NPASS Compound

Structure

NPC16388 OpenBabel06302216142D 34 38 0 0 1 0 0 0 0 0999 V2000 -0.5198 -0.5930 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2636 0.3736 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.5367 0.2237 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7636 0.4370 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6308 0.7188 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 0.1782 0.1310 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.6782 -0.7350 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6782 -0.7350 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.1782 0.1310 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6782 0.9971 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.1782 0.1310 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6782 -0.7350 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6782 -0.7350 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1782 0.1310 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6782 0.9971 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6782 0.9971 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9872 0.7188 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.4449 0.2450 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.6782 1.6699 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.3218 1.6699 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.6048 1.0077 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5670 2.6393 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.7934 -1.3743 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.7934 -0.4581 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -1.5869 -0.0000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -1.5869 0.9162 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -0.7934 1.3743 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -0.0000 0.9162 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 0.7934 1.3743 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5869 0.9162 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 -0.7934 2.2905 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.3803 1.3743 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.3803 -0.4581 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 1 0 0 0 2 21 1 0 0 0 0 2 3 1 0 0 0 0 2 18 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 5 20 1 0 0 0 0 5 6 1 0 0 0 0 6 7 1 6 0 0 0 6 17 1 0 0 0 0 6 23 1 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 9 10 2 0 0 0 0 9 11 1 0 0 0 0 11 16 2 0 0 0 0 11 12 1 0 0 0 0 12 13 2 0 0 0 0 13 14 1 0 0 0 0 14 15 2 0 0 0 0 15 16 1 0 0 0 0 17 18 1 6 0 0 0 17 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 1 0 0 0 0 20 22 1 6 0 0 0 23 24 1 0 0 0 0 24 31 1 0 0 0 0 24 25 1 0 0 0 0 25 26 1 0 0 0 0 25 34 1 0 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 32 1 0 0 0 0 28 29 1 0 0 0 0 28 31 1 0 0 0 0 29 30 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	482.18
Volume:	449.728
LogP:	0.524
LogD:	0.867
LogS:	-2.737
# Rotatable Bonds:	7
TPSA:	164.37
# H-Bond Aceptor:	11
# H-Bond Donor:	5
# Rings:	5
# Heavy Atoms:	11

MedChem Properties

QED Drug-Likeness Score:	0.317
Synthetic Accessibility Score:	5.846
Fsp3:	0.696
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.998
MDCK Permeability:	0.00017032958567142487
Pgp-inhibitor:	0.005
Pgp-substrate:	0.285
Human Intestinal Absorption (HIA):	0.898
20% Bioavailability (F20%):	0.967
30% Bioavailability (F30%):	0.952

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.246
Plasma Protein Binding (PPB):	32.06329345703125%
Volume Distribution (VD):	0.538
Pgp-substrate:	44.10453796386719%

ADMET: Metabolism

CYP1A2-inhibitor:	0.004
CYP1A2-substrate:	0.955
CYP2C19-inhibitor:	0.01
CYP2C19-substrate:	0.574
CYP2C9-inhibitor:	0.002
CYP2C9-substrate:	0.088
CYP2D6-inhibitor:	0.003
CYP2D6-substrate:	0.114
CYP3A4-inhibitor:	0.031
CYP3A4-substrate:	0.073

ADMET: Excretion

Clearance (CL):	0.994
Half-life (T1/2):	0.718

ADMET: Toxicity

hERG Blockers:	0.018
Human Hepatotoxicity (H-HT):	0.055
Drug-inuced Liver Injury (DILI):	0.906
AMES Toxicity:	0.781
Rat Oral Acute Toxicity:	0.051
Maximum Recommended Daily Dose:	0.008
Skin Sensitization:	0.208
Carcinogencity:	0.85
Eye Corrosion:	0.003
Eye Irritation:	0.012
Respiratory Toxicity:	0.045

Download Data

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

Natural Product: NPC16388

Natural Product ID:	NPC16388
*Common Name:**	DBUHUWAIMGXDHQ-BHZIWHCISA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	DBUHUWAIMGXDHQ-BHZIWHCISA-N
Standard InCHI:	InChI=1S/C23H30O11/c1-21-8-7-14-22(20(33-21)34-23(14,29)10-21,11-30-18(28)12-5-3-2-4-6-12)32-19-17(27)16(26)15(25)13(9-24)31-19/h2-6,13-17,19-20,24-27,29H,7-11H2,1H3/t13?,14?,15?,16?,17?,19?,20-,21+,22-,23+/m0/s1
SMILES:	C[C@@]12CCC3[C@@](COC(=O)c4ccccc4)([C@@H](O2)O[C@@]3(C1)O)OC1C(C(C(C(CO)O1)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	53486337
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0004603] Organic oxygen compounds [CHEMONTID:0000323] Organooxygen compounds [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates [CHEMONTID:0002105] Glycosyl compounds [CHEMONTID:0002207] O-glycosyl compounds

