NPASS Compound

Structure

NPC130818 OpenBabel06302216162D 25 28 0 0 0 0 0 0 0 0999 V2000 3.5491 1.1910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5491 0.1910 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.6831 -0.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8171 0.1910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9511 -0.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9511 -1.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8171 -1.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6831 -1.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5491 -1.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4152 -1.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2812 -1.8090 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.2812 -2.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.1472 -3.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.1472 -4.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2812 -4.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4152 -4.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4152 -3.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5491 -2.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6831 -3.3090 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.2812 -5.8090 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 7.0132 -4.8090 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 7.0132 -5.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -1.6180 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.5878 -0.8090 0.0000 C 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 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 25 1 0 0 0 0 5 6 1 0 0 0 0 6 7 2 0 0 0 0 6 23 1 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 9 18 1 0 0 0 0 9 10 2 0 0 0 0 10 11 1 0 0 0 0 11 12 1 0 0 0 0 12 17 2 0 0 0 0 12 13 1 0 0 0 0 13 14 2 0 0 0 0 14 15 1 0 0 0 0 14 21 1 0 0 0 0 15 16 2 0 0 0 0 15 20 1 0 0 0 0 16 17 1 0 0 0 0 17 18 1 0 0 0 0 18 19 2 0 0 0 0 21 22 1 0 0 0 0 23 24 1 0 0 0 0 24 25 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	342.07
Volume:	326.098
LogP:	2.95
LogD:	2.815
LogS:	-4.464
# Rotatable Bonds:	3
TPSA:	87.36
# H-Bond Aceptor:	7
# H-Bond Donor:	1
# Rings:	4
# Heavy Atoms:	7

MedChem Properties

QED Drug-Likeness Score:	0.783
Synthetic Accessibility Score:	2.465
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:	-4.914
MDCK Permeability:	4.4656942918663844e-05
Pgp-inhibitor:	0.028
Pgp-substrate:	0.013
Human Intestinal Absorption (HIA):	0.003
20% Bioavailability (F20%):	0.003
30% Bioavailability (F30%):	0.009

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.056
Plasma Protein Binding (PPB):	90.67325592041016%
Volume Distribution (VD):	0.544
Pgp-substrate:	8.70307445526123%

ADMET: Metabolism

CYP1A2-inhibitor:	0.922
CYP1A2-substrate:	0.831
CYP2C19-inhibitor:	0.941
CYP2C19-substrate:	0.088
CYP2C9-inhibitor:	0.697
CYP2C9-substrate:	0.901
CYP2D6-inhibitor:	0.933
CYP2D6-substrate:	0.913
CYP3A4-inhibitor:	0.915
CYP3A4-substrate:	0.209

ADMET: Excretion

Clearance (CL):	11.662
Half-life (T1/2):	0.49

ADMET: Toxicity

hERG Blockers:	0.038
Human Hepatotoxicity (H-HT):	0.185
Drug-inuced Liver Injury (DILI):	0.853
AMES Toxicity:	0.076
Rat Oral Acute Toxicity:	0.143
Maximum Recommended Daily Dose:	0.387
Skin Sensitization:	0.43
Carcinogencity:	0.762
Eye Corrosion:	0.004
Eye Irritation:	0.418
Respiratory Toxicity:	0.478

Download Data

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

Natural Product: NPC130818

Natural Product ID:	NPC130818
*Common Name:**	XYFYMIVHOFOGRO-UHFFFAOYSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	XYFYMIVHOFOGRO-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C18H14O7/c1-21-13-5-17-16(24-8-25-17)4-9(13)11-7-23-14-6-15(22-2)12(19)3-10(14)18(11)20/h3-7,19H,8H2,1-2H3
SMILES:	COc1cc2c(cc1c1coc3cc(c(cc3c1=O)O)OC)OCO2
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	44257253
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0002506] Isoflavonoids [CHEMONTID:0002586] O-methylated isoflavonoids [CHEMONTID:0002602] 7-O-methylated isoflavonoids [CHEMONTID:0002689] 7-O-methylisoflavones

*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
NPO20737	Centaurium cachanlahuen	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1007/BF01972262]
NPO20031	Erythrina velutina	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19026536]
NPO23137	Ulex nanus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO23137	Ulex nanus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO23373	Ulmus macrocarpa	Species	Ulmaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO26284	Actaea yunnanensis	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23747	Mildbraediodendron excelsa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24228	Catocarpus oreites	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO22341	Brunsvigia rosea	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23130	Arctostaphylos pumila	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22850	Gelasinospora longispora	Species	Sordariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23137	Ulex nanus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3184	Circinaria calcarea	Species	Megasporaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24368	Helianthus gracilentus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23419	Callitropsis araucarioides	Species	Cupressaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24194	Baccharis intermixta	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23373	Ulmus macrocarpa	Species	Ulmaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20737	Centaurium cachanlahuen	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20031	Erythrina velutina	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24017	Zieria aspalathoides	Species	Rutaceae	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 NPC130818 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	450
0.1-0.2	2080
0.2-0.3	4811
0.3-0.4	11081
0.4-0.5	6778
0.5-0.6	3948
0.6-0.7	5207
0.7-0.8	5101
0.8-0.85	1881
0.85-0.9	1079
0.9-0.95	271
0.95-1	10

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 NPC130818 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	420
0.1-0.2	1006
0.2-0.3	2138
0.3-0.4	2678
0.4-0.5	1650
0.5-0.6	845
0.6-0.7	271
0.7-0.8	105
0.8-0.85	23
0.85-0.9	12
0.9-0.95	2
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