NPASS Compound

Structure

NPC284041 OpenBabel06302215202D 49 53 0 0 1 0 0 0 0 0999 V2000 13.5998 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 13.5998 0.9815 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 12.7498 1.4722 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 11.8998 0.9815 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 11.0498 1.4722 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.1999 0.9815 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.3499 1.4722 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.4999 0.9815 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.6499 1.4722 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.7999 0.9815 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9499 1.4722 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0999 0.9815 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2499 1.4722 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4000 0.9815 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5500 1.4722 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7000 0.9815 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8500 1.4722 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7000 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8500 -0.4907 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8500 -1.4722 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -1.9630 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8500 -1.4722 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8500 -2.4537 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8500 -0.4907 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5500 -0.4907 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5500 -1.4722 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.2499 -0.4907 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7000 -1.9630 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.7000 -2.9444 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5500 -3.4352 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4000 -2.9444 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.2499 -3.4352 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.2499 -4.4167 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0999 -4.9074 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.5907 -5.7574 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6092 -5.7574 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9499 -4.4167 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9499 -3.4352 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0999 -2.9444 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.9499 -2.4537 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0999 -1.9630 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2499 -1.4722 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4000 -1.9630 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.4000 -0.9815 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4000 -3.9259 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 0.4907 0.8500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4907 0.8500 0.0000 C 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 3 4 1 0 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 6 7 1 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 2 0 0 0 0 16 18 1 0 0 0 0 19 18 1 1 0 0 0 19 20 1 0 0 0 0 19 47 1 0 0 0 0 20 21 1 0 0 0 0 21 22 1 0 0 0 0 22 29 1 0 0 0 0 22 23 1 1 0 0 0 22 24 1 0 0 0 0 24 25 1 1 0 0 0 24 47 1 0 0 0 0 25 26 1 0 0 0 0 26 27 1 0 0 0 0 27 44 1 0 0 0 0 27 28 1 1 0 0 0 27 29 1 0 0 0 0 29 30 1 1 0 0 0 30 31 1 0 0 0 0 31 32 1 0 0 0 0 32 44 1 0 0 0 0 32 33 1 0 0 0 0 32 46 1 1 0 0 0 33 34 1 6 0 0 0 33 40 1 0 0 0 0 34 35 1 0 0 0 0 35 36 1 0 0 0 0 35 37 1 0 0 0 0 35 38 1 0 0 0 0 38 39 1 0 0 0 0 39 40 1 0 0 0 0 40 41 1 1 0 0 0 40 42 1 0 0 0 0 42 43 1 0 0 0 0 43 44 1 0 0 0 0 44 45 1 6 0 0 0 47 48 1 0 0 0 0 47 49 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	682.63
Volume:	785.124
LogP:	12.344
LogD:	6.86
LogS:	-8.088
# Rotatable Bonds:	16
TPSA:	46.53
# H-Bond Aceptor:	3
# H-Bond Donor:	1
# Rings:	5
# Heavy Atoms:	3

MedChem Properties

QED Drug-Likeness Score:	0.138
Synthetic Accessibility Score:	4.946
Fsp3:	0.978
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Rejected
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:	-5.211
MDCK Permeability:	6.115511041571153e-06
Pgp-inhibitor:	0.0
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.004
20% Bioavailability (F20%):	0.996
30% Bioavailability (F30%):	0.995

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.051
Plasma Protein Binding (PPB):	94.8807144165039%
Volume Distribution (VD):	1.766
Pgp-substrate:	1.5949081182479858%

ADMET: Metabolism

CYP1A2-inhibitor:	0.008
CYP1A2-substrate:	0.155
CYP2C19-inhibitor:	0.082
CYP2C19-substrate:	0.921
CYP2C9-inhibitor:	0.031
CYP2C9-substrate:	0.892
CYP2D6-inhibitor:	0.048
CYP2D6-substrate:	0.066
CYP3A4-inhibitor:	0.239
CYP3A4-substrate:	0.171

ADMET: Excretion

Clearance (CL):	4.957
Half-life (T1/2):	0.005

ADMET: Toxicity

hERG Blockers:	0.695
Human Hepatotoxicity (H-HT):	0.085
Drug-inuced Liver Injury (DILI):	0.016
AMES Toxicity:	0.0
Rat Oral Acute Toxicity:	0.008
Maximum Recommended Daily Dose:	0.729
Skin Sensitization:	0.954
Carcinogencity:	0.007
Eye Corrosion:	0.278
Eye Irritation:	0.729
Respiratory Toxicity:	0.608

Download Data

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

Natural Product: NPC284041

Natural Product ID:	NPC284041
*Common Name:**	FWTRWEOVLCELMX-DJABKKCQSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	FWTRWEOVLCELMX-DJABKKCQSA-N
Standard InCHI:	InChI=1S/C46H82O3/c1-10-11-12-13-14-15-16-17-18-19-20-21-22-23-39(47)49-38-26-27-43(7)35(41(38,4)5)24-28-44(8)36(43)25-29-46(48)37-34-40(2,3)30-31-42(37,6)32-33-45(44,46)9/h35-38,48H,10-34H2,1-9H3/t35-,36+,37+,38-,42+,43-,44+,45-,46-/m0/s1
SMILES:	CCCCCCCCCCCCCCCC(=O)O[C@H]1CC[C@@]2(C)[C@@H](CC[C@]3(C)[C@@H]2CC[C@@]2([C@@H]4CC(C)(C)CC[C@]4(C)CC[C@@]32C)O)C1(C)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	10508767
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001553] Triterpenoids

*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
NPO18760	Euphorbia parviflora	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9895	Bupleurum tenue	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2261	Chromodoris petechialis	Species	Chromodorididae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8667	Azara microphylla	Species	Salicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9762	Lenzites sepiaria	Species	Coriolaceae	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 NPC284041 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	448
0.1-0.2	3400
0.2-0.3	12781
0.3-0.4	12149
0.4-0.5	5660
0.5-0.6	4745
0.6-0.7	2512
0.7-0.8	922
0.8-0.85	43
0.85-0.9	31
0.9-0.95	4
0.95-1	2

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 NPC284041 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	513
0.1-0.2	3569
0.2-0.3	3406
0.3-0.4	1086
0.4-0.5	282
0.5-0.6	228
0.6-0.7	42
0.7-0.8	24
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