NPASS Compound

Structure

NPC482174 OpenBabel06302216202D 40 43 0 0 1 0 0 0 0 0999 V2000 -3.8917 -5.5628 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1406 -6.1535 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2535 -5.7983 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5023 -6.3890 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1175 -4.8525 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2304 -4.4974 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.8686 -4.2618 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5966 -2.3702 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.6508 -2.2342 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9286 -1.6084 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6594 -0.6916 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.4482 -1.2309 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.2049 -0.6474 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.1217 -0.9166 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8838 0.2526 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9286 0.2253 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.6508 0.8510 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2538 1.7202 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5966 0.9870 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.7326 1.9329 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4658 0.5901 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.9824 -0.2138 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.9824 -1.1693 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.4658 -1.9732 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.0916 -2.6954 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.0299 -2.5145 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8100 -0.6916 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.6375 -0.2138 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.6375 -1.1693 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0916 1.3122 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.0299 1.1314 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.6556 1.8536 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.3424 0.2284 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 -1.5028 -3.1413 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.6892 -3.6425 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7165 -4.5976 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.1516 -3.1885 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4546 -1.7176 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4092 -0.7631 0.0000 O 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 1 0 0 0 8 9 1 0 0 0 0 8 24 1 0 0 0 0 9 10 2 0 0 0 0 9 39 1 0 0 0 0 11 10 1 6 0 0 0 11 16 1 0 0 0 0 11 34 1 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 12 35 1 1 0 0 0 13 14 1 1 0 0 0 13 15 1 0 0 0 0 16 15 1 1 0 0 0 16 17 1 0 0 0 0 16 34 1 0 0 0 0 17 18 2 0 0 0 0 17 19 1 0 0 0 0 19 20 1 1 0 0 0 19 21 1 0 0 0 0 21 22 1 0 0 0 0 21 30 1 1 0 0 0 22 23 1 0 0 0 0 22 27 1 6 0 0 0 23 24 1 0 0 0 0 23 27 1 6 0 0 0 24 25 1 6 0 0 0 25 26 1 0 0 0 0 27 28 1 0 0 0 0 27 29 1 0 0 0 0 30 31 1 0 0 0 0 31 32 2 0 0 0 0 31 33 1 0 0 0 0 35 36 1 0 0 0 0 36 37 2 0 0 0 0 36 38 1 0 0 0 0 39 40 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	562.28
Volume:	565.294
LogP:	3.242
LogD:	2.983
LogS:	-4.261
# Rotatable Bonds:	9
TPSA:	137.96
# H-Bond Aceptor:	10
# H-Bond Donor:	1
# Rings:	4
# Heavy Atoms:	10

MedChem Properties

QED Drug-Likeness Score:	0.169
Synthetic Accessibility Score:	6.012
Fsp3:	0.733
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.195
MDCK Permeability:	7.967653800733387e-05
Pgp-inhibitor:	1.0
Pgp-substrate:	0.055
Human Intestinal Absorption (HIA):	0.627
20% Bioavailability (F20%):	0.071
30% Bioavailability (F30%):	0.96

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.074
Plasma Protein Binding (PPB):	74.8349838256836%
Volume Distribution (VD):	1.673
Pgp-substrate:	20.3870906829834%

ADMET: Metabolism

CYP1A2-inhibitor:	0.019
CYP1A2-substrate:	0.088
CYP2C19-inhibitor:	0.029
CYP2C19-substrate:	0.553
CYP2C9-inhibitor:	0.098
CYP2C9-substrate:	0.011
CYP2D6-inhibitor:	0.012
CYP2D6-substrate:	0.037
CYP3A4-inhibitor:	0.919
CYP3A4-substrate:	0.7

ADMET: Excretion

Clearance (CL):	7.503
Half-life (T1/2):	0.579

ADMET: Toxicity

hERG Blockers:	0.025
Human Hepatotoxicity (H-HT):	0.937
Drug-inuced Liver Injury (DILI):	0.953
AMES Toxicity:	0.137
Rat Oral Acute Toxicity:	0.9
Maximum Recommended Daily Dose:	0.133
Skin Sensitization:	0.341
Carcinogencity:	0.135
Eye Corrosion:	0.193
Eye Irritation:	0.05
Respiratory Toxicity:	0.972

Download Data

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

Natural Product: NPC482174

Natural Product ID:	NPC482174
*Common Name:**	HGDPQMSQQDGHCH-PAFBSFPRSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	HGDPQMSQQDGHCH-PAFBSFPRSA-N
Standard InCHI:	InChI=1S/C30H42O10/c1-10-14(2)27(35)39-23-19(13-31)12-30-26(38-18(6)33)15(3)11-29(30,40-30)25(34)16(4)22(37-17(5)32)20-21(24(23)36-9)28(20,7)8/h10,12,15-16,20-24,26,31H,11,13H2,1-9H3/b14-10-,19-12+/t15-,16+,20-,21+,22-,23+,24+,26-,29-,30-/m0/s1
SMILES:	C/C=C(/C)C(=O)O[C@@H]1/C(=C/[C@]23[C@H]([C@@H](C)C[C@@]2(C(=O)[C@H](C)[C@@H]([C@@H]2[C@H]([C@H]1OC)C2(C)C)OC(=O)C)O3)OC(=O)C)/CO
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	90645362
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001551] Diterpenoids

*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
NPO10031	Euphorbia antiquorum	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11858748]
NPO10031	Euphorbia antiquorum	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24840014]
NPO10031	Euphorbia antiquorum	Species	Euphorbiaceae	Eukaryota	Stems	n.a.	n.a.	PMID[31180680]
NPO10031	Euphorbia antiquorum	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO10031	Euphorbia antiquorum	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO10031	Euphorbia antiquorum	Species	Euphorbiaceae	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

Activity Type	# Activity
Cell Line	2
Individual Protein	2

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT4862	Individual Protein	11-beta-hydroxysteroid dehydrogenase 1	Mus musculus	IC50	=	12000.0	nM	PMID[24840014]
NPT116	Cell Line	HL-60	Homo sapiens	IC50	<	10000.0	nM	PMID[24840014]
NPT81	Cell Line	A549	Homo sapiens	IC50	<	10000.0	nM	PMID[24840014]
NPT178	Individual Protein	Protein-tyrosine phosphatase 1B	Homo sapiens	IC50	<	10000.0	nM	PMID[24840014]

☑ 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 NPC482174 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	284
0.1-0.2	1706
0.2-0.3	5685
0.3-0.4	9421
0.4-0.5	13693
0.5-0.6	7105
0.6-0.7	3687
0.7-0.8	1004
0.8-0.85	73
0.85-0.9	11
0.9-0.95	9
0.95-1	19

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 NPC482174 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	288
0.1-0.2	2355
0.2-0.3	3779
0.3-0.4	1775
0.4-0.5	589
0.5-0.6	229
0.6-0.7	128
0.7-0.8	7
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