NPASS Compound

Structure

Physi-Chem Properties

Molecular Weight:	632.17
Volume:	578.303
LogP:	1.623
LogD:	0.39
LogS:	-3.079
# Rotatable Bonds:	10
TPSA:	231.13
# H-Bond Aceptor:	15
# H-Bond Donor:	7
# Rings:	9
# Heavy Atoms:	15

MedChem Properties

QED Drug-Likeness Score:	0.145
Synthetic Accessibility Score:	6.363
Fsp3:	0.533
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	1
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.585
MDCK Permeability:	1.2503774087235797e-05
Pgp-inhibitor:	0.021
Pgp-substrate:	0.977
Human Intestinal Absorption (HIA):	0.914
20% Bioavailability (F20%):	0.957
30% Bioavailability (F30%):	0.996

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.095
Plasma Protein Binding (PPB):	96.24057006835938%
Volume Distribution (VD):	0.428
Pgp-substrate:	10.165901184082031%

ADMET: Metabolism

CYP1A2-inhibitor:	0.023
CYP1A2-substrate:	0.97
CYP2C19-inhibitor:	0.027
CYP2C19-substrate:	0.061
CYP2C9-inhibitor:	0.139
CYP2C9-substrate:	0.074
CYP2D6-inhibitor:	0.028
CYP2D6-substrate:	0.099
CYP3A4-inhibitor:	0.609
CYP3A4-substrate:	0.08

ADMET: Excretion

Clearance (CL):	3.546
Half-life (T1/2):	0.909

ADMET: Toxicity

hERG Blockers:	0.217
Human Hepatotoxicity (H-HT):	0.045
Drug-inuced Liver Injury (DILI):	0.879
AMES Toxicity:	0.769
Rat Oral Acute Toxicity:	0.005
Maximum Recommended Daily Dose:	0.018
Skin Sensitization:	0.924
Carcinogencity:	0.723
Eye Corrosion:	0.003
Eye Irritation:	0.836
Respiratory Toxicity:	0.051

