NPASS Compound

Structure

NPC97309 OpenBabel06302215242D 44 48 0 0 1 0 0 0 0 0999 V2000 2.8179 2.4624 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8397 2.2545 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1706 2.9977 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4796 3.9487 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4578 4.1566 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1269 3.4135 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1051 3.6214 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7742 2.8782 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7523 3.0862 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0613 4.0372 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.4215 2.3430 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.1124 1.3920 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 5.1343 1.1840 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8253 0.2330 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.4944 -0.5102 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 6.4726 -0.3023 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 6.7816 0.6488 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 7.7597 0.8567 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 7.1417 -1.0454 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.1854 -1.4612 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.2072 -1.6691 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.8005 -2.5827 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8060 -2.4781 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1369 -3.2213 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4459 -4.1723 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -1.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.4641 -1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.4641 -0.0000 0.0000 C 0 0 0 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 1.7321 -1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8660 -1.5000 0.0000 O 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 1 0 0 0 0 0 0 0 0 0 -1.7321 -1.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.7321 -0.0000 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 -0.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 2.0000 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 -2.5981 0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.1925 2.7897 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 4 1 0 0 0 0 3 44 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 6 7 1 0 0 0 0 7 8 2 0 0 0 0 8 9 1 0 0 0 0 9 10 2 0 0 0 0 9 11 1 0 0 0 0 12 11 1 1 0 0 0 12 13 1 0 0 0 0 12 17 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 15 20 1 6 0 0 0 16 17 1 0 0 0 0 16 19 1 1 0 0 0 17 18 1 6 0 0 0 21 20 1 6 0 0 0 21 22 1 0 0 0 0 21 27 1 0 0 0 0 22 23 2 0 0 0 0 23 24 1 0 0 0 0 24 25 1 0 0 0 0 26 23 1 1 0 0 0 26 27 1 0 0 0 0 26 31 1 0 0 0 0 27 28 1 1 0 0 0 28 29 2 0 0 0 0 29 30 1 0 0 0 0 30 31 1 0 0 0 0 31 32 1 6 0 0 0 33 32 1 1 0 0 0 33 34 1 0 0 0 0 33 40 1 0 0 0 0 34 35 1 0 0 0 0 34 43 1 6 0 0 0 35 36 1 0 0 0 0 35 42 1 1 0 0 0 36 37 1 0 0 0 0 36 41 1 6 0 0 0 37 38 1 1 0 0 0 37 40 1 0 0 0 0 38 39 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	624.21
Volume:	580.756
LogP:	0.025
LogD:	-0.259
LogS:	-2.202
# Rotatable Bonds:	10
TPSA:	234.29
# H-Bond Aceptor:	15
# H-Bond Donor:	8
# Rings:	5
# Heavy Atoms:	15

MedChem Properties

QED Drug-Likeness Score:	0.081
Synthetic Accessibility Score:	5.366
Fsp3:	0.552
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.388
MDCK Permeability:	0.00010678460967028514
Pgp-inhibitor:	0.001
Pgp-substrate:	0.997
Human Intestinal Absorption (HIA):	0.955
20% Bioavailability (F20%):	0.3
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.181
Plasma Protein Binding (PPB):	58.6284065246582%
Volume Distribution (VD):	0.454
Pgp-substrate:	25.820783615112305%

ADMET: Metabolism

CYP1A2-inhibitor:	0.017
CYP1A2-substrate:	0.01
CYP2C19-inhibitor:	0.017
CYP2C19-substrate:	0.061
CYP2C9-inhibitor:	0.004
CYP2C9-substrate:	0.045
CYP2D6-inhibitor:	0.003
CYP2D6-substrate:	0.099
CYP3A4-inhibitor:	0.047
CYP3A4-substrate:	0.043

ADMET: Excretion

Clearance (CL):	1.014
Half-life (T1/2):	0.881

ADMET: Toxicity

hERG Blockers:	0.155
Human Hepatotoxicity (H-HT):	0.131
Drug-inuced Liver Injury (DILI):	0.961
AMES Toxicity:	0.1
Rat Oral Acute Toxicity:	0.458
Maximum Recommended Daily Dose:	0.054
Skin Sensitization:	0.714
Carcinogencity:	0.571
Eye Corrosion:	0.003
Eye Irritation:	0.013
Respiratory Toxicity:	0.612

Download Data

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

Natural Product: NPC97309

Natural Product ID:	NPC97309
*Common Name:**	QMXKOUSEDUDBEY-LNYAFLLHSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	QMXKOUSEDUDBEY-LNYAFLLHSA-N
Standard InCHI:	InChI=1S/C29H36O15/c30-10-14-9-17(16-7-8-39-27(21(14)16)44-29-26(38)24(36)22(34)18(11-31)43-29)42-28-25(37)23(35)19(12-40-28)41-20(33)6-3-13-1-4-15(32)5-2-13/h1-9,16-19,21-32,34-38H,10-12H2/b6-3+/t16-,17+,18+,19+,21+,22+,23-,24-,25+,26+,27-,28-,29-/m0/s1
SMILES:	c1cc(ccc1/C=C/C(=O)O[C@@H]1CO[C@H]([C@@H]([C@H]1O)O)O[C@@H]1C=C(CO)[C@@H]2[C@H]1C=CO[C@H]2O[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:	102445639
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

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Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO12373	Vinca minor	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6413	Viguiera stenoloba	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11342	Sideritis trojana	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9162	Nicotiana affinis	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11625	Markhamia stipulata	Species	Bignoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13327	Phomopsis leptostromiformis	Species	Valsaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO944	Senecio sandersonii	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12598	Osteospermum fruticosum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7135	Mollugo spergula	Species	Molluginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15456	Sideritis soluta	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

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☑ 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

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Organism ID	NP ID	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference
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☑ 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

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
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☑ 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 NPC97309 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	296
0.1-0.2	1239
0.2-0.3	2949
0.3-0.4	7499
0.4-0.5	10286
0.5-0.6	9875
0.6-0.7	8644
0.7-0.8	1631
0.8-0.85	181
0.85-0.9	68
0.9-0.95	28
0.95-1	1

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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 NPC97309 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	239
0.1-0.2	727
0.2-0.3	1616
0.3-0.4	2999
0.4-0.5	2058
0.5-0.6	1200
0.6-0.7	298
0.7-0.8	12
0.8-0.85	0
0.85-0.9	1
0.9-0.95	0
0.95-1	0

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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