NPASS Compound

Structure

NPC490420 OpenBabel06302216222D 56 62 0 0 1 0 0 0 0 0999 V2000 0.1620 -1.6968 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.4088 -0.8952 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -1.3885 -0.9887 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.9593 -0.1871 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -2.7872 -0.7192 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7714 -0.7192 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.5993 -0.1871 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.3430 -0.8316 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.0081 0.7081 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8680 1.6822 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.6416 2.2906 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.5016 3.2647 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.5552 1.9248 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.3288 2.5331 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.6953 0.9507 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.6089 0.5849 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.9217 0.3423 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2236 2.4260 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2793 2.7032 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0473 3.6596 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7595 4.3387 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5275 5.2951 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.7038 4.0615 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.4160 4.7406 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.9358 3.1051 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.8801 2.8278 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.3350 2.4260 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8030 3.2539 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.6906 1.6822 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.5505 0.7081 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -0.5708 0.8016 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -0.5615 1.7857 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0245 2.5764 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5463 3.3780 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.9633 2.8715 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7679 3.8361 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5055 4.4876 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3100 5.4521 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.4385 4.1746 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1761 4.8261 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.6339 3.2101 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5000 2.5840 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.8964 2.5585 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4672 1.7569 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3241 2.2408 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3335 3.2249 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.1717 1.7407 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0286 2.2246 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.1623 0.7566 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0099 0.2564 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.3054 0.2727 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4578 0.7728 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8718 -0.0178 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4427 -0.8195 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.9330 -0.3130 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.0000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 56 1 0 0 0 0 2 3 1 0 0 0 0 3 4 1 0 0 0 0 4 30 1 0 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 6 7 1 0 0 0 0 7 8 2 0 0 0 0 7 9 1 0 0 0 0 9 17 1 0 0 0 0 9 10 2 0 0 0 0 10 11 1 0 0 0 0 10 18 1 0 0 0 0 11 12 1 0 0 0 0 11 13 2 0 0 0 0 13 14 1 0 0 0 0 13 15 1 0 0 0 0 15 16 1 0 0 0 0 15 17 2 0 0 0 0 18 25 1 0 0 0 0 18 19 2 0 0 0 0 19 20 1 0 0 0 0 19 27 1 0 0 0 0 20 21 2 0 0 0 0 21 22 1 0 0 0 0 21 23 1 0 0 0 0 23 24 1 0 0 0 0 23 25 2 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 30 31 1 0 0 0 0 31 56 1 0 0 0 0 31 32 1 0 0 0 0 32 33 1 0 0 0 0 33 34 2 0 0 0 0 33 35 1 0 0 0 0 35 43 1 0 0 0 0 35 36 2 0 0 0 0 36 37 1 0 0 0 0 37 38 1 0 0 0 0 37 39 2 0 0 0 0 39 40 1 0 0 0 0 39 41 1 0 0 0 0 41 42 1 0 0 0 0 41 43 2 0 0 0 0 43 44 1 0 0 0 0 44 52 1 0 0 0 0 44 45 2 0 0 0 0 45 46 1 0 0 0 0 45 47 1 0 0 0 0 47 48 1 0 0 0 0 47 49 2 0 0 0 0 49 50 1 0 0 0 0 49 51 1 0 0 0 0 51 52 2 0 0 0 0 52 53 1 0 0 0 0 53 54 2 0 0 0 0 53 55 1 0 0 0 0 55 56 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	784.08
Volume:	687.926
LogP:	1.504
LogD:	1.085
LogS:	-3.61
# Rotatable Bonds:	0
TPSA:	377.42
# H-Bond Aceptor:	22
# H-Bond Donor:	13
# Rings:	7
# Heavy Atoms:	22

MedChem Properties

QED Drug-Likeness Score:	0.066
Synthetic Accessibility Score:	5.422
Fsp3:	0.176
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Rejected
Chelating Alert:	1
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-7.048
MDCK Permeability:	5.993570994178299e-06
Pgp-inhibitor:	0.382
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	1.0
20% Bioavailability (F20%):	0.936
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0
Plasma Protein Binding (PPB):	88.25810241699219%
Volume Distribution (VD):	0.453
Pgp-substrate:	37.95095443725586%

