NPASS Compound

Structure

NPC298366 OpenBabel06302215182D 24 28 0 0 1 0 0 0 0 0999 V2000 1.8660 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0000 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 1.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.0000 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7321 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7321 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6831 -0.3090 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.2709 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6831 1.3090 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.9659 0.7412 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2247 -0.2247 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.6730 1.4483 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6390 1.1895 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3461 1.8966 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0872 2.8625 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1213 3.1213 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4142 2.4142 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4483 2.6730 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.2588 1.9659 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.2247 2.2247 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.7944 3.5696 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.8978 0.2235 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 8 2 0 0 0 0 1 2 1 0 0 0 0 2 5 2 0 0 0 0 2 3 1 0 0 0 0 4 3 1 6 0 0 0 4 21 1 0 0 0 0 4 5 1 0 0 0 0 4 12 1 0 0 0 0 5 6 1 0 0 0 0 6 7 2 0 0 0 0 7 11 1 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 12 13 2 0 0 0 0 12 14 1 0 0 0 0 14 19 2 0 0 0 0 14 15 1 0 0 0 0 15 16 2 0 0 0 0 15 24 1 0 0 0 0 16 17 1 0 0 0 0 17 18 2 0 0 0 0 17 23 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 1 0 0 0 0 21 22 1 1 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	328.06
Volume:	302.882
LogP:	2.407
LogD:	1.811
LogS:	-3.728
# Rotatable Bonds:	0
TPSA:	105.45
# H-Bond Aceptor:	7
# H-Bond Donor:	3
# Rings:	5
# Heavy Atoms:	7

MedChem Properties

QED Drug-Likeness Score:	0.667
Synthetic Accessibility Score:	4.221
Fsp3:	0.235
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.417
MDCK Permeability:	9.081489224627148e-06
Pgp-inhibitor:	0.006
Pgp-substrate:	0.422
Human Intestinal Absorption (HIA):	0.007
20% Bioavailability (F20%):	0.284
30% Bioavailability (F30%):	0.573

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.04
Plasma Protein Binding (PPB):	96.26143646240234%
Volume Distribution (VD):	0.744
Pgp-substrate:	2.6625468730926514%

ADMET: Metabolism

CYP1A2-inhibitor:	0.872
CYP1A2-substrate:	0.344
CYP2C19-inhibitor:	0.773
CYP2C19-substrate:	0.123
CYP2C9-inhibitor:	0.617
CYP2C9-substrate:	0.812
CYP2D6-inhibitor:	0.938
CYP2D6-substrate:	0.449
CYP3A4-inhibitor:	0.882
CYP3A4-substrate:	0.162

ADMET: Excretion

Clearance (CL):	9.634
Half-life (T1/2):	0.589

ADMET: Toxicity

hERG Blockers:	0.033
Human Hepatotoxicity (H-HT):	0.258
Drug-inuced Liver Injury (DILI):	0.631
AMES Toxicity:	0.932
Rat Oral Acute Toxicity:	0.684
Maximum Recommended Daily Dose:	0.936
Skin Sensitization:	0.704
Carcinogencity:	0.915
Eye Corrosion:	0.003
Eye Irritation:	0.425
Respiratory Toxicity:	0.824

Download Data

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

Natural Product: NPC298366

Natural Product ID:	NPC298366
*Common Name:**	KEAXKVGKQLXEGB-SJORKVTESA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	KEAXKVGKQLXEGB-SJORKVTESA-N
Standard InCHI:	InChI=1S/C17H12O7/c18-8-2-10(19)14-13(3-8)24-16(21)17(15(14)20)5-7-1-11-12(4-9(7)17)23-6-22-11/h1-4,16,18-19,21H,5-6H2/t16-,17+/m1/s1
SMILES:	c1c2C[C@]3(c2cc2c1OCO2)C(=O)c1c(cc(cc1O[C@H]3O)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:0002506] Isoflavonoids [CHEMONTID:0001612] Isoflavans [CHEMONTID:0001828] Isoflavanols

*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
NPO9383	Scilla scilloides	Species	Hyacinthaceae	Eukaryota	n.a.	bulb	n.a.	PMID[12237544]
NPO28718	Penicillium terrestre	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18163588]
NPO29396	Bidens bipinnata	Species	Asteraceae	Eukaryota	n.a.	whole plant	n.a.	PMID[25282892]
NPO29250	Coprinus comatus	Species	Agaricaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26338495]
NPO29125	Ulex europaeus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO9383	Scilla scilloides	Species	Hyacinthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO29396	Bidens bipinnata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO9383	Scilla scilloides	Species	Hyacinthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO29396	Bidens bipinnata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO29125	Ulex europaeus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO29396	Bidens bipinnata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29250	Coprinus comatus	Species	Agaricaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29481	Streptomyces reticuli	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO29499	Chionodoxa luciliae	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO29125	Ulex europaeus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11162	Aplidium glabrum	Species	Polyclinidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18245	Coprinellus micaceus	Species	Psathyrellaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9383	Scilla scilloides	Species	Hyacinthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29213	Bulbine narcissifolia	Species	Asphodelaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29278	Sicyos angulatus	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28718	Penicillium terrestre	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29534	Sarcomelicope leiocarpa	Species	Rutaceae	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 NPC298366 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	422
0.1-0.2	1855
0.2-0.3	3901
0.3-0.4	10164
0.4-0.5	8412
0.5-0.6	3533
0.6-0.7	5423
0.7-0.8	6674
0.8-0.85	2120
0.85-0.9	185
0.9-0.95	7
0.95-1	1

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 NPC298366 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	386
0.1-0.2	984
0.2-0.3	1921
0.3-0.4	2655
0.4-0.5	1780
0.5-0.6	903
0.6-0.7	370
0.7-0.8	122
0.8-0.85	28
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