NPASS Compound

Structure

NPC84713 OpenBabel06302215392D 34 39 0 0 1 0 0 0 0 0999 V2000 0.8774 -1.4833 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0003 -0.9768 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8776 -0.4707 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8458 -1.4650 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8458 -2.4424 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6923 -2.9311 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5386 -2.4424 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5386 -1.4651 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.3845 -0.9767 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2309 -1.4654 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2309 -2.4427 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.1081 -1.9363 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0773 -2.9314 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.0768 -3.9078 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2309 -4.3961 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3851 -2.9311 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.5079 -3.4375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9229 -2.4433 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.5762 -3.1688 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.4681 -2.7717 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -8.3136 -3.2599 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -8.8018 -4.1054 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.2899 -4.9509 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.3136 -4.9509 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.2899 -3.2599 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.3660 -1.8007 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.4110 -1.5977 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.0139 -0.7058 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.6922 -0.9764 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.5582 -0.4764 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6925 0.0005 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8464 0.4887 0.0000 C 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 0.8660 0.5001 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 33 1 0 0 0 0 2 3 1 0 0 0 0 2 4 1 0 0 0 0 4 5 1 6 0 0 0 4 29 1 0 0 0 0 5 6 1 0 0 0 0 6 7 2 0 0 0 0 7 16 1 0 0 0 0 7 8 1 0 0 0 0 8 9 1 6 0 0 0 8 29 1 0 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 11 16 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 13 18 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 6 0 0 0 18 19 1 6 0 0 0 18 27 1 0 0 0 0 20 19 1 6 0 0 0 20 21 1 0 0 0 0 20 26 1 0 0 0 0 21 22 1 0 0 0 0 21 25 1 1 0 0 0 22 23 1 0 0 0 0 22 24 1 0 0 0 0 22 25 1 0 0 0 0 26 27 1 0 0 0 0 27 28 1 1 0 0 0 29 30 1 6 0 0 0 29 31 1 0 0 0 0 31 32 1 0 0 0 0 32 33 1 0 0 0 0 33 34 2 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	470.34
Volume:	505.985
LogP:	6.108
LogD:	4.628
LogS:	-5.204
# Rotatable Bonds:	2
TPSA:	59.06
# H-Bond Aceptor:	4
# H-Bond Donor:	1
# Rings:	6
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.393
Synthetic Accessibility Score:	5.076
Fsp3:	0.9
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
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:	-4.953
MDCK Permeability:	1.1965712474193424e-05
Pgp-inhibitor:	0.984
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.004
20% Bioavailability (F20%):	0.924
30% Bioavailability (F30%):	0.89

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.091
Plasma Protein Binding (PPB):	93.80170440673828%
Volume Distribution (VD):	1.494
Pgp-substrate:	3.134218692779541%

ADMET: Metabolism

CYP1A2-inhibitor:	0.015
CYP1A2-substrate:	0.661
CYP2C19-inhibitor:	0.086
CYP2C19-substrate:	0.938
CYP2C9-inhibitor:	0.19
CYP2C9-substrate:	0.067
CYP2D6-inhibitor:	0.017
CYP2D6-substrate:	0.109
CYP3A4-inhibitor:	0.727
CYP3A4-substrate:	0.805

ADMET: Excretion

Clearance (CL):	8.144
Half-life (T1/2):	0.106

ADMET: Toxicity

hERG Blockers:	0.06
Human Hepatotoxicity (H-HT):	0.277
Drug-inuced Liver Injury (DILI):	0.049
AMES Toxicity:	0.025
Rat Oral Acute Toxicity:	0.655
Maximum Recommended Daily Dose:	0.879
Skin Sensitization:	0.187
Carcinogencity:	0.311
Eye Corrosion:	0.006
Eye Irritation:	0.03
Respiratory Toxicity:	0.983

Download Data

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

Natural Product: NPC84713

Natural Product ID:	NPC84713
*Common Name:**	ZWXPNDUTGNVQEU-STEPOWRLSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	ZWXPNDUTGNVQEU-STEPOWRLSA-N
Standard InCHI:	InChI=1S/C30H46O4/c1-26(2)22-9-8-20-19(28(22,5)13-12-23(26)31)11-15-29(6)18(10-14-30(20,29)7)17-16-21(33-25(17)32)24-27(3,4)34-24/h8,17-19,21-22,24-25,32H,9-16H2,1-7H3/t17-,18-,19-,21+,22-,24-,25+,28+,29-,30+/m0/s1
SMILES:	CC1(C)[C@@H]2CC=C3[C@H](CC[C@@]4(C)[C@@H](CC[C@]34C)[C@@H]3C[C@H]([C@H]4C(C)(C)O4)O[C@H]3O)[C@@]2(C)CCC1=O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	44575793
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
NPO9965	Eurycoma longifolia	Species	Simaroubaceae	Eukaryota	Roots	n.a.	n.a.	PMID[14575431]
NPO18932	Melia azedarach	Species	Meliaceae	Eukaryota	n.a.	Brazilian	n.a.	PMID[15387656]
NPO18932	Melia azedarach	Species	Meliaceae	Eukaryota	n.a.	ripe fruit	n.a.	PMID[16205005]
NPO9965	Eurycoma longifolia	Species	Simaroubaceae	Eukaryota	n.a.	root	n.a.	PMID[1800638]
NPO9965	Eurycoma longifolia	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19299148]
NPO9965	Eurycoma longifolia	Species	Simaroubaceae	Eukaryota	roots	n.a.	n.a.	PMID[19299148]
NPO9965	Eurycoma longifolia	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19919052]
NPO4899	Streptomyces fungicidicus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	PMID[20353165]
NPO9965	Eurycoma longifolia	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24467387]
NPO9965	Eurycoma longifolia	Species	Simaroubaceae	Eukaryota	roots	n.a.	n.a.	PMID[25066952]
NPO9965	Eurycoma longifolia	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25905468]
NPO18932	Melia azedarach	Species	Meliaceae	Eukaryota	Fruits	n.a.	n.a.	PMID[33253570]
NPO18932	Melia azedarach	Species	Meliaceae	Eukaryota	Seeds	n.a.	n.a.	PMID[3701342]
NPO9965	Eurycoma longifolia	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO18932	Melia azedarach	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO9965	Eurycoma longifolia	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO18932	Melia azedarach	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO18932	Melia azedarach	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO18932.3	Melia azedarach l. var. japonica mak.	Varieties	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO18932	Melia azedarach	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO9965	Eurycoma longifolia	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1469	Cyperus compressus	Species	Cyperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8937	Ferreirea spectabilis	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO10266	Alaria nana	Species	Alariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18932	Melia azedarach	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4899	Streptomyces fungicidicus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO9736	Artemisia arctica	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7417	Pieris melete	Species	Pieridae	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 NPC84713 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 NPC84713 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