NPASS Compound

Structure

NPC139403 OpenBabel06302215142D 22 23 0 0 1 0 0 0 0 0999 V2000 -0.2514 0.5646 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9945 -0.1045 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8605 0.3955 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2673 1.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0594 2.2872 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.3162 2.9563 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3217 3.0608 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5443 2.5608 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.9511 1.6473 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.9456 1.7518 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4456 2.6178 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3523 0.8383 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3305 0.6303 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6092 0.1691 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.7431 0.6691 0.0000 C 0 0 1 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 1.2875 3.2300 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.5241 1.9781 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9254 2.7872 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.9254 3.7872 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0594 4.2872 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.7914 4.2872 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 16 1 0 0 0 0 2 3 2 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 5 19 1 6 0 0 0 6 7 2 0 0 0 0 6 18 1 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 8 17 1 1 0 0 0 9 10 1 6 0 0 0 9 15 1 0 0 0 0 10 11 2 0 0 0 0 10 12 1 0 0 0 0 12 13 2 0 0 0 0 12 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 1 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	306.15
Volume:	316.244
LogP:	1.36
LogD:	1.59
LogS:	-2.74
# Rotatable Bonds:	2
TPSA:	72.83
# H-Bond Aceptor:	5
# H-Bond Donor:	1
# Rings:	2
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.456
Synthetic Accessibility Score:	4.775
Fsp3:	0.529
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	2
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.804
MDCK Permeability:	7.735566032351926e-05
Pgp-inhibitor:	0.002
Pgp-substrate:	0.004
Human Intestinal Absorption (HIA):	0.964
20% Bioavailability (F20%):	0.169
30% Bioavailability (F30%):	0.959

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.578
Plasma Protein Binding (PPB):	82.10883331298828%
Volume Distribution (VD):	0.822
Pgp-substrate:	18.672752380371094%

ADMET: Metabolism

CYP1A2-inhibitor:	0.055
CYP1A2-substrate:	0.061
CYP2C19-inhibitor:	0.044
CYP2C19-substrate:	0.167
CYP2C9-inhibitor:	0.057
CYP2C9-substrate:	0.142
CYP2D6-inhibitor:	0.025
CYP2D6-substrate:	0.156
CYP3A4-inhibitor:	0.131
CYP3A4-substrate:	0.245

ADMET: Excretion

Clearance (CL):	7.511
Half-life (T1/2):	0.365

ADMET: Toxicity

hERG Blockers:	0.009
Human Hepatotoxicity (H-HT):	0.717
Drug-inuced Liver Injury (DILI):	0.754
AMES Toxicity:	0.193
Rat Oral Acute Toxicity:	0.857
Maximum Recommended Daily Dose:	0.967
Skin Sensitization:	0.842
Carcinogencity:	0.213
Eye Corrosion:	0.021
Eye Irritation:	0.03
Respiratory Toxicity:	0.973

Download Data

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

Natural Product: NPC139403

Natural Product ID:	NPC139403
*Common Name:**	DYURAIYPGNPHCD-RMZQFRPTSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	DYURAIYPGNPHCD-RMZQFRPTSA-N
Standard InCHI:	InChI=1S/C17H22O5/c1-9-5-6-14(21-12(4)18)10(2)8-13(19)16-11(3)17(20)22-15(16)7-9/h5,8,13-16,19H,3,6-7H2,1-2,4H3/b9-5+,10-8+/t13-,14+,15+,16+/m1/s1
SMILES:	C/C/1=CC[C@@H](/C(=C/[C@H]([C@@H]2C(=C)C(=O)O[C@H]2C1)O)/C)OC(=O)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001283] Terpene lactones [CHEMONTID:0001543] Sesquiterpene lactones [CHEMONTID:0001771] Germacranolides and derivatives

*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
NPO19629	Laurencia scoparia	Species	Rhodomelaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11754610]
NPO11074	Mycale izuensis	Species	Mycalidae	Eukaryota	n.a.	n.a.	n.a.	PMID[12088446]
NPO18159	Crypteronia paniculata	Species	Crypteroniaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12502343]
NPO18159	Crypteronia paniculata	Species	Crypteroniaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15787463]
NPO19629	Laurencia scoparia	Species	Rhodomelaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16872159]
NPO15112	Premna oligotricha	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8450316]
NPO17110	Barleria prionitis	Species	Acanthaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9784173]
NPO17989	Astragalus falcatus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO17989	Astragalus falcatus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO19081	Iris halophila	Species	Iridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18159	Crypteronia paniculata	Species	Crypteroniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19007	Lycopodium fastigiatum	Species	Lycopodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18837	Ulva rigida	Species	Ulvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17486	Alpinia javanica	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23391	Nidula niveotomentosa	Species	Nidulariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17989	Astragalus falcatus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15112	Premna oligotricha	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19433	Trichocline caulescens	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9841	Picramnia hirsuta	Species	Picramniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16972	Penicillium spiculisporum	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19629	Laurencia scoparia	Species	Rhodomelaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17110	Barleria prionitis	Species	Acanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11074	Mycale izuensis	Species	Mycalidae	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 NPC139403 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	165
0.1-0.2	1152
0.2-0.3	5037
0.3-0.4	13367
0.4-0.5	11683
0.5-0.6	6785
0.6-0.7	3376
0.7-0.8	922
0.8-0.85	87
0.85-0.9	51
0.9-0.95	47
0.95-1	25

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 NPC139403 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	147
0.1-0.2	1716
0.2-0.3	3786
0.3-0.4	2410
0.4-0.5	683
0.5-0.6	334
0.6-0.7	50
0.7-0.8	24
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
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