NPASS Compound

Structure

NPC202224 OpenBabel06302215182D 36 39 0 0 1 0 0 0 0 0999 V2000 5.1962 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 4.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 5.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8660 1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7321 1.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.7321 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8660 -0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8660 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -2.0000 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 -2.5981 -0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 2.5000 0.0000 O 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 8 2 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 24 1 0 0 0 0 5 6 1 0 0 0 0 6 7 2 0 0 0 0 6 12 1 0 0 0 0 7 8 1 0 0 0 0 7 11 1 0 0 0 0 8 9 1 0 0 0 0 9 10 1 0 0 0 0 12 13 2 0 0 0 0 12 14 1 0 0 0 0 14 15 2 0 0 0 0 14 25 1 0 0 0 0 15 16 1 0 0 0 0 15 24 1 0 0 0 0 16 21 2 0 0 0 0 16 17 1 0 0 0 0 17 18 2 0 0 0 0 18 19 1 0 0 0 0 19 20 2 0 0 0 0 19 23 1 0 0 0 0 20 21 1 0 0 0 0 20 22 1 0 0 0 0 26 25 1 6 0 0 0 26 27 1 0 0 0 0 26 33 1 0 0 0 0 27 28 1 0 0 0 0 27 36 1 1 0 0 0 28 29 1 0 0 0 0 28 35 1 6 0 0 0 29 30 1 0 0 0 0 29 34 1 6 0 0 0 30 31 1 6 0 0 0 30 33 1 0 0 0 0 31 32 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	508.12
Volume:	465.32
LogP:	0.661
LogD:	0.181
LogS:	-3.59
# Rotatable Bonds:	6
TPSA:	208.74
# H-Bond Aceptor:	13
# H-Bond Donor:	7
# Rings:	4
# Heavy Atoms:	13

MedChem Properties

QED Drug-Likeness Score:	0.215
Synthetic Accessibility Score:	4.046
Fsp3:	0.348
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	2
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.208
MDCK Permeability:	1.4376742001331877e-05
Pgp-inhibitor:	0.34
Pgp-substrate:	0.962
Human Intestinal Absorption (HIA):	0.442
20% Bioavailability (F20%):	0.005
30% Bioavailability (F30%):	0.381

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.035
Plasma Protein Binding (PPB):	82.83229064941406%
Volume Distribution (VD):	0.909
Pgp-substrate:	21.42947769165039%

ADMET: Metabolism

CYP1A2-inhibitor:	0.069
CYP1A2-substrate:	0.599
CYP2C19-inhibitor:	0.016
CYP2C19-substrate:	0.062
CYP2C9-inhibitor:	0.033
CYP2C9-substrate:	0.182
CYP2D6-inhibitor:	0.039
CYP2D6-substrate:	0.177
CYP3A4-inhibitor:	0.056
CYP3A4-substrate:	0.017

ADMET: Excretion

Clearance (CL):	4.587
Half-life (T1/2):	0.869

ADMET: Toxicity

hERG Blockers:	0.211
Human Hepatotoxicity (H-HT):	0.11
Drug-inuced Liver Injury (DILI):	0.978
AMES Toxicity:	0.782
Rat Oral Acute Toxicity:	0.049
Maximum Recommended Daily Dose:	0.008
Skin Sensitization:	0.556
Carcinogencity:	0.025
Eye Corrosion:	0.003
Eye Irritation:	0.126
Respiratory Toxicity:	0.025

Download Data

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

Natural Product: NPC202224

Natural Product ID:	NPC202224
*Common Name:**	QJJFDGNJOXCQPD-LTGKLFRMSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	QJJFDGNJOXCQPD-LTGKLFRMSA-N
Standard InCHI:	InChI=1S/C23H24O13/c1-32-12-6-11-14(16(28)21(12)33-2)17(29)22(20(34-11)8-3-4-9(25)10(26)5-8)36-23-19(31)18(30)15(27)13(7-24)35-23/h3-6,13,15,18-19,23-28,30-31H,7H2,1-2H3/t13-,15+,18+,19-,23+/m1/s1
SMILES:	COc1cc2c(c(c1OC)O)c(=O)c(c(c1ccc(c(c1)O)O)o2)O[C@H]1[C@@H]([C@H]([C@H]([C@@H](CO)O1)O)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:0000334] Flavonoids [CHEMONTID:0001111] Flavonoid glycosides [CHEMONTID:0001583] Flavonoid O-glycosides [CHEMONTID:0003531] Flavonoid-3-O-glycosides

*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
NPO17829	Ibervillea sonorae	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1055/s-2007-967117]
NPO20756	Aspergillus unilateralis	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15602607]
NPO21518	Senecio tricephalus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17829	Ibervillea sonorae	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21969	Veronicastrum virginicum	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20399	Turbinellus floccosus	Species	Gomphaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3676	Fusarium sambucinum	Species	Nectriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9599	Delphinium hybr	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20756	Aspergillus unilateralis	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11698	Drosera spatulata	Species	Droseraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19601	Albizia amara	Species	Fabaceae	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 NPC202224 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	444
0.1-0.2	1773
0.2-0.3	4156
0.3-0.4	9775
0.4-0.5	8387
0.5-0.6	4259
0.6-0.7	5245
0.7-0.8	5274
0.8-0.85	1537
0.85-0.9	1157
0.9-0.95	503
0.95-1	187

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 NPC202224 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	395
0.1-0.2	942
0.2-0.3	1978
0.3-0.4	2688
0.4-0.5	1794
0.5-0.6	894
0.6-0.7	301
0.7-0.8	117
0.8-0.85	17
0.85-0.9	14
0.9-0.95	9
0.95-1	1

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