NPASS Compound

Structure

NPC110879 OpenBabel06302215232D 27 28 0 0 1 0 0 0 0 0999 V2000 6.0981 0.3660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5981 1.2321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0981 2.0981 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.5981 1.2321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0981 0.3660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5981 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0981 -1.3660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9641 -1.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9641 -0.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5981 -2.2321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -2.2321 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.0981 -1.3660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -0.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.5981 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8660 -1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0000 -2.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8660 -1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8660 -0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7321 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.0981 -3.0981 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 2 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 2 0 0 0 0 6 13 1 0 0 0 0 6 7 1 0 0 0 0 7 8 1 0 0 0 0 7 9 1 0 0 0 0 7 10 1 0 0 0 0 10 11 1 0 0 0 0 11 12 1 0 0 0 0 11 27 1 6 0 0 0 12 13 1 0 0 0 0 13 14 1 6 0 0 0 13 15 1 0 0 0 0 16 15 1 1 0 0 0 16 17 1 0 0 0 0 16 23 1 0 0 0 0 17 18 1 0 0 0 0 17 26 1 6 0 0 0 18 19 1 0 0 0 0 18 25 1 1 0 0 0 19 20 1 0 0 0 0 19 24 1 6 0 0 0 20 21 1 1 0 0 0 20 23 1 0 0 0 0 21 22 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	386.19
Volume:	382.48
LogP:	-0.211
LogD:	-0.142
LogS:	-1.272
# Rotatable Bonds:	4
TPSA:	136.68
# H-Bond Aceptor:	8
# H-Bond Donor:	5
# Rings:	2
# Heavy Atoms:	8

MedChem Properties

QED Drug-Likeness Score:	0.32
Synthetic Accessibility Score:	4.943
Fsp3:	0.789
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
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:	-5.031
MDCK Permeability:	4.7174882638501e-05
Pgp-inhibitor:	0.83
Pgp-substrate:	0.982
Human Intestinal Absorption (HIA):	0.793
20% Bioavailability (F20%):	0.004
30% Bioavailability (F30%):	0.539

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.193
Plasma Protein Binding (PPB):	61.64122009277344%
Volume Distribution (VD):	0.934
Pgp-substrate:	32.87580490112305%

ADMET: Metabolism

CYP1A2-inhibitor:	0.005
CYP1A2-substrate:	0.426
CYP2C19-inhibitor:	0.012
CYP2C19-substrate:	0.769
CYP2C9-inhibitor:	0.007
CYP2C9-substrate:	0.049
CYP2D6-inhibitor:	0.001
CYP2D6-substrate:	0.047
CYP3A4-inhibitor:	0.007
CYP3A4-substrate:	0.07

ADMET: Excretion

Clearance (CL):	1.51
Half-life (T1/2):	0.801

ADMET: Toxicity

hERG Blockers:	0.037
Human Hepatotoxicity (H-HT):	0.246
Drug-inuced Liver Injury (DILI):	0.032
AMES Toxicity:	0.469
Rat Oral Acute Toxicity:	0.016
Maximum Recommended Daily Dose:	0.57
Skin Sensitization:	0.883
Carcinogencity:	0.796
Eye Corrosion:	0.009
Eye Irritation:	0.107
Respiratory Toxicity:	0.845

Download Data

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

Natural Product: NPC110879

Natural Product ID:	NPC110879
*Common Name:**	XTODSGVDHGMKSN-JAAWGWRJSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	XTODSGVDHGMKSN-JAAWGWRJSA-N
Standard InCHI:	InChI=1S/C19H30O8/c1-10(21)5-6-13-18(2,3)7-11(22)8-19(13,4)27-17-16(25)15(24)14(23)12(9-20)26-17/h5,11-12,14-17,20,22-25H,7-9H2,1-4H3/t6-,11-,12+,14+,15-,16+,17-,19+/m0/s1
SMILES:	CC(=O)C=C=C1C(C)(C)C[C@@H](C[C@@]1(C)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)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

*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
NPO16098	Boronia pinnata	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11076549]
NPO22142	Hippocratea excelsa	Species	n.a.	n.a.	n.a.	root	n.a.	PMID[17385912]
NPO22142	Hippocratea excelsa	Species	n.a.	n.a.	root bark	n.a.	n.a.	PMID[17385912]
NPO6655	Streptomyces niveus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	PMID[19762445]
NPO6364	Pongamiopsis pervilleana	Species	Fabaceae	Eukaryota	n.a.	Madagascar Dry Forest	n.a.	PMID[20804165]
NPO22142	Hippocratea excelsa	Species	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[2292687]
NPO7890	Cleistanthus indochinensis	Species	Phyllanthaceae	Eukaryota	fruits	n.a.	n.a.	PMID[22938151]
NPO19408	Eupatorium compositifolium	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO7282	Rauvolfia serpentina	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15319	Glochidion sphaerogynum	Species	Phyllanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO19408	Eupatorium compositifolium	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO7282	Rauvolfia serpentina	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO4549	Leonotis leonitis	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6364	Pongamiopsis pervilleana	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24550	Connarus paniculatus	Species	Connaraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2941	Salsola foetida	Species	Chenopodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22142	Hippocratea excelsa	Species	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO12835	Cyrtomium falcatum	Species	Dryopteridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15319	Glochidion sphaerogynum	Species	Phyllanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1379	Lecanora carpinea	Species	Lecanoraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21904	Tarenaya spinosa	Species	Cleomaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12101	Ajuga genevensis	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6655	Streptomyces niveus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO8679	Streptomyces sparsogenes	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO19408	Eupatorium compositifolium	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16098	Boronia pinnata	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17282	Pinguicula vulgaris	Species	Lentibulariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7890	Cleistanthus indochinensis	Species	Phyllanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1118	Elymus repens	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7282	Rauvolfia serpentina	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23083	Senecio magnificus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO262	Heliotropium ellipticum	Species	Heliotropiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4943	Metapenaeus endeavouri	Species	Penaeidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15005	Sargassum muticum	Species	Sargassaceae	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 NPC110879 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	215
0.1-0.2	2080
0.2-0.3	6142
0.3-0.4	13327
0.4-0.5	10170
0.5-0.6	7340
0.6-0.7	3224
0.7-0.8	196
0.8-0.85	2
0.85-0.9	0
0.9-0.95	0
0.95-1	1

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 NPC110879 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	204
0.1-0.2	2518
0.2-0.3	4066
0.3-0.4	1589
0.4-0.5	449
0.5-0.6	283
0.6-0.7	40
0.7-0.8	1
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