NPASS Compound

Structure

NPC160240 OpenBabel06302216002D 31 33 0 0 1 0 0 0 0 0999 V2000 -1.7321 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -3.5000 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 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -0.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.7321 -0.0000 0.0000 C 0 0 1 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 -0.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 2.5000 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 -4.3301 2.5000 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 -5.1962 1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 1.0000 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 -0.0000 1.0000 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 0.5000 -0.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -0.5000 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 -1.7321 -2.0000 0.0000 O 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 -3.4641 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -3.5000 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 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 4 1 0 0 0 0 3 5 1 0 0 0 0 5 6 2 0 0 0 0 5 7 1 0 0 0 0 8 7 1 6 0 0 0 8 9 1 0 0 0 0 8 22 1 0 0 0 0 9 10 1 0 0 0 0 9 25 1 6 0 0 0 10 20 2 0 0 0 0 10 11 1 0 0 0 0 11 12 2 0 0 0 0 11 21 1 0 0 0 0 12 13 1 0 0 0 0 13 14 2 0 0 0 0 14 20 1 0 0 0 0 14 15 1 0 0 0 0 15 16 2 0 0 0 0 16 17 1 0 0 0 0 17 18 2 0 0 0 0 17 19 1 0 0 0 0 19 20 1 0 0 0 0 21 22 1 0 0 0 0 22 23 1 0 0 0 0 22 24 1 0 0 0 0 25 26 1 0 0 0 0 26 27 2 0 0 0 0 26 28 1 0 0 0 0 28 29 1 0 0 0 0 29 30 1 0 0 0 0 29 31 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	496.36
Volume:	537.941
LogP:	5.955
LogD:	4.51
LogS:	-5.188
# Rotatable Bonds:	1
TPSA:	55.76
# H-Bond Aceptor:	4
# H-Bond Donor:	1
# Rings:	6
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.381
Synthetic Accessibility Score:	5.097
Fsp3:	0.844
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.395
MDCK Permeability:	2.238705928903073e-05
Pgp-inhibitor:	0.002
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.002
20% Bioavailability (F20%):	0.716
30% Bioavailability (F30%):	0.027

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.817
Plasma Protein Binding (PPB):	87.54310607910156%
Volume Distribution (VD):	0.919
Pgp-substrate:	9.334859848022461%

ADMET: Metabolism

CYP1A2-inhibitor:	0.008
CYP1A2-substrate:	0.516
CYP2C19-inhibitor:	0.016
CYP2C19-substrate:	0.867
CYP2C9-inhibitor:	0.142
CYP2C9-substrate:	0.117
CYP2D6-inhibitor:	0.006
CYP2D6-substrate:	0.23
CYP3A4-inhibitor:	0.39
CYP3A4-substrate:	0.303

ADMET: Excretion

Clearance (CL):	3.646
Half-life (T1/2):	0.167

ADMET: Toxicity

hERG Blockers:	0.008
Human Hepatotoxicity (H-HT):	0.447
Drug-inuced Liver Injury (DILI):	0.046
AMES Toxicity:	0.01
Rat Oral Acute Toxicity:	0.194
Maximum Recommended Daily Dose:	0.884
Skin Sensitization:	0.066
Carcinogencity:	0.378
Eye Corrosion:	0.012
Eye Irritation:	0.03
Respiratory Toxicity:	0.983

Download Data

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

Natural Product: NPC160240

Natural Product ID:	NPC160240
*Common Name:**	UFUVJROSOIXJGR-IULGZIFLSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	UFUVJROSOIXJGR-IULGZIFLSA-N
Standard InCHI:	InChI=1S/C24H28O7/c1-7-14(4)23(27)30-22-21(29-18(26)12-13(2)3)19-16(31-24(22,5)6)10-8-15-9-11-17(25)28-20(15)19/h7-11,13,21-22H,12H2,1-6H3/b14-7-/t21-,22-/m1/s1
SMILES:	C/C=C(/C)C(=O)O[C@@H]1[C@@H](c2c(ccc3ccc(=O)oc23)OC1(C)C)OC(=O)CC(C)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	5320692
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000145] Coumarins and derivatives [CHEMONTID:0003484] Pyranocoumarins [CHEMONTID:0003485] Angular pyranocoumarins

*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
NPO26621	Streptomyces uncialis	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	PMID[18646774]
NPO15394	Angelica decursiva	Species	Apiaceae	Eukaryota	n.a.	root	n.a.	PMID[22784551]
NPO15394	Angelica decursiva	Species	Apiaceae	Eukaryota	n.a.	root	n.a.	PMID[25068578]
NPO25369	Levisticum officinale	Species	Apiaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO25369	Levisticum officinale	Species	Apiaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO25369	Levisticum officinale	Species	Apiaceae	Eukaryota	Plant	n.a.	n.a.	Database[FooDB]
NPO25369	Levisticum officinale	Species	Apiaceae	Eukaryota	Root	n.a.	n.a.	Database[FooDB]
NPO25369	Levisticum officinale	Species	Apiaceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO15394	Angelica decursiva	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO25369	Levisticum officinale	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO14267	Seseli tortuosum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO4340	Peucedanum praeruptorum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO25369	Levisticum officinale	Species	Apiaceae	Eukaryota	n.a.	n.a.		Database[Phenol-Explorer]
NPO25369	Levisticum officinale	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15394	Angelica decursiva	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO14267	Seseli tortuosum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4340	Peucedanum praeruptorum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15394	Angelica decursiva	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO4340	Peucedanum praeruptorum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO14267	Seseli tortuosum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO4340	Peucedanum praeruptorum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO15394	Angelica decursiva	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO21159	Monoon membranifolium	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12008	Aplidium californicum	Species	Polyclinidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26014	Amphidinium corpulentum	Species	Gymnodiniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26235	Achillea ageratum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9129	Ircinia campana	Species	Irciniidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12370	Pulmonaria officinalis	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23122	Trichoderma citrinoviride	Species	Hypocreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14267	Seseli tortuosum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4340	Peucedanum praeruptorum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13650	Dysidea frondosa	Species	Dysideidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26365	Gomphidius glutinosus	Species	Gomphidiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26621	Streptomyces uncialis	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO26830	Hyaena hyaena	Species	Hyaenidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8979	Strychnos malacoclados	Species	Loganiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26092	Agathosma abrupta	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15394	Angelica decursiva	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8094	Cotoneaster veitchii	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25369	Levisticum officinale	Species	Apiaceae	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 NPC160240 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	416
0.1-0.2	1646
0.2-0.3	4074
0.3-0.4	9180
0.4-0.5	9424
0.5-0.6	4062
0.6-0.7	5920
0.7-0.8	5532
0.8-0.85	1848
0.85-0.9	392
0.9-0.95	154
0.95-1	49

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 NPC160240 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	360
0.1-0.2	951
0.2-0.3	1755
0.3-0.4	2640
0.4-0.5	1889
0.5-0.6	1034
0.6-0.7	361
0.7-0.8	116
0.8-0.85	34
0.85-0.9	8
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