NPASS Compound

Structure

NPC192709 OpenBabel06302216012D 27 29 0 0 1 0 0 0 0 0999 V2000 2.1369 3.2213 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8060 2.4781 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.8005 2.5827 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2072 1.6691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1854 1.4612 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 1.0000 0.0000 C 0 0 2 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 1.7321 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 1.0000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 2.5981 1.5000 0.0000 C 0 0 2 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 1 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 4.3301 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 1 0 0 0 2 3 1 0 0 0 0 2 11 1 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 6 4 1 6 0 0 0 6 7 1 0 0 0 0 6 11 1 0 0 0 0 7 8 2 0 0 0 0 7 24 1 0 0 0 0 8 9 1 0 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 10 12 1 0 0 0 0 13 12 1 6 0 0 0 13 14 1 0 0 0 0 13 20 1 0 0 0 0 14 15 1 0 0 0 0 14 23 1 1 0 0 0 15 16 1 0 0 0 0 15 22 1 6 0 0 0 16 17 1 0 0 0 0 16 21 1 1 0 0 0 17 18 1 6 0 0 0 17 20 1 0 0 0 0 18 19 1 0 0 0 0 24 25 2 0 0 0 0 24 26 1 0 0 0 0 26 27 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	388.14
Volume:	356.912
LogP:	-0.503
LogD:	-0.497
LogS:	-1.386
# Rotatable Bonds:	5
TPSA:	151.98
# H-Bond Aceptor:	10
# H-Bond Donor:	4
# Rings:	3
# Heavy Atoms:	10

MedChem Properties

QED Drug-Likeness Score:	0.392
Synthetic Accessibility Score:	4.657
Fsp3:	0.765
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.8
MDCK Permeability:	7.056028698571026e-05
Pgp-inhibitor:	0.038
Pgp-substrate:	0.039
Human Intestinal Absorption (HIA):	0.916
20% Bioavailability (F20%):	0.011
30% Bioavailability (F30%):	0.967

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.25
Plasma Protein Binding (PPB):	28.867563247680664%
Volume Distribution (VD):	0.473
Pgp-substrate:	52.02687454223633%

ADMET: Metabolism

CYP1A2-inhibitor:	0.01
CYP1A2-substrate:	0.447
CYP2C19-inhibitor:	0.025
CYP2C19-substrate:	0.587
CYP2C9-inhibitor:	0.002
CYP2C9-substrate:	0.03
CYP2D6-inhibitor:	0.003
CYP2D6-substrate:	0.092
CYP3A4-inhibitor:	0.008
CYP3A4-substrate:	0.17

ADMET: Excretion

Clearance (CL):	1.532
Half-life (T1/2):	0.799

ADMET: Toxicity

hERG Blockers:	0.018
Human Hepatotoxicity (H-HT):	0.233
Drug-inuced Liver Injury (DILI):	0.848
AMES Toxicity:	0.216
Rat Oral Acute Toxicity:	0.076
Maximum Recommended Daily Dose:	0.053
Skin Sensitization:	0.261
Carcinogencity:	0.336
Eye Corrosion:	0.003
Eye Irritation:	0.022
Respiratory Toxicity:	0.043

Download Data

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

Natural Product: NPC192709

Natural Product ID:	NPC192709
*Common Name:**	HLXRWTJXGMHOFN-RQHBHZFSSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	HLXRWTJXGMHOFN-RQHBHZFSSA-N
Standard InCHI:	InChI=1S/C17H24O10/c1-6-3-8(19)11-7(15(23)24-2)5-25-16(10(6)11)27-17-14(22)13(21)12(20)9(4-18)26-17/h5-6,9-14,16-18,20-22H,3-4H2,1-2H3/t6-,9+,10+,11-,12+,13-,14+,16?,17-/m0/s1
SMILES:	C[C@H]1CC(=O)[C@@H]2C(=COC([C@H]12)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)C(=O)OC
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	17751048
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0002049] Terpene glycosides [CHEMONTID:0004081] Iridoid 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
NPO11577	Buddleja officinalis	Species	Scrophulariaceae	Eukaryota	flowers	bought from a drugstore in Beijing	n.a.	PMID[10514305]
NPO27625	Buddleja globosa	Species	Scrophulariaceae	Eukaryota	Roots	London	n.a.	PMID[10514305]
NPO27625	Buddleja globosa	Species	Scrophulariaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11000021]
NPO11577	Buddleja officinalis	Species	Scrophulariaceae	Eukaryota	flower buds	n.a.	n.a.	PMID[14738377]
NPO11577	Buddleja officinalis	Species	Scrophulariaceae	Eukaryota	flowers	n.a.	n.a.	PMID[21524582]
NPO12588	Cornus officinalis	Species	Cornaceae	Eukaryota	Fruits	n.a.	n.a.	PMID[29140705]
NPO2838	Verbena officinalis	Species	Verbenaceae	Eukaryota	Root	n.a.	n.a.	Database[FooDB]
NPO2838	Verbena officinalis	Species	Verbenaceae	Eukaryota	Stem	n.a.	n.a.	Database[FooDB]
NPO2838	Verbena officinalis	Species	Verbenaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO2838	Verbena officinalis	Species	Verbenaceae	Eukaryota	Flower	n.a.	n.a.	Database[FooDB]
NPO2838	Verbena officinalis	Species	Verbenaceae	Eukaryota	Leaf	n.a.	n.a.	Database[FooDB]
NPO2838	Verbena officinalis	Species	Verbenaceae	Eukaryota	Plant	n.a.	n.a.	Database[FooDB]
NPO11577	Buddleja officinalis	Species	Scrophulariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO12588	Cornus officinalis	Species	Cornaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO2838	Verbena officinalis	Species	Verbenaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO28552	Verbena stricta	Species	Verbenaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO27625	Buddleja globosa	Species	Scrophulariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO2838	Verbena officinalis	Species	Verbenaceae	Eukaryota	n.a.	n.a.		Database[Phenol-Explorer]
NPO2838	Verbena officinalis	Species	Verbenaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11577	Buddleja officinalis	Species	Scrophulariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27625	Buddleja globosa	Species	Scrophulariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO28552	Verbena stricta	Species	Verbenaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12588	Cornus officinalis	Species	Cornaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12588	Cornus officinalis	Species	Cornaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO11577	Buddleja officinalis	Species	Scrophulariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO2838	Verbena officinalis	Species	Verbenaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO2838	Verbena officinalis	Species	Verbenaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO12588	Cornus officinalis	Species	Cornaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO11577	Buddleja officinalis	Species	Scrophulariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO12588	Cornus officinalis	Species	Cornaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28552	Verbena stricta	Species	Verbenaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2838	Verbena officinalis	Species	Verbenaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11577	Buddleja officinalis	Species	Scrophulariaceae	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 NPC192709 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	221
0.1-0.2	1457
0.2-0.3	5275
0.3-0.4	9650
0.4-0.5	12232
0.5-0.6	7616
0.6-0.7	5643
0.7-0.8	543
0.8-0.85	40
0.85-0.9	6
0.9-0.95	12
0.95-1	2

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 NPC192709 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	209
0.1-0.2	2047
0.2-0.3	3870
0.3-0.4	1977
0.4-0.5	609
0.5-0.6	318
0.6-0.7	118
0.7-0.8	2
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