NPASS Compound

Structure

NPC49556 OpenBabel06302215402D 23 27 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 -0.9659 0.7412 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6730 1.4483 0.0000 O 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 -2.1213 3.1213 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8625 4.0872 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8966 4.3461 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1895 3.6390 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4483 2.6730 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2588 1.9659 0.0000 C 0 0 0 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 0.7765 3.8978 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5696 4.7944 0.0000 O 0 0 0 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 1 20 2 0 0 0 0 1 2 1 0 0 0 0 2 17 2 0 0 0 0 2 3 1 0 0 0 0 4 3 1 6 0 0 0 4 13 1 0 0 0 0 4 5 1 0 0 0 0 4 17 1 0 0 0 0 5 6 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 9 16 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 11 15 1 0 0 0 0 12 13 1 0 0 0 0 13 14 2 0 0 0 0 17 18 1 0 0 0 0 18 19 2 0 0 0 0 19 23 1 0 0 0 0 19 20 1 0 0 0 0 20 21 1 0 0 0 0 21 22 1 0 0 0 0 22 23 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	312.06
Volume:	294.092
LogP:	2.704
LogD:	2.742
LogS:	-4.151
# Rotatable Bonds:	0
TPSA:	85.22
# H-Bond Aceptor:	6
# H-Bond Donor:	2
# Rings:	5
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.773
Synthetic Accessibility Score:	3.882
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:	-5.0
MDCK Permeability:	1.70643597812159e-05
Pgp-inhibitor:	0.022
Pgp-substrate:	0.091
Human Intestinal Absorption (HIA):	0.005
20% Bioavailability (F20%):	0.219
30% Bioavailability (F30%):	0.336

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.02
Plasma Protein Binding (PPB):	96.80426025390625%
Volume Distribution (VD):	0.872
Pgp-substrate:	2.789597988128662%

ADMET: Metabolism

CYP1A2-inhibitor:	0.97
CYP1A2-substrate:	0.296
CYP2C19-inhibitor:	0.945
CYP2C19-substrate:	0.108
CYP2C9-inhibitor:	0.713
CYP2C9-substrate:	0.875
CYP2D6-inhibitor:	0.955
CYP2D6-substrate:	0.424
CYP3A4-inhibitor:	0.9
CYP3A4-substrate:	0.253

ADMET: Excretion

Clearance (CL):	17.911
Half-life (T1/2):	0.299

ADMET: Toxicity

hERG Blockers:	0.022
Human Hepatotoxicity (H-HT):	0.184
Drug-inuced Liver Injury (DILI):	0.341
AMES Toxicity:	0.731
Rat Oral Acute Toxicity:	0.223
Maximum Recommended Daily Dose:	0.816
Skin Sensitization:	0.158
Carcinogencity:	0.902
Eye Corrosion:	0.003
Eye Irritation:	0.354
Respiratory Toxicity:	0.221

Download Data

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

Natural Product: NPC49556

Natural Product ID:	NPC49556
*Common Name:**	SAXOGBBWXWKZKR-QGZVFWFLSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	SAXOGBBWXWKZKR-QGZVFWFLSA-N
Standard InCHI:	InChI=1S/C17H12O6/c18-9-2-11(19)15-14(3-9)21-6-17(16(15)20)5-8-1-12-13(4-10(8)17)23-7-22-12/h1-4,18-19H,5-7H2/t17-/m1/s1
SMILES:	c1c2C[C@@]3(COc4cc(cc(c4C3=O)O)O)c2cc2c1OCO2
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	133561796
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0002506] Isoflavonoids [CHEMONTID:0001612] Isoflavans [CHEMONTID:0001827] Isoflavanones

*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]
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]
NPO29125	Ulex europaeus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO29125	Ulex europaeus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
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]
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]
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]

☑ 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 NPC49556 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	1873
0.2-0.3	4059
0.3-0.4	10197
0.4-0.5	8160
0.5-0.6	3423
0.6-0.7	5385
0.7-0.8	6566
0.8-0.85	2338
0.85-0.9	262
0.9-0.95	11
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 NPC49556 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	381
0.1-0.2	992
0.2-0.3	1872
0.3-0.4	2658
0.4-0.5	1789
0.5-0.6	910
0.6-0.7	396
0.7-0.8	122
0.8-0.85	29
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