NPASS Compound

Structure

NPC252041 OpenBabel06302216142D 27 29 0 0 1 0 0 0 0 0999 V2000 0.4067 0.9135 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4013 0.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0704 1.5522 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7614 2.5032 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6092 -0.1691 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.7431 -0.6691 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.7431 -1.6691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6092 -2.1691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4752 -1.6691 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.4752 -0.6691 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.3412 -0.1691 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.2072 -0.6691 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.2072 -1.6691 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 5.0733 -2.1691 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 5.9393 -1.6691 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 5.9393 -0.6691 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 6.8053 -0.1691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.6713 -0.6691 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.0733 -0.1691 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.8053 -2.1691 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.0733 -3.1691 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.3412 -2.1691 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.1229 -2.1691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9889 -1.6691 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.1229 -3.1691 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.9781 -0.2079 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 26 1 0 0 0 0 1 2 2 0 0 0 0 2 3 1 0 0 0 0 3 4 1 0 0 0 0 5 2 1 1 0 0 0 5 6 1 0 0 0 0 5 10 1 0 0 0 0 6 7 1 1 0 0 0 6 26 1 0 0 0 0 7 8 2 0 0 0 0 7 23 1 0 0 0 0 8 9 1 0 0 0 0 9 10 1 0 0 0 0 10 11 1 6 0 0 0 12 11 1 6 0 0 0 12 13 1 0 0 0 0 12 19 1 0 0 0 0 13 14 1 0 0 0 0 13 22 1 1 0 0 0 14 15 1 0 0 0 0 14 21 1 6 0 0 0 15 16 1 0 0 0 0 15 20 1 1 0 0 0 16 17 1 6 0 0 0 16 19 1 0 0 0 0 17 18 1 0 0 0 0 23 24 2 0 0 0 0 23 25 1 0 0 0 0 26 27 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	390.12
Volume:	348.406
LogP:	-1.195
LogD:	-0.639
LogS:	-0.537
# Rotatable Bonds:	5
TPSA:	186.37
# H-Bond Aceptor:	11
# H-Bond Donor:	7
# Rings:	3
# Heavy Atoms:	11

MedChem Properties

QED Drug-Likeness Score:	0.233
Synthetic Accessibility Score:	4.828
Fsp3:	0.688
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	1
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.425
MDCK Permeability:	0.00019750712090171874
Pgp-inhibitor:	0.0
Pgp-substrate:	0.116
Human Intestinal Absorption (HIA):	0.317
20% Bioavailability (F20%):	0.053
30% Bioavailability (F30%):	0.998

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.278
Plasma Protein Binding (PPB):	19.066020965576172%
Volume Distribution (VD):	0.274
Pgp-substrate:	66.50562286376953%

ADMET: Metabolism

CYP1A2-inhibitor:	0.015
CYP1A2-substrate:	0.016
CYP2C19-inhibitor:	0.014
CYP2C19-substrate:	0.048
CYP2C9-inhibitor:	0.002
CYP2C9-substrate:	0.034
CYP2D6-inhibitor:	0.01
CYP2D6-substrate:	0.099
CYP3A4-inhibitor:	0.011
CYP3A4-substrate:	0.017

ADMET: Excretion

Clearance (CL):	1.466
Half-life (T1/2):	0.908

ADMET: Toxicity

hERG Blockers:	0.026
Human Hepatotoxicity (H-HT):	0.107
Drug-inuced Liver Injury (DILI):	0.974
AMES Toxicity:	0.065
Rat Oral Acute Toxicity:	0.357
Maximum Recommended Daily Dose:	0.005
Skin Sensitization:	0.122
Carcinogencity:	0.935
Eye Corrosion:	0.003
Eye Irritation:	0.091
Respiratory Toxicity:	0.915

Download Data

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

Natural Product: NPC252041

Natural Product ID:	NPC252041
*Common Name:**	ZVXWFPTVHBWJOU-AWQYILTISA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	ZVXWFPTVHBWJOU-AWQYILTISA-N
Standard InCHI:	InChI=1S/C16H22O11/c17-2-5-1-7(19)10-6(14(23)24)4-25-15(9(5)10)27-16-13(22)12(21)11(20)8(3-18)26-16/h1,4,7-13,15-22H,2-3H2,(H,23,24)/t7-,8-,9-,10+,11-,12+,13-,15+,16+/m1/s1
SMILES:	C1=C(CO)[C@@H]2[C@@H](C(=CO[C@H]2O[C@H]2[C@@H]([C@H]([C@@H]([C@@H](CO)O2)O)O)O)C(=O)O)[C@@H]1O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	21602023
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0002049] Terpene glycosides [CHEMONTID:0004081] Iridoid O-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
NPO10429	Gentiana scabra	Species	Gentianaceae	Eukaryota	n.a.	rhizome	n.a.	PMID[17404979]
NPO12604	Phakellia dendyi	Species	Bubaridae	Eukaryota	n.a.	Byron Strait, Papua New Guinea	2003	PMID[18327911]
NPO10429	Gentiana scabra	Species	Gentianaceae	Eukaryota	n.a.	root	n.a.	PMID[26129938]
NPO40024	Arcytophyllum thymifolium	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[27509358]
NPO10429	Gentiana scabra	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO11045	Paederia scandens	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO11045	Paederia scandens	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO10429	Gentiana scabra	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11045	Paederia scandens	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO10429	Gentiana scabra	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO10429	Gentiana scabra	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO7081	Sidastrum tehuacanum	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17497	Bohadschia koellikeri	Species	Holothuriidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11045	Paederia scandens	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3220	Aberia caffra	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO13955	Lippia javanica	Species	Verbenaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18170	Aconitum miyabei	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25931	Psammogeton canescens	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18375	Bauhinia tomentosa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3040	Acanthella carteri	Species	Melastomataceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19265	Metarhizium viride	Species	Clavicipitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19124	Guevaria sodiroi	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO6819	Cardopatium corymbosum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12604	Phakellia dendyi	Species	Bubaridae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22168	Scutellaria rivularis	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3034	Lonchocarpus yucatanensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13581	Daphnandra repandula	Species	Atherospermataceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10429	Gentiana scabra	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18057	Chlorobium phaeobacteroides	Species	Chlorobiaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO1540	Scopolia tangutica	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16962	Dipsacus laciniatus	Species	Caprifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24096	Furcraea macrophylla	Species	Asparagaceae	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 NPC252041 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 NPC252041 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