ADMET: Metabolism

CYP1A2-inhibitor:	0.015
CYP1A2-substrate:	0.006
CYP2C19-inhibitor:	0.006
CYP2C19-substrate:	0.022
CYP2C9-inhibitor:	0.339
CYP2C9-substrate:	0.019
CYP2D6-inhibitor:	0.0
CYP2D6-substrate:	0.071
CYP3A4-inhibitor:	0.009
CYP3A4-substrate:	0.005

ADMET: Excretion

Clearance (CL):	9.075
Half-life (T1/2):	0.963

ADMET: Toxicity

hERG Blockers:	0.022
Human Hepatotoxicity (H-HT):	0.042
Drug-inuced Liver Injury (DILI):	0.992
AMES Toxicity:	0.102
Rat Oral Acute Toxicity:	0.0
Maximum Recommended Daily Dose:	0.023
Skin Sensitization:	0.942
Carcinogencity:	0.007
Eye Corrosion:	0.003
Eye Irritation:	0.912
Respiratory Toxicity:	0.001

Download Data

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

Natural Product: NPC490420

Natural Product ID:	NPC490420
*Common Name:**	Pedunculagin
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	IYMHVUYNBVWXKH-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C34H24O22/c35-10-1-6-15(23(43)19(10)39)16-7(2-11(36)20(40)24(16)44)31(48)54-27-14(5-52-30(6)47)53-34(51)29-28(27)55-32(49)8-3-12(37)21(41)25(45)17(8)18-9(33(50)56-29)4-13(38)22(42)26(18)46/h1-4,14,27-29,34-46,51H,5H2
SMILES:	OC1OC2COC(=O)C3=C(C(O)=C(O)C(O)=C3)C3=C(C=C(O)C(O)=C3O)C(=O)OC2C2OC(=O)C3=CC(O)=C(O)C(O)=C3C3=C(O)C(O)=C(O)C=C3C(=O)OC12
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:0000238] Tannins [CHEMONTID:0001710] Hydrolyzable tannins

*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
NPO21349	Punica granatum	Species	Lythraceae	Eukaryota	n.a.	fruit	n.a.	DOI[10.1007/s00217-007-0799-1]
NPO21349	Punica granatum	Species	Lythraceae	Eukaryota	n.a.	flower	n.a.	DOI[10.1016/j.foodchem.2011.01.077]
NPO21349	Punica granatum	Species	Lythraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11520216]
NPO21349	Punica granatum	Species	Lythraceae	Eukaryota	Seeds	n.a.	n.a.	PMID[15620261]
NPO21349	Punica granatum	Species	Lythraceae	Eukaryota	Leaf	n.a.	n.a.	Database[FooDB]
NPO21349	Punica granatum	Species	Lythraceae	Eukaryota	Pericarp	n.a.	n.a.	Database[FooDB]
NPO21349	Punica granatum	Species	Lythraceae	Eukaryota	Root Bark	n.a.	n.a.	Database[FooDB]
NPO21349	Punica granatum	Species	Lythraceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO21349	Punica granatum	Species	Lythraceae	Eukaryota	Stem Bark	n.a.	n.a.	Database[FooDB]
NPO21349	Punica granatum	Species	Lythraceae	Eukaryota	Twig	n.a.	n.a.	Database[FooDB]
NPO21349	Punica granatum	Species	Lythraceae	Eukaryota	n.a.	n.a.		Database[FooDB]
NPO21349	Punica granatum	Species	Lythraceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO21349	Punica granatum	Species	Lythraceae	Eukaryota	Bark	n.a.	n.a.	Database[FooDB]
NPO21349	Punica granatum	Species	Lythraceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO21349	Punica granatum	Species	Lythraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO21349	Punica granatum	Species	Lythraceae	Eukaryota	n.a.	n.a.		Database[Phenol-Explorer]
NPO21349	Punica granatum	Species	Lythraceae	Eukaryota	Fruits	n.a.		Database[Phenol-Explorer]
NPO21349	Punica granatum	Species	Lythraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO21349	Punica granatum	Species	Lythraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO21349	Punica granatum	Species	Lythraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO21349	Punica granatum	Species	Lythraceae	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
NPO21349	NPC490420	Other	Stem Bark	8	8	8	mg/100g	Database [DUKE]

☑ 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 NPC490420 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 NPC490420 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