NPASS Compound

Structure

NPC45931 OpenBabel06302215372D 25 26 0 0 0 0 0 0 0 0999 V2000 2.5981 -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 0.8660 -2.5000 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 0.0000 -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 -1.7321 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 2.0000 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 -0.8660 0.5000 0.0000 C 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 0.8660 0.5000 0.0000 O 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 0.0000 2.0000 0.0000 O 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 -0.8660 -2.5000 0.0000 O 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 1.7321 -4.0000 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 25 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 5 18 2 0 0 0 0 5 6 1 0 0 0 0 6 7 2 0 0 0 0 6 23 1 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 8 17 2 0 0 0 0 9 10 2 0 0 0 0 10 11 1 0 0 0 0 11 16 2 0 0 0 0 11 12 1 0 0 0 0 12 13 2 0 0 0 0 13 14 1 0 0 0 0 14 15 2 0 0 0 0 15 16 1 0 0 0 0 17 18 1 0 0 0 0 17 20 1 0 0 0 0 18 19 1 0 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 23 24 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	338.15
Volume:	366.092
LogP:	5.501
LogD:	3.396
LogS:	-4.064
# Rotatable Bonds:	6
TPSA:	66.76
# H-Bond Aceptor:	4
# H-Bond Donor:	2
# Rings:	2
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.588
Synthetic Accessibility Score:	2.487
Fsp3:	0.19
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	1
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.925
MDCK Permeability:	1.705173599475529e-05
Pgp-inhibitor:	0.002
Pgp-substrate:	0.006
Human Intestinal Absorption (HIA):	0.01
20% Bioavailability (F20%):	0.015
30% Bioavailability (F30%):	0.852

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.045
Plasma Protein Binding (PPB):	97.48331451416016%
Volume Distribution (VD):	0.33
Pgp-substrate:	1.8362114429473877%

ADMET: Metabolism

CYP1A2-inhibitor:	0.304
CYP1A2-substrate:	0.134
CYP2C19-inhibitor:	0.142
CYP2C19-substrate:	0.062
CYP2C9-inhibitor:	0.762
CYP2C9-substrate:	0.54
CYP2D6-inhibitor:	0.288
CYP2D6-substrate:	0.139
CYP3A4-inhibitor:	0.098
CYP3A4-substrate:	0.091

ADMET: Excretion

Clearance (CL):	2.895
Half-life (T1/2):	0.584

ADMET: Toxicity

hERG Blockers:	0.115
Human Hepatotoxicity (H-HT):	0.867
Drug-inuced Liver Injury (DILI):	0.975
AMES Toxicity:	0.008
Rat Oral Acute Toxicity:	0.174
Maximum Recommended Daily Dose:	0.017
Skin Sensitization:	0.179
Carcinogencity:	0.17
Eye Corrosion:	0.003
Eye Irritation:	0.053
Respiratory Toxicity:	0.898

Download Data

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

Natural Product: NPC45931

Natural Product ID:	NPC45931
*Common Name:**	XPDYDSQPCFQSLH-ZHACJKMWSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	XPDYDSQPCFQSLH-ZHACJKMWSA-N
Standard InCHI:	InChI=1S/C21H22O4/c1-14(2)9-12-17-18(25-3)13-16(19(20(17)22)21(23)24)11-10-15-7-5-4-6-8-15/h4-11,13,22H,12H2,1-3H3,(H,23,24)/b11-10+
SMILES:	CC(=CCc1c(cc(/C=C/c2ccccc2)c(c1O)C(=O)O)OC)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	9819225
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000253] Stilbenes

*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
NPO12682	Euphorbia helioscopia	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18321057]
NPO12682	Euphorbia helioscopia	Species	Euphorbiaceae	Eukaryota	n.a.	whole plant	n.a.	PMID[19099222]
NPO12682	Euphorbia helioscopia	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[30724086]
NPO12682	Euphorbia helioscopia	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31550154]
NPO12682	Euphorbia helioscopia	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO12682	Euphorbia helioscopia	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12682	Euphorbia helioscopia	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO12682	Euphorbia helioscopia	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
EC50	5
MIC	15
Others	10

Activity Type	# Activity
Cell Line	4
Organism	20
Others	6

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT113	Cell Line	RAW264.7	Mus musculus	Inhibition	=	30.19	%	PMID[31550154]
NPT113	Cell Line	RAW264.7	Mus musculus	Inhibition	=	40.92	%	PMID[31255927]
NPT113	Cell Line	RAW264.7	Mus musculus	Inhibition	=	30.63	%	PMID[31255927]
NPT113	Cell Line	RAW264.7	Mus musculus	Inhibition	=	21.16	%	PMID[31255927]
NPT79	Organism	Bacillus subtilis	Bacillus subtilis	MIC	=	32.0	ug.mL-1	PMID[26093280]
NPT17	Organism	Staphylococcus epidermidis	Staphylococcus epidermidis	MIC	=	16.0	ug.mL-1	PMID[26093280]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	=	16.0	ug.mL-1	PMID[26093280]
NPT19	Organism	Escherichia coli	Escherichia coli	MIC	>	128.0	ug.mL-1	PMID[26093280]
NPT766	Organism	Proteus vulgaris	Proteus vulgaris	MIC	>	64.0	ug.mL-1	PMID[26093280]
NPT18	Organism	Pseudomonas aeruginosa	Pseudomonas aeruginosa	MIC	>	64.0	ug.mL-1	PMID[26093280]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	=	32.0	ug.mL-1	PMID[26093280]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	=	8.0	ug.mL-1	PMID[26093280]
NPT18	Organism	Pseudomonas aeruginosa	Pseudomonas aeruginosa	Activity	=	-41.0	%	PMID[30444360]
NPT2	Others	Unspecified		Ratio EC50	=	1.3	n.a.	PMID[27783522]
NPT191	Organism	Hepatitis C virus	Hepatitis C virus	EC50	=	8590.0	nM	PMID[27783522]
NPT191	Organism	Hepatitis C virus	Hepatitis C virus	EC50	=	3800.0	nM	PMID[27783522]
NPT191	Organism	Hepatitis C virus	Hepatitis C virus	EC50	=	6440.0	nM	PMID[27783522]
NPT191	Organism	Hepatitis C virus	Hepatitis C virus	EC50	=	3030.0	nM	PMID[27783522]
NPT2	Others	Unspecified		Ratio CC50/EC50	=	40.0	n.a.	PMID[27783522]
NPT2	Others	Unspecified		EC50	=	3170.0	nM	PMID[27783522]
NPT2	Others	Unspecified		CC50	=	90990.0	nM	PMID[27783522]

☑ 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 NPC45931 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	349
0.1-0.2	1572
0.2-0.3	3654
0.3-0.4	8756
0.4-0.5	9666
0.5-0.6	3307
0.6-0.7	5730
0.7-0.8	6465
0.8-0.85	2179
0.85-0.9	861
0.9-0.95	146
0.95-1	12

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 NPC45931 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	314
0.1-0.2	980
0.2-0.3	1497
0.3-0.4	2538
0.4-0.5	1946
0.5-0.6	1167
0.6-0.7	485
0.7-0.8	176
0.8-0.85	34
0.85-0.9	8
0.9-0.95	5
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