Download Data

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

Natural Product: NPC491280

Natural Product ID:	NPC491280
*Common Name:**	Galloylpaeoniflorin
IUPAC Name:	[(2R,3S,4S,5R,6S)-6-[[(1R,2S,3R,5R,6R,8S)-2-(benzoyloxymethyl)-6-hydroxy-8-methyl-9,10-dioxatetracyclo[4.3.1.02,5.03,8]decan-3-yl]oxy]-3,4,5-trihydroxyoxan-2-yl]methyl 3,4,5-trihydroxybenzoate
Synonyms:
Standard InCHIKey:	KLFIUQCKSSAFFU-QHOIGUMUSA-N
Standard InCHI:	InChI=1S/C30H32O15/c1-27-11-29(39)18-9-30(27,28(18,26(44-27)45-29)12-41-23(37)13-5-3-2-4-6-13)43-25-22(36)21(35)20(34)17(42-25)10-40-24(38)14-7-15(31)19(33)16(32)8-14/h2-8,17-18,20-22,25-26,31-36,39H,9-12H2,1H3/t17-,18-,20-,21+,22-,25+,26-,27+,28+,29-,30+/m1/s1
SMILES:	C[C@]12C[C@@]3([C@@H]4C[C@]1([C@@]4([C@H](O2)O3)COC(=O)C5=CC=CC=C5)O[C@H]6[C@@H]([C@H]([C@@H]([C@H](O6)COC(=O)C7=CC(=C(C(=C7)O)O)O)O)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	101604718
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0002049] Terpene 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
NPO9798	Paeonia lactiflora	Species	Paeoniaceae	Eukaryota	Seeds	Anhui province, China		DOI[10.1016/j.foodres.2020.109416]
NPO9798	Paeonia lactiflora	Species	Paeoniaceae	Eukaryota	Seeds	Gansu province, China		DOI[10.1016/j.foodres.2020.109416]
NPO9798	Paeonia lactiflora	Species	Paeoniaceae	Eukaryota	Seeds	Henan province, China		DOI[10.1016/j.foodres.2020.109416]
NPO9798	Paeonia lactiflora	Species	Paeoniaceae	Eukaryota	Seeds	Shandong province, China		DOI[10.1016/j.foodres.2020.109416]
NPO9798	Paeonia lactiflora	Species	Paeoniaceae	Eukaryota	Seeds	Shanxi province, China		DOI[10.1016/j.foodres.2020.109416]
NPO9798	Paeonia lactiflora	Species	Paeoniaceae	Eukaryota	n.a.	root	n.a.	DOI[10.2174/092986712800229032]
NPO9798	Paeonia lactiflora	Species	Paeoniaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19402674]
NPO9798	Paeonia lactiflora	Species	Paeoniaceae	Eukaryota	n.a.	root	n.a.	PMID[19721258]
NPO9798	Paeonia lactiflora	Species	Paeoniaceae	Eukaryota	n.a.	root	n.a.	PMID[19772486]
NPO9798	Paeonia lactiflora	Species	Paeoniaceae	Eukaryota	Roots	n.a.	n.a.	PMID[20806783]
NPO9798	Paeonia lactiflora	Species	Paeoniaceae	Eukaryota	n.a.	root	n.a.	PMID[21782011]
NPO15265	Paeonia rockii	Species	Paeoniaceae	Eukaryota	n.a.	root	n.a.	PMID[21954959]
NPO15265	Paeonia rockii	Species	Paeoniaceae	Eukaryota	roots	Whitessence Srl, Viterbo, Italy	2005-OCT	PMID[21954959]
NPO9798	Paeonia lactiflora	Species	Paeoniaceae	Eukaryota	n.a.	root	n.a.	PMID[22190295]
NPO15265	Paeonia rockii	Species	Paeoniaceae	Eukaryota	n.a.	seed	n.a.	PMID[23497864]
NPO9798	Paeonia lactiflora	Species	Paeoniaceae	Eukaryota	n.a.	seed	n.a.	PMID[23497864]
NPO9798	Paeonia lactiflora	Species	Paeoniaceae	Eukaryota	n.a.	root	n.a.	PMID[26838074]
NPO9798	Paeonia lactiflora	Species	Paeoniaceae	Eukaryota	n.a.	root	n.a.	PMID[27313650]
NPO9798	Paeonia lactiflora	Species	Paeoniaceae	Eukaryota	n.a.	root	n.a.	PMID[27429639]
NPO9798	Paeonia lactiflora	Species	Paeoniaceae	Eukaryota	Roots	n.a.	n.a.	PMID[29741372]
NPO15265	Paeonia rockii	Species	Paeoniaceae	Eukaryota	Seeds	LanZhou, GanSu, China	early autumn (from August to the beginning of September	PMID[32545196]
NPO9798	Paeonia lactiflora	Species	Paeoniaceae	Eukaryota	Seeds	HeZe, ShanDong, China	early autumn (from August to the beginning of September	PMID[32545196]
NPO15265	Paeonia rockii	Species	Paeoniaceae	Eukaryota	Seeds	DingXi, GanSu, China	early autumn (from August to the beginning of September	PMID[32545196]
NPO9798	Paeonia lactiflora	Species	Paeoniaceae	Eukaryota	Roots	n.a.	n.a.	PMID[32951423]
NPO9798	Paeonia lactiflora	Species	Paeoniaceae	Eukaryota	Seeds	Xinjiang,China		PMID[33063333]
NPO15265	Paeonia rockii	Species	Paeoniaceae	Eukaryota	Seeds	Yangling, Shaanxi, China	40 days after pollination	PMID[33131958]
NPO15265	Paeonia rockii	Species	Paeoniaceae	Eukaryota	Seeds	Yangling, Shaanxi, China	50 days after pollination	PMID[33131958]
NPO15265	Paeonia rockii	Species	Paeoniaceae	Eukaryota	Seeds	Yangling, Shaanxi, China	60 days after pollination	PMID[33131958]
NPO15265	Paeonia rockii	Species	Paeoniaceae	Eukaryota	Seeds	Yangling, Shaanxi, China	70 days after pollination	PMID[33131958]
NPO15265	Paeonia rockii	Species	Paeoniaceae	Eukaryota	Fruits	Yangling, Shaanxi, China	10 days after pollination	PMID[33131958]
