NPASS Compound

Structure

NPC208128 OpenBabel06302216212D 26 28 0 0 1 0 0 0 0 0999 V2000 -3.1758 -3.6286 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1829 -3.5092 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5831 -4.3093 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9761 -5.2288 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3763 -6.0290 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.5903 -4.1899 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0096 -4.9901 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.1972 -3.2704 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.7971 -2.4703 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.7782 -2.6635 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5410 -2.0169 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.5356 -1.9124 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5111 -1.0174 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.3288 -0.4417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0341 0.5138 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0342 0.5288 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4586 1.3465 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7110 -0.4175 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.7431 -0.6691 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.3364 -1.5827 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.6581 -1.4781 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3272 -2.2213 0.0000 C 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 1.7796 -0.0933 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 -3.1288 -2.8259 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 3 4 1 0 0 0 0 3 6 1 0 0 0 0 4 5 1 0 0 0 0 6 7 2 0 0 0 0 6 8 1 0 0 0 0 9 8 1 6 0 0 0 9 10 1 0 0 0 0 9 20 1 0 0 0 0 10 11 1 0 0 0 0 11 12 1 6 0 0 0 11 13 1 0 0 0 0 11 26 1 0 0 0 0 13 14 1 6 0 0 0 13 18 1 0 0 0 0 14 15 1 0 0 0 0 15 16 2 0 0 0 0 16 17 1 0 0 0 0 18 16 1 6 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 19 25 1 1 0 0 0 20 21 1 6 0 0 0 21 22 2 0 0 0 0 21 23 1 0 0 0 0 23 24 2 0 0 0 0 23 25 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	362.17
Volume:	368.366
LogP:	0.582
LogD:	1.081
LogS:	-2.262
# Rotatable Bonds:	4
TPSA:	93.06
# H-Bond Aceptor:	6
# H-Bond Donor:	2
# Rings:	3
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.451
Synthetic Accessibility Score:	4.941
Fsp3:	0.6
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	2
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.74
MDCK Permeability:	2.0574112568283454e-05
Pgp-inhibitor:	0.045
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.289
20% Bioavailability (F20%):	0.084
30% Bioavailability (F30%):	0.806

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.024
Plasma Protein Binding (PPB):	74.13241577148438%
Volume Distribution (VD):	1.261
Pgp-substrate:	15.636380195617676%

ADMET: Metabolism

CYP1A2-inhibitor:	0.137
CYP1A2-substrate:	0.112
CYP2C19-inhibitor:	0.15
CYP2C19-substrate:	0.56
CYP2C9-inhibitor:	0.257
CYP2C9-substrate:	0.086
CYP2D6-inhibitor:	0.019
CYP2D6-substrate:	0.066
CYP3A4-inhibitor:	0.724
CYP3A4-substrate:	0.224

ADMET: Excretion

Clearance (CL):	5.292
Half-life (T1/2):	0.905

ADMET: Toxicity

hERG Blockers:	0.032
Human Hepatotoxicity (H-HT):	0.938
Drug-inuced Liver Injury (DILI):	0.935
AMES Toxicity:	0.045
Rat Oral Acute Toxicity:	0.327
Maximum Recommended Daily Dose:	0.188
Skin Sensitization:	0.809
Carcinogencity:	0.079
Eye Corrosion:	0.086
Eye Irritation:	0.393
Respiratory Toxicity:	0.8

Download Data

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

Natural Product: NPC208128

Natural Product ID:	NPC208128
*Common Name:**	QYKCTVZWKZFZNA-SIPRDXAKSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	QYKCTVZWKZFZNA-SIPRDXAKSA-N
Standard InCHI:	InChI=1S/C20H26O6/c1-5-12(9-21)19(23)25-14-8-20(4,24)13-7-6-10(2)15(13)17-16(14)11(3)18(22)26-17/h5-6,13-17,21,24H,3,7-9H2,1-2,4H3/b12-5-/t13-,14-,15+,16-,17-,20-/m1/s1
SMILES:	C/C=C(/CO)C(=O)O[C@@H]1C[C@](C)([C@@H]2CC=C(C)[C@@H]2[C@@H]2[C@@H]1C(=C)C(=O)O2)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:0001283] Terpene lactones [CHEMONTID:0001543] Sesquiterpene lactones [CHEMONTID:0001770] Guaianolides and derivatives

*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
NPO23542	Omphalotus illudens	Species	Omphalotaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11087609]
NPO23542	Omphalotus illudens	Species	Omphalotaceae	Eukaryota	mature fruiting bodies	n.a.	n.a.	PMID[14510611]
NPO23832	Cyclea sutchuenensis	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO3885	Ampulloclitocybe clavipes	Species	Tricholomataceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO23832	Cyclea sutchuenensis	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO23832	Cyclea sutchuenensis	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO23918	Cochlearia armoracia	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23542	Omphalotus illudens	Species	Omphalotaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23832	Cyclea sutchuenensis	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3885	Ampulloclitocybe clavipes	Species	Tricholomataceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24088	Senecio glutinosus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23316	Lappula anocarpa	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17405	Cinnamomum iners	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21959	Syncarpia glomulifera	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22805	Saussurea japonica	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23959	Echium humile	Species	Boraginaceae	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 NPC208128 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	219
0.1-0.2	1252
0.2-0.3	4660
0.3-0.4	8863
0.4-0.5	14516
0.5-0.6	7424
0.6-0.7	4213
0.7-0.8	1276
0.8-0.85	211
0.85-0.9	44
0.9-0.95	12
0.95-1	7

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 NPC208128 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	203
0.1-0.2	1837
0.2-0.3	3671
0.3-0.4	2276
0.4-0.5	744
0.5-0.6	330
0.6-0.7	62
0.7-0.8	23
0.8-0.85	2
0.85-0.9	1
0.9-0.95	1
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