NPASS Compound

Structure

NPC154159 OpenBabel06302215282D 42 47 0 0 1 0 0 0 0 0999 V2000 1.6960 -0.9792 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5439 -1.4688 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5439 -2.4479 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6960 -2.9375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8480 -2.4479 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8480 -1.4688 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.9792 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8480 -1.4687 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.6960 -0.9792 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6960 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5439 0.4896 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5439 1.4688 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6960 1.9583 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8480 1.4688 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8480 2.4479 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8480 3.4271 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 3.9167 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 4.8958 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8480 5.3854 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6960 4.8958 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6960 3.9167 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5439 3.4271 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5439 2.4479 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.3919 1.9583 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2399 2.4479 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0879 1.9583 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0879 0.9792 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2399 0.4896 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3919 0.9792 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2399 -0.4896 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.9359 0.4896 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6960 1.9583 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6960 0.9792 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8480 6.3646 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8480 3.4271 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8480 0.4896 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 -1.6960 2.9375 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.3919 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8480 -2.4479 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6960 -3.9167 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.3919 -2.9375 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 4 1 0 0 0 0 3 42 1 0 0 0 0 4 5 2 0 0 0 0 4 41 1 0 0 0 0 5 6 1 0 0 0 0 7 6 1 6 0 0 0 7 8 1 0 0 0 0 7 37 1 0 0 0 0 8 9 1 0 0 0 0 8 40 1 6 0 0 0 9 10 1 0 0 0 0 10 36 2 0 0 0 0 10 11 1 0 0 0 0 11 12 2 0 0 0 0 11 39 1 0 0 0 0 12 13 1 0 0 0 0 13 14 2 0 0 0 0 13 38 1 0 0 0 0 14 36 1 0 0 0 0 15 14 1 6 0 0 0 15 16 1 0 0 0 0 15 32 1 0 0 0 0 16 21 2 0 0 0 0 16 17 1 0 0 0 0 17 18 2 0 0 0 0 17 35 1 0 0 0 0 18 19 1 0 0 0 0 19 20 2 0 0 0 0 19 34 1 0 0 0 0 20 21 1 0 0 0 0 21 22 1 0 0 0 0 22 23 1 0 0 0 0 23 24 1 1 0 0 0 23 32 1 0 0 0 0 24 29 2 0 0 0 0 24 25 1 0 0 0 0 25 26 2 0 0 0 0 26 27 1 0 0 0 0 27 28 2 0 0 0 0 27 31 1 0 0 0 0 28 29 1 0 0 0 0 28 30 1 0 0 0 0 32 33 1 1 0 0 0 36 37 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	578.14
Volume:	549.942
LogP:	2.055
LogD:	1.743
LogS:	-4.245
# Rotatable Bonds:	3
TPSA:	220.76
# H-Bond Aceptor:	12
# H-Bond Donor:	10
# Rings:	6
# Heavy Atoms:	12

MedChem Properties

QED Drug-Likeness Score:	0.159
Synthetic Accessibility Score:	4.519
Fsp3:	0.2
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Rejected
Chelating Alert:	1
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.847
MDCK Permeability:	4.788759270013543e-06
Pgp-inhibitor:	0.044
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.793
20% Bioavailability (F20%):	0.7
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.005
Plasma Protein Binding (PPB):	87.88815307617188%
Volume Distribution (VD):	0.417
Pgp-substrate:	10.58641529083252%

ADMET: Metabolism

CYP1A2-inhibitor:	0.036
CYP1A2-substrate:	0.098
CYP2C19-inhibitor:	0.024
CYP2C19-substrate:	0.043
CYP2C9-inhibitor:	0.616
CYP2C9-substrate:	0.949
CYP2D6-inhibitor:	0.004
CYP2D6-substrate:	0.224
CYP3A4-inhibitor:	0.065
CYP3A4-substrate:	0.196

ADMET: Excretion

Clearance (CL):	15.07
Half-life (T1/2):	0.718

ADMET: Toxicity

hERG Blockers:	0.11
Human Hepatotoxicity (H-HT):	0.115
Drug-inuced Liver Injury (DILI):	0.82
AMES Toxicity:	0.313
Rat Oral Acute Toxicity:	0.444
Maximum Recommended Daily Dose:	0.37
Skin Sensitization:	0.968
Carcinogencity:	0.039
Eye Corrosion:	0.003
Eye Irritation:	0.925
Respiratory Toxicity:	0.031

Download Data

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

Natural Product: NPC154159

Natural Product ID:	NPC154159
*Common Name:**	XFZJEEAOWLFHDH-OMNZJWBCSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	XFZJEEAOWLFHDH-OMNZJWBCSA-N
Standard InCHI:	InChI=1S/C30H26O12/c31-13-7-20(37)24-23(8-13)41-29(12-2-4-16(33)19(36)6-12)27(40)26(24)25-21(38)10-17(34)14-9-22(39)28(42-30(14)25)11-1-3-15(32)18(35)5-11/h1-8,10,22,26-29,31-40H,9H2/t22-,26+,27+,28-,29+/m1/s1
SMILES:	c1cc(c(cc1[C@@H]1[C@@H](Cc2c(cc(c([C@@H]3c4c(cc(cc4O[C@@H](c4ccc(c(c4)O)O)[C@H]3O)O)O)c2O1)O)O)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	13269091
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0001586] Biflavonoids and polyflavonoids

*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
NPO8561	Liparis loeselii	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO17165	Teucrium heterophyllum	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16080	Cedrela fissilis	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13761	Plexaurella nutans	Species	Plexauridae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14281	Anaxagorea dolichocarpa	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO870	Aglaia tsangii	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8561	Liparis loeselii	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16781	Dorycnium suffruticosum	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17525	Baccharis sagittalis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26159	Pseudocyphellaria faveolata	Species	Lobariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17773	Senecio ambraceus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4024	Pedicularis procera	Species	Orobanchaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9505	Magnolia pterocarpa	Species	Magnoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27966	Stigmatella erecta	Species	Archangiaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO6863	Dendrobates azureus	Species	Dendrobatidae	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 NPC154159 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	540
0.1-0.2	1744
0.2-0.3	4830
0.3-0.4	11566
0.4-0.5	6377
0.5-0.6	4254
0.6-0.7	6403
0.7-0.8	5525
0.8-0.85	875
0.85-0.9	446
0.9-0.95	101
0.95-1	36

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 NPC154159 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	441
0.1-0.2	880
0.2-0.3	2029
0.3-0.4	2681
0.4-0.5	1562
0.5-0.6	865
0.6-0.7	569
0.7-0.8	111
0.8-0.85	7
0.85-0.9	3
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