NPASS Compound

Structure

NPC305392 OpenBabel06302215192D 27 30 0 0 1 0 0 0 0 0999 V2000 -5.0733 -5.1691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2072 -4.6691 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.3412 -5.1691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3412 -6.1691 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.4752 -4.6691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2072 -3.6691 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.0733 -3.1691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0733 -2.1691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9393 -1.6691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.8053 -2.1691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.8053 -3.1691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9393 -3.6691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7564 -3.4781 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.3442 -2.6691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7564 -1.8601 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.3412 -3.1691 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.3412 -2.1691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2072 -1.6691 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.4752 -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 -0.7431 -1.6691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7431 -0.6691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6092 -0.1691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4752 -0.6691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4013 0.8090 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.4067 0.9135 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 2 1 1 1 0 0 0 2 3 1 0 0 0 0 2 6 1 0 0 0 0 3 4 2 0 0 0 0 3 5 1 0 0 0 0 6 7 1 0 0 0 0 6 16 1 1 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 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 21 22 1 0 0 0 0 22 27 1 0 0 0 0 22 23 2 0 0 0 0 23 24 1 0 0 0 0 23 25 1 0 0 0 0 25 26 1 0 0 0 0 26 27 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	370.11
Volume:	360.69
LogP:	3.42
LogD:	3.321
LogS:	-4.892
# Rotatable Bonds:	6
TPSA:	80.29
# H-Bond Aceptor:	7
# H-Bond Donor:	0
# Rings:	4
# Heavy Atoms:	7

MedChem Properties

QED Drug-Likeness Score:	0.747
Synthetic Accessibility Score:	3.193
Fsp3:	0.3
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.762
MDCK Permeability:	6.344797293422744e-05
Pgp-inhibitor:	0.508
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.002
20% Bioavailability (F20%):	0.058
30% Bioavailability (F30%):	0.466

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.071
Plasma Protein Binding (PPB):	99.44315338134766%
Volume Distribution (VD):	0.702
Pgp-substrate:	2.5372326374053955%

ADMET: Metabolism

CYP1A2-inhibitor:	0.935
CYP1A2-substrate:	0.249
CYP2C19-inhibitor:	0.981
CYP2C19-substrate:	0.152
CYP2C9-inhibitor:	0.931
CYP2C9-substrate:	0.9
CYP2D6-inhibitor:	0.986
CYP2D6-substrate:	0.891
CYP3A4-inhibitor:	0.972
CYP3A4-substrate:	0.366

ADMET: Excretion

Clearance (CL):	17.153
Half-life (T1/2):	0.264

ADMET: Toxicity

hERG Blockers:	0.14
Human Hepatotoxicity (H-HT):	0.258
Drug-inuced Liver Injury (DILI):	0.944
AMES Toxicity:	0.049
Rat Oral Acute Toxicity:	0.039
Maximum Recommended Daily Dose:	0.015
Skin Sensitization:	0.153
Carcinogencity:	0.816
Eye Corrosion:	0.008
Eye Irritation:	0.213
Respiratory Toxicity:	0.051

Download Data

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

Natural Product: NPC305392

Natural Product ID:	NPC305392
*Common Name:**	NYJDPARBGPGZBE-WYRIXSBYSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	NYJDPARBGPGZBE-WYRIXSBYSA-N
Standard InCHI:	InChI=1S/C20H18O7/c1-11(12(2)21)19(13-3-5-15-17(7-13)25-9-23-15)27-20(22)14-4-6-16-18(8-14)26-10-24-16/h3-8,11,19H,9-10H2,1-2H3/t11-,19+/m1/s1
SMILES:	C[C@H](C(=O)C)[C@@H](c1ccc2c(c1)OCO2)OC(=O)c1ccc2c(c1)OCO2
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0000296] Benzodioxoles

*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
NPO4562	Lonchocarpus urucu	Species	Fabaceae	Eukaryota	n.a.	root	n.a.	PMID[10075742]
NPO9740	Dacrycarpus imbricatus	Species	Podocarpaceae	Eukaryota	Twigs	n.a.	n.a.	PMID[32786878]
NPO6017	Artemisia arbuscula	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO9740	Dacrycarpus imbricatus	Species	Podocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO6017	Artemisia arbuscula	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13443	Doris montereyensis	Species	Dorididae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9094	Citrus reshni	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO378	Myristica argentea	Species	Myristicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO790	Cybister confusus	Species	Dytiscidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2622	Cheilanthes mysurensis	Species	Pteridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1477	Egregia menziesii	Species	Lessoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4562	Lonchocarpus urucu	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8794	Aconitum fauriei	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO182	Cylas formicarius	Species	Brentidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6559	Duddingtonia flagrans	Species	n.a.	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9234	Cynoctonum wilfordii	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO9740	Dacrycarpus imbricatus	Species	Podocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6017	Artemisia arbuscula	Species	Asteraceae	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 NPC305392 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	384
0.1-0.2	1493
0.2-0.3	3645
0.3-0.4	8363
0.4-0.5	10198
0.5-0.6	3881
0.6-0.7	6928
0.7-0.8	7358
0.8-0.85	378
0.85-0.9	62
0.9-0.95	4
0.95-1	3

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 NPC305392 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	318
0.1-0.2	892
0.2-0.3	1662
0.3-0.4	2647
0.4-0.5	1922
0.5-0.6	1103
0.6-0.7	473
0.7-0.8	129
0.8-0.85	3
0.85-0.9	1
0.9-0.95	0
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