NPASS Compound

Structure

NPC191077 OpenBabel06302215422D 28 29 0 0 1 0 0 0 0 0999 V2000 -2.5981 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.3301 -0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.3301 -1.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.1962 -2.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.0622 -1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.9282 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 -0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 1.0000 0.0000 C 0 0 0 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 0.8660 -0.5000 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 -1.0000 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5000 -0.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 2.5000 0.0000 C 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 17 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 6 5 1 1 0 0 0 6 7 1 0 0 0 0 6 13 1 0 0 0 0 7 8 1 0 0 0 0 7 16 1 6 0 0 0 8 9 1 0 0 0 0 8 15 1 1 0 0 0 9 10 1 0 0 0 0 9 14 1 6 0 0 0 10 11 1 1 0 0 0 10 13 1 0 0 0 0 11 12 1 0 0 0 0 17 18 2 0 0 0 0 19 18 1 1 0 0 0 19 20 1 0 0 0 0 19 25 1 0 0 0 0 20 21 2 0 0 0 0 20 28 1 0 0 0 0 21 22 1 0 0 0 0 22 23 2 0 0 0 0 22 24 1 0 0 0 0 24 25 1 0 0 0 0 25 26 1 0 0 0 0 25 27 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	396.21
Volume:	405.645
LogP:	0.75
LogD:	-0.651
LogS:	-1.652
# Rotatable Bonds:	6
TPSA:	116.45
# H-Bond Aceptor:	7
# H-Bond Donor:	4
# Rings:	2
# Heavy Atoms:	7

MedChem Properties

QED Drug-Likeness Score:	0.495
Synthetic Accessibility Score:	4.486
Fsp3:	0.667
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:	-5.451
MDCK Permeability:	7.857081982365344e-06
Pgp-inhibitor:	0.835
Pgp-substrate:	0.985
Human Intestinal Absorption (HIA):	0.871
20% Bioavailability (F20%):	0.007
30% Bioavailability (F30%):	0.035

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.172
Plasma Protein Binding (PPB):	55.66789245605469%
Volume Distribution (VD):	1.069
Pgp-substrate:	37.012081146240234%

ADMET: Metabolism

CYP1A2-inhibitor:	0.017
CYP1A2-substrate:	0.091
CYP2C19-inhibitor:	0.016
CYP2C19-substrate:	0.586
CYP2C9-inhibitor:	0.003
CYP2C9-substrate:	0.302
CYP2D6-inhibitor:	0.005
CYP2D6-substrate:	0.461
CYP3A4-inhibitor:	0.005
CYP3A4-substrate:	0.262

ADMET: Excretion

Clearance (CL):	1.318
Half-life (T1/2):	0.913

ADMET: Toxicity

hERG Blockers:	0.037
Human Hepatotoxicity (H-HT):	0.17
Drug-inuced Liver Injury (DILI):	0.058
AMES Toxicity:	0.69
Rat Oral Acute Toxicity:	0.541
Maximum Recommended Daily Dose:	0.25
Skin Sensitization:	0.586
Carcinogencity:	0.281
Eye Corrosion:	0.003
Eye Irritation:	0.018
Respiratory Toxicity:	0.843

