NPASS Compound

Structure

NPC306375 OpenBabel06302216162D 61 67 0 0 1 0 0 0 0 0999 V2000 -1.7321 -0.0000 0.0000 C 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 2 0 0 0 0 0 0 0 0 0 0.8660 0.5000 0.0000 C 0 0 2 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 1.7321 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.4641 -1.0000 0.0000 C 0 0 2 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 4.3301 -2.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.4641 -3.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.5981 -2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -4.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -5.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -6.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -5.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -6.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -5.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -6.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -7.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -7.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 -7.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 -6.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -5.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 -7.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -6.0000 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 5.1962 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 -2.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 6.9282 -3.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 7.7942 -2.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 7.7942 -1.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 6.9282 -1.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 6.9282 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 8.6603 -1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 8.6603 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 9.5263 -2.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 10.3923 -3.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 11.2583 -2.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 11.2583 -1.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 10.3923 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.5263 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 12.1244 -1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 12.1244 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 10.3923 -4.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 -4.0000 0.0000 O 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 3.4641 0.0000 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 1 1 1 0 0 0 2 3 1 0 0 0 0 2 58 1 0 0 0 0 3 4 1 0 0 0 0 3 61 1 6 0 0 0 4 5 1 0 0 0 0 4 60 1 1 0 0 0 5 6 1 0 0 0 0 5 59 1 1 0 0 0 6 7 1 6 0 0 0 6 58 1 0 0 0 0 7 8 1 0 0 0 0 9 8 1 1 0 0 0 9 10 1 0 0 0 0 9 14 1 0 0 0 0 10 11 1 0 0 0 0 10 57 1 1 0 0 0 11 12 1 0 0 0 0 11 56 1 1 0 0 0 12 13 1 0 0 0 0 12 36 1 6 0 0 0 13 14 1 0 0 0 0 13 15 1 1 0 0 0 15 16 1 0 0 0 0 16 26 2 0 0 0 0 16 17 1 0 0 0 0 17 18 2 0 0 0 0 17 19 1 0 0 0 0 19 24 2 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 35 1 0 0 0 0 21 22 1 0 0 0 0 22 23 2 0 0 0 0 22 34 1 0 0 0 0 23 24 1 0 0 0 0 24 25 1 0 0 0 0 25 26 1 0 0 0 0 26 27 1 0 0 0 0 27 32 2 0 0 0 0 27 28 1 0 0 0 0 28 29 2 0 0 0 0 29 30 1 0 0 0 0 30 31 2 0 0 0 0 30 33 1 0 0 0 0 31 32 1 0 0 0 0 37 36 1 6 0 0 0 37 38 1 0 0 0 0 37 43 1 0 0 0 0 38 39 1 0 0 0 0 38 55 1 1 0 0 0 39 40 1 0 0 0 0 39 45 1 1 0 0 0 40 41 1 0 0 0 0 40 44 1 6 0 0 0 41 42 1 1 0 0 0 41 43 1 0 0 0 0 46 45 1 6 0 0 0 46 47 1 0 0 0 0 46 51 1 0 0 0 0 47 48 1 0 0 0 0 47 54 1 1 0 0 0 48 49 1 0 0 0 0 48 53 1 6 0 0 0 49 50 1 0 0 0 0 49 52 1 6 0 0 0 50 51 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	386.25
Volume:	414.049
LogP:	3.034
LogD:	3.17
LogS:	-3.066
# Rotatable Bonds:	4
TPSA:	74.6
# H-Bond Aceptor:	4
# H-Bond Donor:	2
# Rings:	4
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.717
Synthetic Accessibility Score:	4.649
Fsp3:	0.75
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
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:	-4.898
MDCK Permeability:	4.1261435399064794e-05
Pgp-inhibitor:	0.942
Pgp-substrate:	0.963
Human Intestinal Absorption (HIA):	0.168
20% Bioavailability (F20%):	0.008
30% Bioavailability (F30%):	0.025

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.84
Plasma Protein Binding (PPB):	90.40705871582031%
Volume Distribution (VD):	0.653
Pgp-substrate:	5.762156963348389%

ADMET: Metabolism

CYP1A2-inhibitor:	0.01
CYP1A2-substrate:	0.215
CYP2C19-inhibitor:	0.023
CYP2C19-substrate:	0.838
CYP2C9-inhibitor:	0.096
CYP2C9-substrate:	0.107
CYP2D6-inhibitor:	0.002
CYP2D6-substrate:	0.232
CYP3A4-inhibitor:	0.054
CYP3A4-substrate:	0.616

ADMET: Excretion

Clearance (CL):	3.294
Half-life (T1/2):	0.91

ADMET: Toxicity

hERG Blockers:	0.017
Human Hepatotoxicity (H-HT):	0.174
Drug-inuced Liver Injury (DILI):	0.22
AMES Toxicity:	0.144
Rat Oral Acute Toxicity:	0.843
Maximum Recommended Daily Dose:	0.98
Skin Sensitization:	0.934
Carcinogencity:	0.424
Eye Corrosion:	0.021
Eye Irritation:	0.801
Respiratory Toxicity:	0.971

