NPASS Compound

Structure

NPC10305 OpenBabel06302216032D 21 23 0 0 0 0 0 0 0 0999 V2000 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 0.8660 -0.5000 0.0000 C 0 0 0 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 0.0000 -2.0000 0.0000 C 0 0 0 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 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -1.5000 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 -3.4641 0.0000 0.0000 C 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 -5.1962 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 1.0000 0.0000 C 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 -1.7321 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -0.5000 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 0.0000 -3.0000 0.0000 O 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 20 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 5 21 1 0 0 0 0 6 19 2 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 10 2 0 0 0 0 10 11 1 0 0 0 0 10 18 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 16 17 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	208.22
Volume:	256.803
LogP:	6.744
LogD:	5.38
LogS:	-6.309
# Rotatable Bonds:	4
TPSA:	0.0
# H-Bond Aceptor:	0
# H-Bond Donor:	0
# Rings:	1
# Heavy Atoms:	0

MedChem Properties

QED Drug-Likeness Score:	0.557
Synthetic Accessibility Score:	2.888
Fsp3:	0.867
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.429
MDCK Permeability:	1.2035136023769155e-05
Pgp-inhibitor:	0.166
Pgp-substrate:	0.002
Human Intestinal Absorption (HIA):	0.003
20% Bioavailability (F20%):	0.948
30% Bioavailability (F30%):	0.796

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.341
Plasma Protein Binding (PPB):	97.77301788330078%
Volume Distribution (VD):	5.03
Pgp-substrate:	2.5368316173553467%

ADMET: Metabolism

CYP1A2-inhibitor:	0.428
CYP1A2-substrate:	0.332
CYP2C19-inhibitor:	0.418
CYP2C19-substrate:	0.642
CYP2C9-inhibitor:	0.659
CYP2C9-substrate:	0.895
CYP2D6-inhibitor:	0.06
CYP2D6-substrate:	0.076
CYP3A4-inhibitor:	0.169
CYP3A4-substrate:	0.217

ADMET: Excretion

Clearance (CL):	11.936
Half-life (T1/2):	0.042

ADMET: Toxicity

hERG Blockers:	0.071
Human Hepatotoxicity (H-HT):	0.425
Drug-inuced Liver Injury (DILI):	0.499
AMES Toxicity:	0.007
Rat Oral Acute Toxicity:	0.013
Maximum Recommended Daily Dose:	0.013
Skin Sensitization:	0.94
Carcinogencity:	0.121
Eye Corrosion:	0.965
Eye Irritation:	0.979
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: NPC10305

Natural Product ID:	NPC10305
*Common Name:**	PXFLNHWWYOVFDA-UHFFFAOYSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	PXFLNHWWYOVFDA-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C16H12O5/c1-20-9-6-12(18)16-13(19)8-14(21-15(16)7-9)10-4-2-3-5-11(10)17/h2-8,17-18H,1H3
SMILES:	COc1cc(c2c(=O)cc(c3ccccc3O)oc2c1)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	15559079
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0002585] O-methylated flavonoids [CHEMONTID:0002592] 7-O-methylated flavonoids

*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
NPO17551	Phytolacca americana	Species	Phytolaccaceae	Eukaryota	roots	n.a.	n.a.	PMID[18177012]
NPO17551	Phytolacca americana	Species	Phytolaccaceae	Eukaryota	Seeds	n.a.	n.a.	PMID[26595875]
NPO17551	Phytolacca americana	Species	Phytolaccaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO17551	Phytolacca americana	Species	Phytolaccaceae	Eukaryota	Shoot	n.a.	n.a.	Database[FooDB]
NPO17551	Phytolacca americana	Species	Phytolaccaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO17551	Phytolacca americana	Species	Phytolaccaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO17551	Phytolacca americana	Species	Phytolaccaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO17551	Phytolacca americana	Species	Phytolaccaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO17551	Phytolacca americana	Species	Phytolaccaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO4008	Blaps lethifera	Species	Tenebrionidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17278	Mitragyna parvifolia	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20300	Trapa maeotica	Species	Lythraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17551	Phytolacca americana	Species	Phytolaccaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19471	Ascobulla ulla	Species	n.a.	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18879	Drosera auriculata	Species	Droseraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19661	Nectria cinnabarina	Species	Nectriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18552	Cucumaria conicospermium	Species	Cucumariidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17665	Aria tomentosa	Species	Rosaceae	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 NPC10305 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	453
0.1-0.2	1936
0.2-0.3	4943
0.3-0.4	12045
0.4-0.5	5395
0.5-0.6	4390
0.6-0.7	5772
0.7-0.8	4072
0.8-0.85	1835
0.85-0.9	1292
0.9-0.95	504
0.95-1	60

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 NPC10305 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	431
0.1-0.2	992
0.2-0.3	1535
0.3-0.4	2708
0.4-0.5	1837
0.5-0.6	1139
0.6-0.7	326
0.7-0.8	115
0.8-0.85	39
0.85-0.9	19
0.9-0.95	8
0.95-1	1

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