NPASS Compound

Structure

NPC201219 OpenBabel06302215122D 31 33 0 0 1 0 0 0 0 0999 V2000 3.7017 -5.6126 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8031 -4.6473 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6898 -4.2525 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.0179 -4.0768 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.1194 -3.1115 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3341 -2.5410 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3341 -1.5704 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2572 -1.2705 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.8277 -0.4853 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8277 0.4853 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.7771 0.2835 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2572 1.2705 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8277 2.0557 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.3341 1.5704 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4111 1.2705 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8406 0.4853 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.5656 2.2860 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8406 -0.4853 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.4111 -1.2705 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8406 -2.0557 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.4111 -2.8410 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1111 -3.7640 0.0000 O 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 4.4772 1.2066 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.4265 1.0048 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0760 1.7261 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.7265 0.0817 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8277 -2.0557 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.7930 -1.9543 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1878 -1.0676 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.3635 -2.7395 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 2 4 1 0 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 6 21 1 0 0 0 0 6 7 2 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 8 28 1 6 0 0 0 9 10 1 0 0 0 0 10 11 1 1 0 0 0 10 12 1 0 0 0 0 10 24 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 0 0 0 0 16 23 1 0 0 0 0 16 17 1 1 0 0 0 16 18 1 0 0 0 0 18 19 1 0 0 0 0 18 23 1 1 0 0 0 19 7 1 6 0 0 0 19 20 1 0 0 0 0 20 21 1 0 0 0 0 21 22 2 0 0 0 0 24 25 1 0 0 0 0 25 26 2 0 0 0 0 25 27 1 0 0 0 0 28 29 1 0 0 0 0 29 30 2 0 0 0 0 29 31 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	438.15
Volume:	418.186
LogP:	1.829
LogD:	1.599
LogS:	-2.831
# Rotatable Bonds:	7
TPSA:	141.87
# H-Bond Aceptor:	10
# H-Bond Donor:	1
# Rings:	3
# Heavy Atoms:	10

MedChem Properties

QED Drug-Likeness Score:	0.423
Synthetic Accessibility Score:	5.205
Fsp3:	0.619
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.252
MDCK Permeability:	8.044375135796145e-05
Pgp-inhibitor:	0.576
Pgp-substrate:	0.105
Human Intestinal Absorption (HIA):	0.673
20% Bioavailability (F20%):	0.733
30% Bioavailability (F30%):	0.961

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.938
Plasma Protein Binding (PPB):	62.28483581542969%
Volume Distribution (VD):	0.54
Pgp-substrate:	34.51220703125%

ADMET: Metabolism

CYP1A2-inhibitor:	0.008
CYP1A2-substrate:	0.098
CYP2C19-inhibitor:	0.014
CYP2C19-substrate:	0.419
CYP2C9-inhibitor:	0.034
CYP2C9-substrate:	0.244
CYP2D6-inhibitor:	0.022
CYP2D6-substrate:	0.118
CYP3A4-inhibitor:	0.066
CYP3A4-substrate:	0.512

ADMET: Excretion

Clearance (CL):	3.729
Half-life (T1/2):	0.942

ADMET: Toxicity

hERG Blockers:	0.006
Human Hepatotoxicity (H-HT):	0.921
Drug-inuced Liver Injury (DILI):	0.966
AMES Toxicity:	0.826
Rat Oral Acute Toxicity:	0.902
Maximum Recommended Daily Dose:	0.049
Skin Sensitization:	0.406
Carcinogencity:	0.62
Eye Corrosion:	0.004
Eye Irritation:	0.04
Respiratory Toxicity:	0.739

