NPASS Compound

Structure

NPC303655 OpenBabel06302215512D 28 29 0 0 1 0 0 0 0 0999 V2000 1.7321 -0.0000 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 0.8660 -1.5000 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 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7321 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2321 -2.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2321 -2.8660 0.0000 C 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 -2.5981 -0.5000 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 -0.8660 -0.5000 0.0000 C 0 0 1 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 1 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 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 2.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.0000 3.0000 0.0000 C 0 0 2 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 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 4.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 4.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 4.5000 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 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 14 1 0 0 0 0 2 3 2 0 0 0 0 3 4 1 0 0 0 0 5 4 1 1 0 0 0 5 6 1 0 0 0 0 5 12 1 0 0 0 0 6 7 1 0 0 0 0 6 8 1 0 0 0 0 6 9 1 0 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 11 12 1 0 0 0 0 12 13 1 1 0 0 0 12 14 1 0 0 0 0 14 15 1 1 0 0 0 15 16 1 0 0 0 0 17 16 1 6 0 0 0 17 18 1 0 0 0 0 17 26 1 0 0 0 0 18 19 1 6 0 0 0 18 23 1 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 23 24 2 0 0 0 0 23 25 1 0 0 0 0 26 27 2 0 0 0 0 26 28 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	396.21
Volume:	405.645
LogP:	2.834
LogD:	7.364
LogS:	-3.393
# Rotatable Bonds:	8
TPSA:	121.13
# H-Bond Aceptor:	7
# H-Bond Donor:	3
# Rings:	2
# Heavy Atoms:	7

MedChem Properties

QED Drug-Likeness Score:	0.537
Synthetic Accessibility Score:	4.364
Fsp3:	0.762
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	1
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.124
MDCK Permeability:	0.00017039384692907333
Pgp-inhibitor:	0.0
Pgp-substrate:	0.004
Human Intestinal Absorption (HIA):	0.509
20% Bioavailability (F20%):	0.131
30% Bioavailability (F30%):	0.017

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.073
Plasma Protein Binding (PPB):	81.07415008544922%
Volume Distribution (VD):	0.273
Pgp-substrate:	18.32622528076172%

ADMET: Metabolism

CYP1A2-inhibitor:	0.003
CYP1A2-substrate:	0.061
CYP2C19-inhibitor:	0.008
CYP2C19-substrate:	0.045
CYP2C9-inhibitor:	0.013
CYP2C9-substrate:	0.839
CYP2D6-inhibitor:	0.025
CYP2D6-substrate:	0.068
CYP3A4-inhibitor:	0.011
CYP3A4-substrate:	0.007

ADMET: Excretion

Clearance (CL):	1.469
Half-life (T1/2):	0.775

ADMET: Toxicity

hERG Blockers:	0.003
Human Hepatotoxicity (H-HT):	0.196
Drug-inuced Liver Injury (DILI):	0.094
AMES Toxicity:	0.003
Rat Oral Acute Toxicity:	0.149
Maximum Recommended Daily Dose:	0.017
Skin Sensitization:	0.264
Carcinogencity:	0.263
Eye Corrosion:	0.867
Eye Irritation:	0.398
Respiratory Toxicity:	0.858

Download Data

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

Natural Product: NPC303655

Natural Product ID:	NPC303655
*Common Name:**	PGTQRMPLONEWBV-YIBSWQHHSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	PGTQRMPLONEWBV-YIBSWQHHSA-N
Standard InCHI:	InChI=1S/C21H32O7/c1-12-6-7-15-20(2,3)8-5-9-21(15,4)14(12)11-28-17(19(26)27)13(18(24)25)10-16(22)23/h6,13-15,17H,5,7-11H2,1-4H3,(H,22,23)(H,24,25)(H,26,27)/t13-,14-,15-,17+,21+/m0/s1
SMILES:	CC1=CC[C@H]2C(C)(C)CCC[C@]2(C)[C@H]1CO[C@H]([C@H](CC(=O)O)C(=O)O)C(=O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000264] Organic acids and derivatives [CHEMONTID:0000265] Carboxylic acids and derivatives [CHEMONTID:0001986] Tricarboxylic acids 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
NPO9046	Aigialus parvus	Species	Aigialaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19299148]
NPO14259	Euphorbia milii	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO13752	Acacia mollissima	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO14259	Euphorbia milii	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO17993	Antitrogus parvulus	Species	Scarabaeidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14259	Euphorbia milii	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9046	Aigialus parvus	Species	Aigialaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO640	Gloriosa modesta	Species	Colchicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12172	Bauerella baueri	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO15162	Henricia sanguinolenta	Species	Echinasteridae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6091	Gluta usitata	Species	Anacardiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13752	Acacia mollissima	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5283	Schefflera actinophylla	Species	Araliaceae	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 NPC303655 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	204
0.1-0.2	1243
0.2-0.3	4653
0.3-0.4	10529
0.4-0.5	12381
0.5-0.6	7000
0.6-0.7	6044
0.7-0.8	634
0.8-0.85	9
0.85-0.9	0
0.9-0.95	0
0.95-1	0

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 NPC303655 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	180
0.1-0.2	1698
0.2-0.3	3765
0.3-0.4	2264
0.4-0.5	767
0.5-0.6	306
0.6-0.7	161
0.7-0.8	9
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