NPO15265	Paeonia rockii	Species	Paeoniaceae	Eukaryota	Seeds	Yangling, Shaanxi, China	80 days after pollination	PMID[33131958]
NPO15265	Paeonia rockii	Species	Paeoniaceae	Eukaryota	Fruits	Yangling, Shaanxi, China	20 days after pollination	PMID[33131958]
NPO15265	Paeonia rockii	Species	Paeoniaceae	Eukaryota	Seeds	Yangling, Shaanxi, China	90 days after pollination	PMID[33131958]
NPO15265	Paeonia rockii	Species	Paeoniaceae	Eukaryota	Fruits	Yangling, Shaanxi, China	30 days after pollination	PMID[33131958]
NPO15265	Paeonia rockii	Species	Paeoniaceae	Eukaryota	Fruits	Yangling, Shaanxi, China	40 days after pollination	PMID[33131958]
NPO15265	Paeonia rockii	Species	Paeoniaceae	Eukaryota	Fruits	Yangling, Shaanxi, China	50 days after pollination	PMID[33131958]
NPO15265	Paeonia rockii	Species	Paeoniaceae	Eukaryota	Fruits	Yangling, Shaanxi, China	60 days after pollination	PMID[33131958]
NPO15265	Paeonia rockii	Species	Paeoniaceae	Eukaryota	Seeds	Yangling, Shaanxi, China	Maturation	PMID[33131958]
NPO15265	Paeonia rockii	Species	Paeoniaceae	Eukaryota	Fruits	Yangling, Shaanxi, China	70 days after pollination	PMID[33131958]
NPO15265	Paeonia rockii	Species	Paeoniaceae	Eukaryota	Fruits	Yangling, Shaanxi, China	80 days after pollination	PMID[33131958]
NPO15265	Paeonia rockii	Species	Paeoniaceae	Eukaryota	Fruits	Yangling, Shaanxi, China	90 days after pollination	PMID[33131958]
NPO15265	Paeonia rockii	Species	Paeoniaceae	Eukaryota	Fruits	Yangling, Shaanxi, China	Maturation	PMID[33131958]
NPO15265	Paeonia rockii	Species	Paeoniaceae	Eukaryota	Seeds	Yangling, Shaanxi, China	10 days after pollination	PMID[33131958]
NPO15265	Paeonia rockii	Species	Paeoniaceae	Eukaryota	Seeds	Yangling, Shaanxi, China	20 days after pollination	PMID[33131958]
NPO15265	Paeonia rockii	Species	Paeoniaceae	Eukaryota	Seeds	Yangling, Shaanxi, China	30 days after pollination	PMID[33131958]
NPO9798	Paeonia lactiflora	Species	Paeoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO9798	Paeonia lactiflora	Species	Paeoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9798	Paeonia lactiflora	Species	Paeoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO9798	Paeonia lactiflora	Species	Paeoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO15265	Paeonia rockii	Species	Paeoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9798	Paeonia lactiflora	Species	Paeoniaceae	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
NPO15265	NPC491280	Naturally dried; obtain oils by crushing seeds using screw press	Seeds	0.275 ± 0.000	n.a.	n.a.	μg/g	PMID[32545196]
NPO15265	NPC491280	Naturally dried; obtain oils by crushing seeds using screw press	Seeds	0.444 ± 0.003	n.a.	n.a.	μg/g	PMID[32545196]
NPO30287	NPC491280	Naturally dried; obtain oils by crushing seeds using screw press	Seeds	0.216 ± 0.003	n.a.	n.a.	μg/g	PMID[32545196]
NPO30287	NPC491280	Naturally dried; obtain oils by crushing seeds using screw press	Seeds	0.166 ± 0.002	n.a.	n.a.	μg/g	PMID[32545196]
NPO30287	NPC491280	Naturally dried; obtain oils by crushing seeds using screw press	Seeds	0.055 ± 0.000	n.a.	n.a.	μg/g	PMID[32545196]
NPO30287	NPC491280	Naturally dried; obtain oils by crushing seeds using screw press	Seeds	0.185 ± 0.000	n.a.	n.a.	μg/g	PMID[32545196]
NPO30287	NPC491280	Naturally dried; obtain oils by crushing seeds using screw press	Seeds	0.153 + 0.002	n.a.	n.a.	μg/g	PMID[32545196]
NPO30287	NPC491280	Naturally dried; obtain oils by crushing seeds using screw press	Seeds	0.260 ± 0.001	n.a.	n.a.	μg/g	PMID[32545196]
NPO30287	NPC491280	Naturally dried; obtain oils by crushing seeds using screw press	Seeds	0.133 ± 0.0031	n.a.	n.a.	μg/g	PMID[32545196]
NPO30287	NPC491280	Naturally dried; obtain oils by crushing seeds using screw press	Seeds	0.217 + 0.003	n.a.	n.a.	μg/g	PMID[32545196]
NPO9798	NPC491280	Naturally dried; obtain oils by crushing seeds using screw press	Seeds	0.252 ± 0.012	n.a.	n.a.	μg/g	PMID[32545196]
NPO9798	NPC491280	Naturally dried; obtain oils by crushing seeds using screw press	Seeds	0.368 + 0.002	n.a.	n.a.	μg/g	PMID[32545196]

☑ 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 NPC491280 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 NPC491280 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