
0.6-0.7	190
0.7-0.8	121
0.8-0.85	1
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