NPASS Compound

Structure

NPC195001 OpenBabel06302215152D 26 28 0 0 0 0 0 0 0 0999 V2000 5.1962 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 2.0000 0.0000 C 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 1.7321 0.0000 0.0000 C 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 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 0.0000 2.0000 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 -0.8660 1.5000 0.0000 C 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 -1.7321 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 -3.4641 0.0000 0.0000 C 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 -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 -0.0000 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -0.0000 0.0000 O 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 1 2 1 0 0 0 0 2 3 1 0 0 0 0 2 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 6 11 2 0 0 0 0 6 7 1 0 0 0 0 7 8 2 0 0 0 0 7 25 1 0 0 0 0 8 9 1 0 0 0 0 9 23 1 0 0 0 0 9 10 2 0 0 0 0 10 11 1 0 0 0 0 10 13 1 0 0 0 0 11 12 1 0 0 0 0 13 14 2 0 0 0 0 13 15 1 0 0 0 0 15 21 2 0 0 0 0 15 16 1 0 0 0 0 16 17 2 0 0 0 0 16 23 1 0 0 0 0 17 18 1 0 0 0 0 18 19 1 0 0 0 0 18 20 2 0 0 0 0 20 21 1 0 0 0 0 21 22 1 0 0 0 0 23 24 2 0 0 0 0 25 26 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	352.13
Volume:	366.326
LogP:	5.568
LogD:	3.667
LogS:	-6.428
# Rotatable Bonds:	3
TPSA:	83.83
# H-Bond Aceptor:	5
# H-Bond Donor:	2
# Rings:	3
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.748
Synthetic Accessibility Score:	2.826
Fsp3:	0.238
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.989
MDCK Permeability:	1.4001218914927449e-05
Pgp-inhibitor:	0.066
Pgp-substrate:	0.007
Human Intestinal Absorption (HIA):	0.031
20% Bioavailability (F20%):	0.004
30% Bioavailability (F30%):	0.799

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.024
Plasma Protein Binding (PPB):	101.07280731201172%
Volume Distribution (VD):	0.349
Pgp-substrate:	0.6853914856910706%

ADMET: Metabolism

CYP1A2-inhibitor:	0.863
CYP1A2-substrate:	0.884
CYP2C19-inhibitor:	0.308
CYP2C19-substrate:	0.135
CYP2C9-inhibitor:	0.752
CYP2C9-substrate:	0.703
CYP2D6-inhibitor:	0.522
CYP2D6-substrate:	0.241
CYP3A4-inhibitor:	0.43
CYP3A4-substrate:	0.188

ADMET: Excretion

Clearance (CL):	5.64
Half-life (T1/2):	0.086

ADMET: Toxicity

hERG Blockers:	0.008
Human Hepatotoxicity (H-HT):	0.053
Drug-inuced Liver Injury (DILI):	0.961
AMES Toxicity:	0.823
Rat Oral Acute Toxicity:	0.198
Maximum Recommended Daily Dose:	0.915
Skin Sensitization:	0.181
Carcinogencity:	0.78
Eye Corrosion:	0.003
Eye Irritation:	0.942
Respiratory Toxicity:	0.15

Download Data

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

Natural Product: NPC195001

Natural Product ID:	NPC195001
*Common Name:**	FMUNWYQUOSZHBF-AATRIKPKSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	FMUNWYQUOSZHBF-AATRIKPKSA-N
Standard InCHI:	InChI=1S/C21H20O5/c1-10(2)5-6-12-16(26-4)9-14-18(20(12)24)21(25)17-13(19(14)23)7-11(3)8-15(17)22/h5-10,22,24H,1-4H3/b6-5+
SMILES:	CC(C)/C=C/c1c(cc2c(c1O)C(=O)c1c(cc(C)cc1O)C2=O)OC
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	5378723
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0002448] Benzenoids [CHEMONTID:0000018] Anthracenes [CHEMONTID:0000151] Anthraquinones

*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
NPO10596	Vismia sp.	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12828475]
NPO25801	Harungana madagascariensis	Species	Hypericaceae	Eukaryota	stem bark	n.a.	n.a.	PMID[16499321]
NPO25801	Harungana madagascariensis	Species	Hypericaceae	Eukaryota	Leaves	n.a.	n.a.	PMID[17352491]
NPO13029	Sorbus aucuparia	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18635332]
NPO13475	Clinopodium chinense	Species	Lamiaceae	Eukaryota	n.a.	aerial part	n.a.	PMID[23178306]
NPO13475	Clinopodium chinense	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26408136]
NPO25801	Harungana madagascariensis	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26727375]
NPO13029	Sorbus aucuparia	Species	Rosaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO13029	Sorbus aucuparia	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO13475	Clinopodium chinense	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO10596	Vismia sp.	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13475	Clinopodium chinense	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO25801	Harungana madagascariensis	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13029	Sorbus aucuparia	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13029	Sorbus aucuparia	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO13475	Clinopodium chinense	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25801	Harungana madagascariensis	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14855	Vismia laurentii	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13029	Sorbus aucuparia	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18459	Streptomyces olivoreticuli	Species	Streptomycetaceae	Bacteria	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 NPC195001 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 NPC195001 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