NPASS Compound

Structure

NPC242035 OpenBabel06302215422D 24 26 0 0 0 0 0 0 0 0999 V2000 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 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 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 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 1.0000 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 2.5000 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 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 -1.7321 -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 -0.0000 -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 -4.3301 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -2.0000 0.0000 O 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 1 2 1 0 0 0 0 2 3 1 0 0 0 0 3 8 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 7 2 0 0 0 0 6 10 1 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 10 19 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 18 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 15 23 1 0 0 0 0 16 17 2 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 2 0 0 0 0 21 22 1 0 0 0 0 23 24 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	328.09
Volume:	325.865
LogP:	2.701
LogD:	2.649
LogS:	-3.803
# Rotatable Bonds:	4
TPSA:	78.13
# H-Bond Aceptor:	6
# H-Bond Donor:	1
# Rings:	3
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.792
Synthetic Accessibility Score:	2.154
Fsp3:	0.167
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:	-4.749
MDCK Permeability:	4.1274892282672226e-05
Pgp-inhibitor:	0.051
Pgp-substrate:	0.959
Human Intestinal Absorption (HIA):	0.006
20% Bioavailability (F20%):	0.004
30% Bioavailability (F30%):	0.066

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.085
Plasma Protein Binding (PPB):	86.46207427978516%
Volume Distribution (VD):	0.523
Pgp-substrate:	11.058761596679688%

ADMET: Metabolism

CYP1A2-inhibitor:	0.694
CYP1A2-substrate:	0.962
CYP2C19-inhibitor:	0.738
CYP2C19-substrate:	0.162
CYP2C9-inhibitor:	0.619
CYP2C9-substrate:	0.879
CYP2D6-inhibitor:	0.514
CYP2D6-substrate:	0.924
CYP3A4-inhibitor:	0.783
CYP3A4-substrate:	0.414

ADMET: Excretion

Clearance (CL):	7.091
Half-life (T1/2):	0.793

ADMET: Toxicity

hERG Blockers:	0.054
Human Hepatotoxicity (H-HT):	0.182
Drug-inuced Liver Injury (DILI):	0.847
AMES Toxicity:	0.064
Rat Oral Acute Toxicity:	0.22
Maximum Recommended Daily Dose:	0.371
Skin Sensitization:	0.675
Carcinogencity:	0.106
Eye Corrosion:	0.004
Eye Irritation:	0.448
Respiratory Toxicity:	0.538

Download Data

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

Natural Product: NPC242035

Natural Product ID:	NPC242035
*Common Name:**	XZJYWKSINSUIPD-UHFFFAOYSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	XZJYWKSINSUIPD-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C18H16O6/c1-21-14-5-4-10(6-13(14)19)12-9-24-15-8-17(23-3)16(22-2)7-11(15)18(12)20/h4-9,19H,1-3H3
SMILES:	COc1ccc(cc1O)c1coc2cc(c(cc2c1=O)OC)OC
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0002506] Isoflavonoids [CHEMONTID:0002586] O-methylated isoflavonoids [CHEMONTID:0002606] 4'-O-methylated isoflavonoids [CHEMONTID:0003651] 3'-hydroxy,4'-methoxyisoflavonoids

*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
NPO28689	Armillaria mellea	Species	Physalacriaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19795841]
NPO28689	Armillaria mellea	Species	Physalacriaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[4040154]
NPO28689	Armillaria mellea	Species	Physalacriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO28761	Tricholoma populinum	Species	Tricholomataceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28647	Fleischmannia deborabellae	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28624	Canthium gilfillanii	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28328	Cortispongilla barroisi	Species	Malawispongiidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28672	Ficus cunia	Species	Ficidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22882	Biancaea millettii	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29071	Anacardium giganteum	Species	Anacardiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28689	Armillaria mellea	Species	Physalacriaceae	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 NPC242035 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	464
0.1-0.2	1957
0.2-0.3	4843
0.3-0.4	11320
0.4-0.5	6198
0.5-0.6	3755
0.6-0.7	5154
0.7-0.8	5003
0.8-0.85	2040
0.85-0.9	1146
0.9-0.95	661
0.95-1	156

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 NPC242035 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	432
0.1-0.2	991
0.2-0.3	1898
0.3-0.4	2632
0.4-0.5	1734
0.5-0.6	950
0.6-0.7	351
0.7-0.8	111
0.8-0.85	30
0.85-0.9	14
0.9-0.95	6
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