Download Data

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

Natural Product: NPC306375

Natural Product ID:	NPC306375
*Common Name:**	ALGKOJZNIQBASA-PJQWMBFESA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	ALGKOJZNIQBASA-PJQWMBFESA-N
Standard InCHI:	InChI=1S/C38H48O23/c1-11-21(43)26(48)29(51)35(55-11)54-10-19-24(46)27(49)34(61-37-30(52)32(22(44)12(2)56-37)59-36-28(50)23(45)17(42)9-53-36)38(58-19)60-33-25(47)20-16(41)7-15(40)8-18(20)57-31(33)13-3-5-14(39)6-4-13/h3-8,11-12,17,19,21-24,26-30,32,34-46,48-52H,9-10H2,1-2H3/t11-,12-,17-,19-,21-,22-,23-,24+,26+,27+,28+,29+,30+,32+,34-,35+,36-,37-,38+/m0/s1
SMILES:	C[C@H]1[C@@H]([C@H]([C@H]([C@H](OC[C@H]2[C@H]([C@H]([C@@H]([C@H](O2)Oc2c(=O)c3c(cc(cc3oc2c2ccc(cc2)O)O)O)O[C@H]2[C@@H]([C@@H]([C@H]([C@H](C)O2)O)O[C@H]2[C@@H]([C@H]([C@H](CO2)O)O)O)O)O)O)O1)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0001111] Flavonoid glycosides [CHEMONTID:0001583] Flavonoid O-glycosides [CHEMONTID:0003531] Flavonoid-3-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
NPO20440	Chrysanthemum x morifolium	Species	Asteraceae	Eukaryota	Flowers	n.a.	n.a.	DOI[10.1016/j.foodchem.2009.03.042]
NPO20440	Chrysanthemum x morifolium	Species	Asteraceae	Eukaryota	Flowers	n.a.	n.a.	DOI[10.3136/fstr.15.499]
NPO20440	Chrysanthemum x morifolium	Species	Asteraceae	Eukaryota	Flowers	n.a.	n.a.	DOI[10.5897/AJB10.140]
NPO20440	Chrysanthemum x morifolium	Species	Asteraceae	Eukaryota	Flowers	n.a.	n.a.	DOI[10.5897/AJB2010.000-3252]
NPO22471	Maytenus cuzcoina	Species	Celastraceae	Eukaryota	root bark;leaves	Huayllabamba-Urquillos, Province of Urabamba, Cusco (Peru); Parque Nacional El Imposible, El Salvador	n.a.	PMID[16038541]
NPO20440	Chrysanthemum x morifolium	Species	Asteraceae	Eukaryota	Flowers	Tongxiang, China	n.a.	PMID[24621197]
NPO11296	Arthrinium arundinis	Species	Apiosporaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25626143]
NPO22471	Maytenus cuzcoina	Species	Celastraceae	Eukaryota	root bark	Urubamba, Cusco, Peru	n.a.	PMID[25927586]
NPO20440	Chrysanthemum x morifolium	Species	Asteraceae	Eukaryota	Flowers	n.a.	n.a.	PMID[28248102]
NPO22524	Ranunculus sceleratus	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO20440	Chrysanthemum x morifolium	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO22524	Ranunculus sceleratus	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO22409	Cyanostegia microphylla	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO20440	Chrysanthemum x morifolium	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO1118	Elymus repens	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22806	Euphorbia leuconeura	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22409	Cyanostegia microphylla	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13457	Acacia pachyphloia	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16652	Centipeda cunninghami	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19626	Lavandula dentata	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21358	Pyrus ussuriensis	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22593	Graphis rikuzensis	Species	Aclididae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20702	Discodermia dissoluta	Species	Theonellidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22524	Ranunculus sceleratus	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11296	Arthrinium arundinis	Species	Apiosporaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22471	Maytenus cuzcoina	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20440	Chrysanthemum x morifolium	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9876	Isocoma pluriflora	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20567	Montipora mollis	Species	Acroporidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22006	Maytenus aquifolium	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2217	Valeriana wolgensis	Species	Caprifoliaceae	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 NPC306375 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	453
0.1-0.2	1756
0.2-0.3	4147
0.3-0.4	9533
0.4-0.5	8615
0.5-0.6	5624
0.6-0.7	5965
0.7-0.8	5115
0.8-0.85	788
0.85-0.9	446
0.9-0.95	220
0.95-1	35

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 NPC306375 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	401
0.1-0.2	944
0.2-0.3	1998
0.3-0.4	2809
0.4-0.5	1854
0.5-0.6	788
0.6-0.7	238
0.7-0.8	94
0.8-0.85	15
0.85-0.9	5
0.9-0.95	4
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