Download Data

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

Natural Product: NPC201219

Natural Product ID:	NPC201219
*Common Name:**	JNLNEIIZZQABDP-ZBWGKUOUSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	JNLNEIIZZQABDP-ZBWGKUOUSA-N
Standard InCHI:	InChI=1S/C21H26O10/c1-10(22)27-9-13-16-14(28-11(2)23)8-21(5,30-12(3)24)15(25)6-7-20(4)18(31-20)17(16)29-19(13)26/h14,17-18H,6-9H2,1-5H3/t14-,17-,18+,20+,21+/m0/s1
SMILES:	CC(=O)OCC1=C2[C@H](C[C@](C)(C(=O)CC[C@]3(C)[C@@H]([C@H]2OC1=O)O3)OC(=O)C)OC(=O)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	442250
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001283] Terpene lactones

*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
NPO21865	Biemna laboutei	Species	Biemnidae	Eukaryota	n.a.	n.a.	n.a.	PMID[24601655]
NPO12126	Coix lacryma-jobi	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO12126	Coix lacryma-jobi	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12354	Sargassum pallidum	Species	Sargassaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO12126	Coix lacryma-jobi	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO12354	Sargassum pallidum	Species	Sargassaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO21865	Biemna laboutei	Species	Biemnidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12126	Coix lacryma-jobi	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12354	Sargassum pallidum	Species	Sargassaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15463	Vernonia fruticulosa	Species	Asteraceae	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

Activity Type	# Activity
IC50	4
Others	8

Activity Type	# Activity
Organism	2
SINGLE PROTEIN	10

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT21851	SINGLE PROTEIN	Dihydroorotate dehydrogenase (fumarate)	Leishmania major	IC50	=	30900.0	nM	PMID[449423]
NPT21851	SINGLE PROTEIN	Dihydroorotate dehydrogenase (fumarate)	Leishmania major	IC50	=	31622.78	nM	PMID[449423]
NPT21851	SINGLE PROTEIN	Dihydroorotate dehydrogenase (fumarate)	Leishmania major	Inhibition	=	41.0	%	PMID[449423]
NPT21852	SINGLE PROTEIN	Dihydroorotate dehydrogenase	Homo sapiens	Inhibition	=	0.0	%	PMID[449423]
NPT21851	SINGLE PROTEIN	Dihydroorotate dehydrogenase (fumarate)	Leishmania major	Delta Tm	=	-0.21	degrees C	PMID[449423]
NPT21851	SINGLE PROTEIN	Dihydroorotate dehydrogenase (fumarate)	Leishmania major	Delta Tm	=	-0.41	degrees C	PMID[449423]
NPT21851	SINGLE PROTEIN	Dihydroorotate dehydrogenase (fumarate)	Leishmania major	Delta Tm	=	-0.7	degrees C	PMID[449423]
NPT21851	SINGLE PROTEIN	Dihydroorotate dehydrogenase (fumarate)	Leishmania major	Delta Tm	=	-0.27	degrees C	PMID[449423]
NPT21851	SINGLE PROTEIN	Dihydroorotate dehydrogenase (fumarate)	Leishmania major	Delta Tm	=	-0.47	degrees C	PMID[449423]
NPT21851	SINGLE PROTEIN	Dihydroorotate dehydrogenase (fumarate)	Leishmania major	Delta Tm	=	-0.64	degrees C	PMID[449423]
NPT634	Organism	Leishmania amazonensis	Leishmania amazonensis	IC50	=	46100.0	nM	PMID[449423]
NPT1208	Organism	Leishmania braziliensis	Leishmania braziliensis	IC50	=	27900.0	nM	PMID[449423]

☑ 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 NPC201219 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	313
0.1-0.2	2481
0.2-0.3	6865
0.3-0.4	12675
0.4-0.5	13217
0.5-0.6	5134
0.6-0.7	1661
0.7-0.8	331
0.8-0.85	13
0.85-0.9	2
0.9-0.95	2
0.95-1	3

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 NPC201219 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	361
0.1-0.2	3026
0.2-0.3	3588
0.3-0.4	1493
0.4-0.5	520
0.5-0.6	144
0.6-0.7	15
0.7-0.8	3
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