Download Data

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

Natural Product: NPC191077

Natural Product ID:	NPC191077
*Common Name:**	ZQNWZSDLRNNPNH-QXRHVDDYSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	ZQNWZSDLRNNPNH-QXRHVDDYSA-N
Standard InCHI:	InChI=1S/C21H32O7/c1-12(5-6-15-13(2)9-14(23)10-21(15,3)4)7-8-27-20-19(26)18(25)17(24)16(11-22)28-20/h5-7,9,15-20,22,24-26H,8,10-11H2,1-4H3/b6-5+,12-7+/t15-,16+,17+,18-,19+,20+/m0/s1
SMILES:	C/C(=CCO[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)/C=C/[C@H]1C(=CC(=O)CC1(C)C)C
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
NPO22761	Gentiana cruciata	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1016/S0031-9422(00)88887-1]
NPO25472	Garcinia cowa	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1071/CH03175]
NPO14117	Diplodia sapinea	Species	Botryosphaeriaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[10075753]
NPO24512	Xestospongia testudinaria	Species	Petrosiidae	Eukaryota	n.a.	n.a.	n.a.	PMID[10543913]
NPO25046	Aplidium meridianum	Species	Polyclinidae	Eukaryota	n.a.	South Georgia Islands, South Atlantic	n.a.	PMID[15026054]
NPO25472	Garcinia cowa	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19299148]
NPO25391	Vitex glabrata	Species	Lamiaceae	Eukaryota	leaves	Chantaburi Province, Thailand	2007-Nov	PMID[19943620]
NPO25472	Garcinia cowa	Species	Clusiaceae	Eukaryota	twigs	n.a.	n.a.	PMID[20058933]
NPO28887	Eupomatia laurina	Species	Eupomatiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21504145]
NPO24745	Salvia cavaleriei	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24256484]
NPO25472	Garcinia cowa	Species	Clusiaceae	Eukaryota	flowers	Pakook, Muang District, Chiang Rai Province, Thailand	2013-Feb	PMID[25651042]
NPO25472	Garcinia cowa	Species	Clusiaceae	Eukaryota	young fruits	Khokkhon, Tha Bo District, Nong Khai Province, Thailand	2011-Aug	PMID[25651042]
NPO25416	Uncaria cordata	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[27128898]
NPO22780	Sphaeranthus africanus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[30074787]
NPO25472	Garcinia cowa	Species	Clusiaceae	Eukaryota	Leaves	n.a.	n.a.	PMID[31860303]
NPO25046	Aplidium meridianum	Species	Polyclinidae	Eukaryota	n.a.	n.a.	n.a.	PMID[9748381]
NPO25145	Cydonia oblonga	Species	Rosaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO25145	Cydonia oblonga	Species	Rosaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO25145	Cydonia oblonga	Species	Rosaceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO25145	Cydonia oblonga	Species	Rosaceae	Eukaryota	Fruits	n.a.		Database[FooDB]
NPO24601	Rumex dentatus	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO25472	Garcinia cowa	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO25145	Cydonia oblonga	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO13588	Sanguinaria canadensis	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO13767	Woodfordia fruticosa	Species	Lythraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO25416	Uncaria cordata	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO24077	Astragalus pterocarpus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO25145	Cydonia oblonga	Species	Rosaceae	Eukaryota	Fruits	n.a.		Database[Phenol-Explorer]
NPO13588	Sanguinaria canadensis	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO24601	Rumex dentatus	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13767	Woodfordia fruticosa	Species	Lythraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO25145	Cydonia oblonga	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO25472	Garcinia cowa	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO25416	Uncaria cordata	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO24077	Astragalus pterocarpus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO25145	Cydonia oblonga	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO24601	Rumex dentatus	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO13767	Woodfordia fruticosa	Species	Lythraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5027	Peniophora polygonia	Species	Peniophoraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22780	Sphaeranthus africanus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25091	Samadera bidwillii	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14117	Diplodia sapinea	Species	Botryosphaeriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25700	Psiadia punctulata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28887	Eupomatia laurina	Species	Eupomatiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24745	Salvia cavaleriei	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25472	Garcinia cowa	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13588	Sanguinaria canadensis	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23568	Guatteria pogonopus	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18842	Gnaphalium gaudichaudianum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25416	Uncaria cordata	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25625	Hymenophyllum recurvum	Species	Hymenophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25364	Didemnum candidum	Species	Didemnidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22761	Gentiana cruciata	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22293	Bryobium hyacinthoides	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25145	Cydonia oblonga	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24512	Xestospongia testudinaria	Species	Petrosiidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25391	Vitex glabrata	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24077	Astragalus pterocarpus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24601	Rumex dentatus	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25046	Aplidium meridianum	Species	Polyclinidae	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 NPC191077 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	191
0.1-0.2	1075
0.2-0.3	4285
0.3-0.4	7966
0.4-0.5	15068
0.5-0.6	8645
0.6-0.7	4840
0.7-0.8	592
0.8-0.85	18
0.85-0.9	7
0.9-0.95	8
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 NPC191077 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	1296
0.2-0.3	3825
0.3-0.4	2571
0.4-0.5	853
0.5-0.6	344
0.6-0.7	89
0.7-0.8	4
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