NPASS Compound

Structure

NPC205686 OpenBabel06302215382D 23 26 0 0 1 0 0 0 0 0999 V2000 -2.5128 -0.4479 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6697 0.0241 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8394 -0.4700 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8521 -1.4319 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0254 -1.9239 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8140 -1.4539 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6395 -1.9460 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4892 -1.4760 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.5019 -0.5141 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3460 -0.0328 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1710 -0.5361 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1583 -1.4980 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3204 -1.9682 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 3.3587 0.9348 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5159 1.4214 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6778 0.9570 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6650 -0.0107 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8267 -0.4920 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0127 0.9661 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8494 1.4525 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5244 2.3796 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6988 2.8660 0.0000 C 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 19 2 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 6 18 2 0 0 0 0 6 7 1 0 0 0 0 8 7 1 6 0 0 0 8 9 1 0 0 0 0 8 13 1 0 0 0 0 9 17 2 0 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 10 14 2 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 14 15 1 0 0 0 0 15 16 2 0 0 0 0 15 22 1 0 0 0 0 16 17 1 0 0 0 0 16 21 1 0 0 0 0 17 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 22 23 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	313.13
Volume:	315.997
LogP:	1.321
LogD:	2.083
LogS:	-1.676
# Rotatable Bonds:	2
TPSA:	70.95
# H-Bond Aceptor:	5
# H-Bond Donor:	3
# Rings:	4
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.795
Synthetic Accessibility Score:	3.208
Fsp3:	0.333
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	1
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.313
MDCK Permeability:	1.0801450116559863e-05
Pgp-inhibitor:	0.01
Pgp-substrate:	0.963
Human Intestinal Absorption (HIA):	0.016
20% Bioavailability (F20%):	0.006
30% Bioavailability (F30%):	0.046

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.487
Plasma Protein Binding (PPB):	91.12574005126953%
Volume Distribution (VD):	1.378
Pgp-substrate:	9.503802299499512%

ADMET: Metabolism

CYP1A2-inhibitor:	0.432
CYP1A2-substrate:	0.874
CYP2C19-inhibitor:	0.062
CYP2C19-substrate:	0.614
CYP2C9-inhibitor:	0.009
CYP2C9-substrate:	0.541
CYP2D6-inhibitor:	0.13
CYP2D6-substrate:	0.909
CYP3A4-inhibitor:	0.075
CYP3A4-substrate:	0.756

ADMET: Excretion

Clearance (CL):	3.785
Half-life (T1/2):	0.504

ADMET: Toxicity

hERG Blockers:	0.178
Human Hepatotoxicity (H-HT):	0.404
Drug-inuced Liver Injury (DILI):	0.532
AMES Toxicity:	0.575
Rat Oral Acute Toxicity:	0.599
Maximum Recommended Daily Dose:	0.951
Skin Sensitization:	0.725
Carcinogencity:	0.043
Eye Corrosion:	0.003
Eye Irritation:	0.011
Respiratory Toxicity:	0.789

Download Data

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

Natural Product: NPC205686

Natural Product ID:	NPC205686
*Common Name:**	POIRVLZGTSWEMG-LLVKDONJSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	POIRVLZGTSWEMG-LLVKDONJSA-N
Standard InCHI:	InChI=1S/C18H19NO4/c1-22-12-4-3-9-7-11-14-10(5-6-19-11)8-13(23-2)18(21)16(14)15(9)17(12)20/h3-4,8,11,19-21H,5-7H2,1-2H3/t11-/m1/s1
SMILES:	COc1ccc2C[C@@H]3c4c(CCN3)cc(c(c4-c2c1O)O)OC
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000279] Alkaloids and derivatives [CHEMONTID:0000381] Aporphines

*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
NPO10618	Acnistus arborescens	Species	Solanaceae	Eukaryota	leaves	n.a.	n.a.	PMID[15104512]
NPO10618	Acnistus arborescens	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20590148]
NPO15264	Garcinia paucinervis	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20594858]
NPO22043	Hylomecon japonica	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO11640	Berberis fortunei	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO22043	Hylomecon japonica	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO10618	Acnistus arborescens	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO22043	Hylomecon japonica	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO11640	Berberis fortunei	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO15264	Garcinia paucinervis	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10618	Acnistus arborescens	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11640	Berberis fortunei	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16401	Zataria bracteata	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22043	Hylomecon japonica	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8448	Trifolium stellatum	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3994	Haplophyllum latifolium	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16970	Nectandra saligna	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12130	Frullania dilatata	Species	Frullaniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13942	Cryptantha leiocarpa	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13554	Chrysactinia mexicana	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14056	Microstrobos niphophilus	Species	Podocarpaceae	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 NPC205686 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	332
0.1-0.2	1711
0.2-0.3	8036
0.3-0.4	9983
0.4-0.5	5687
0.5-0.6	11367
0.6-0.7	4420
0.7-0.8	768
0.8-0.85	217
0.85-0.9	117
0.9-0.95	42
0.95-1	17

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 NPC205686 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	192
0.1-0.2	755
0.2-0.3	1086
0.3-0.4	2014
0.4-0.5	2644
0.5-0.6	1610
0.6-0.7	665
0.7-0.8	160
0.8-0.85	24
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