NPASS Compound

Structure

NPC26091 OpenBabel06302215502D 30 33 0 0 1 0 0 0 0 0999 V2000 -6.1472 -4.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.1472 -3.3090 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.2812 -2.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4152 -3.3090 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.2812 -1.8090 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.1472 -1.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.0132 -1.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.0132 -2.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.8793 -3.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.7453 -2.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.7453 -1.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.8793 -1.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.6963 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -10.2841 -2.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.6963 -3.1180 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.4152 -1.3090 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.5491 -1.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6831 -1.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6831 -0.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8171 0.1910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9511 -0.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9511 -1.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8171 -1.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -1.6180 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.5878 -0.8090 0.0000 C 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 -4.4152 -0.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5491 0.1910 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.2812 0.1910 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.2812 1.1910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 1 0 0 0 0 3 4 2 0 0 0 0 3 5 1 0 0 0 0 5 6 1 6 0 0 0 5 16 1 0 0 0 0 6 7 1 0 0 0 0 7 12 2 0 0 0 0 7 8 1 0 0 0 0 8 9 2 0 0 0 0 9 10 1 0 0 0 0 10 15 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 11 13 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 16 17 1 6 0 0 0 16 27 1 0 0 0 0 17 18 1 0 0 0 0 18 23 2 0 0 0 0 18 19 1 0 0 0 0 19 20 2 0 0 0 0 20 21 1 0 0 0 0 21 26 1 0 0 0 0 21 22 2 0 0 0 0 22 23 1 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 27 28 2 0 0 0 0 27 29 1 0 0 0 0 29 30 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	414.13
Volume:	404.072
LogP:	3.112
LogD:	3.739
LogS:	-5.378
# Rotatable Bonds:	9
TPSA:	89.52
# H-Bond Aceptor:	8
# H-Bond Donor:	0
# Rings:	4
# Heavy Atoms:	8

MedChem Properties

QED Drug-Likeness Score:	0.639
Synthetic Accessibility Score:	3.233
Fsp3:	0.364
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.811
MDCK Permeability:	3.336562076583505e-05
Pgp-inhibitor:	0.999
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.001
20% Bioavailability (F20%):	0.005
30% Bioavailability (F30%):	0.058

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.849
Plasma Protein Binding (PPB):	92.3670425415039%
Volume Distribution (VD):	1.297
Pgp-substrate:	5.177992343902588%

ADMET: Metabolism

CYP1A2-inhibitor:	0.988
CYP1A2-substrate:	0.516
CYP2C19-inhibitor:	0.979
CYP2C19-substrate:	0.664
CYP2C9-inhibitor:	0.926
CYP2C9-substrate:	0.903
CYP2D6-inhibitor:	0.962
CYP2D6-substrate:	0.902
CYP3A4-inhibitor:	0.991
CYP3A4-substrate:	0.859

ADMET: Excretion

Clearance (CL):	14.574
Half-life (T1/2):	0.253

ADMET: Toxicity

hERG Blockers:	0.303
Human Hepatotoxicity (H-HT):	0.495
Drug-inuced Liver Injury (DILI):	0.852
AMES Toxicity:	0.036
Rat Oral Acute Toxicity:	0.004
Maximum Recommended Daily Dose:	0.222
Skin Sensitization:	0.625
Carcinogencity:	0.793
Eye Corrosion:	0.003
Eye Irritation:	0.039
Respiratory Toxicity:	0.079

Download Data

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

Natural Product: NPC26091

Natural Product ID:	NPC26091
*Common Name:**	YKLDSNGNWJIDLS-HZPDHXFCSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	YKLDSNGNWJIDLS-HZPDHXFCSA-N
Standard InCHI:	InChI=1S/C22H22O8/c1-25-21(23)15(7-13-3-5-17-19(9-13)29-11-27-17)16(22(24)26-2)8-14-4-6-18-20(10-14)30-12-28-18/h3-6,9-10,15-16H,7-8,11-12H2,1-2H3/t15-,16-/m1/s1
SMILES:	COC(=O)[C@H](Cc1ccc2c(c1)OCO2)[C@@H](Cc1ccc2c(c1)OCO2)C(=O)OC
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	46894017
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0001392] Lignans, neolignans and related compounds [CHEMONTID:0001969] Dibenzylbutane lignans

*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
NPO18553.1	Heliopsis helianthoides	Under-species	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[24972328]
NPO18553.1	Heliopsis helianthoides	Under-species	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[25479041]
NPO3631	Euphorbia boetica	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31507181]
NPO15606	Smyrnium olusatrum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO15606	Smyrnium olusatrum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO17854	Neobeguea mahafalensis	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15033	Emiliania huxleyi	Species	0elaerhabdaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16935	Heliopsis buphthalmoides	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18095	Siphocampylus macropodus	Species	Campanulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22240	Microbulbifer variabilis	Species	Microbulbiferaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO15418	Canavalia obtusifolia	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16716	Gracilaria edulis	Species	Gracilariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17463	Geijera balansae	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15606	Smyrnium olusatrum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6745	Montanoa leucantha	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15775	Kielmeyera pumila	Species	Calophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3631	Euphorbia boetica	Species	Euphorbiaceae	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 NPC26091 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 NPC26091 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