*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]
NPO21850	Paeonia delavayi	Species	Paeoniaceae	Eukaryota	n.a.	root	n.a.	PMID[10945272]
NPO22550	Paeonia suffruticosa	Species	Paeoniaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11339628]
NPO22550	Paeonia suffruticosa	Species	Paeoniaceae	Eukaryota	n.a.	bark	n.a.	PMID[17260795]
NPO9798	Paeonia lactiflora	Species	Paeoniaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19402674]
NPO22550	Paeonia suffruticosa	Species	Paeoniaceae	Eukaryota	n.a.	Daejeon, Korea	2007-Jan	PMID[19670875]
NPO30226	Paeonia albiflora	Species	Paeoniaceae	Eukaryota	roots	n.a.	n.a.	PMID[19691309]
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]
NPO22550	Paeonia suffruticosa	Species	Paeoniaceae	Eukaryota	n.a.	seed	n.a.	PMID[20822014]
NPO9798	Paeonia lactiflora	Species	Paeoniaceae	Eukaryota	n.a.	root	n.a.	PMID[21782011]
NPO9798	Paeonia lactiflora	Species	Paeoniaceae	Eukaryota	n.a.	root	n.a.	PMID[22190295]
NPO22550	Paeonia suffruticosa	Species	Paeoniaceae	Eukaryota	n.a.	root	n.a.	PMID[22547314]
NPO21850	Paeonia delavayi	Species	Paeoniaceae	Eukaryota	n.a.	seed	n.a.	PMID[23497864]
NPO9798	Paeonia lactiflora	Species	Paeoniaceae	Eukaryota	n.a.	seed	n.a.	PMID[23497864]
NPO19352	Paeonia obovata	Species	Paeoniaceae	Eukaryota	n.a.	seed	n.a.	PMID[23497864]
NPO22550	Paeonia suffruticosa	Species	Paeoniaceae	Eukaryota	root bark	Bozhou, Anhui Province, China	2010-AUG	PMID[24377852]
NPO22550	Paeonia suffruticosa	Species	Paeoniaceae	Eukaryota	n.a.	flower	n.a.	PMID[24504864]
NPO22550	Paeonia suffruticosa	Species	Paeoniaceae	Eukaryota	Flowers	LuoYang, HeNan, China	n.a.	PMID[24621197]
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]
NPO9798	Paeonia lactiflora	Species	Paeoniaceae	Eukaryota	Seeds	HeZe, ShanDong, 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]
NPO9798	Paeonia lactiflora	Species	Paeoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO21850	Paeonia delavayi	Species	Paeoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO19352	Paeonia obovata	Species	Paeoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO13118	Paeonia officinalis	Species	Paeoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO29741	Paeonia moutan	Species	Paeoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO24267	Paeonia veitchii	Species	Paeoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO30226	Paeonia albiflora	Species	Paeoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO23476	Paeonia lactiflora wild	Species	Paeoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO24267	Paeonia veitchii	Species	Paeoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9798	Paeonia lactiflora	Species	Paeoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO22550	Paeonia suffruticosa	Species	Paeoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13118	Paeonia officinalis	Species	Paeoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO21850	Paeonia delavayi	Species	Paeoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO21458	Radix paeoniae rubra	Species	Lymnaeidae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO19352	Paeonia obovata	Species	Paeoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO22550	Paeonia suffruticosa	Species	Paeoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO29741	Paeonia moutan	Species	Paeoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO30226	Paeonia albiflora	Species	Paeoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO24267	Paeonia veitchii	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[TCM_Taiwan]
NPO9798	Paeonia lactiflora	Species	Paeoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO22550	Paeonia suffruticosa	Species	Paeoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO13118	Paeonia officinalis	Species	Paeoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19352	Paeonia obovata	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]
NPO24267	Paeonia veitchii	Species	Paeoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21850	Paeonia delavayi	Species	Paeoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22550	Paeonia suffruticosa	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

☑ 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 NPC16388 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	290
0.1-0.2	1042
0.2-0.3	2279
0.3-0.4	4484
0.4-0.5	8946
0.5-0.6	12661
0.6-0.7	10325
0.7-0.8	2243
0.8-0.85	238
0.85-0.9	150
0.9-0.95	39
0.95-1	0

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 NPC16388 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	242
0.1-0.2	690
0.2-0.3	1418
0.3-0.4	2825
0.4-0.5	2452
0.5-0.6	1143
0.6-0.7	344
0.7-0.8	36
0.8-0.85	0
0.85-0.9	0
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