NPASS Compound

Structure

NPC211872 OpenBabel06302215342D 22 24 0 0 1 0 0 0 0 0999 V2000 -0.7925 -3.0438 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2090 -2.1789 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.1690 -2.1789 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7676 -1.4283 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.5540 -0.4924 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.3781 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.4641 0.9561 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1010 -0.6316 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0370 -0.4180 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.7237 -1.5144 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.6890 -0.0759 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8241 -0.4924 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7726 -0.3441 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6105 -1.4283 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3456 -1.5144 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7229 -0.6316 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 0.0861 0.9561 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.6890 1.8441 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8577 2.3241 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8577 3.2841 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0263 1.8441 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 6 0 0 0 2 3 1 0 0 0 0 2 14 1 0 0 0 0 4 3 1 1 0 0 0 4 5 1 0 0 0 0 4 10 1 0 0 0 0 5 6 1 0 0 0 0 5 11 1 0 0 0 0 6 7 1 6 0 0 0 6 8 1 0 0 0 0 8 9 2 0 0 0 0 8 10 1 0 0 0 0 11 12 1 0 0 0 0 11 19 1 6 0 0 0 12 17 1 0 0 0 0 12 13 1 1 0 0 0 12 14 1 0 0 0 0 14 15 2 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 17 18 2 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 M END $$$$

Physi-Chem Properties

Molecular Weight:	306.15
Volume:	310.324
LogP:	1.455
LogD:	1.16
LogS:	-2.679
# Rotatable Bonds:	2
TPSA:	69.67
# H-Bond Aceptor:	5
# H-Bond Donor:	0
# Rings:	3
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.548
Synthetic Accessibility Score:	4.662
Fsp3:	0.706
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.607
MDCK Permeability:	5.341732321539894e-05
Pgp-inhibitor:	0.824
Pgp-substrate:	0.006
Human Intestinal Absorption (HIA):	0.046
20% Bioavailability (F20%):	0.032
30% Bioavailability (F30%):	0.621

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.965
Plasma Protein Binding (PPB):	54.625640869140625%
Volume Distribution (VD):	1.159
Pgp-substrate:	44.330352783203125%

ADMET: Metabolism

CYP1A2-inhibitor:	0.049
CYP1A2-substrate:	0.089
CYP2C19-inhibitor:	0.021
CYP2C19-substrate:	0.738
CYP2C9-inhibitor:	0.012
CYP2C9-substrate:	0.072
CYP2D6-inhibitor:	0.007
CYP2D6-substrate:	0.089
CYP3A4-inhibitor:	0.62
CYP3A4-substrate:	0.35

ADMET: Excretion

Clearance (CL):	5.738
Half-life (T1/2):	0.843

ADMET: Toxicity

hERG Blockers:	0.005
Human Hepatotoxicity (H-HT):	0.723
Drug-inuced Liver Injury (DILI):	0.867
AMES Toxicity:	0.015
Rat Oral Acute Toxicity:	0.184
Maximum Recommended Daily Dose:	0.034
Skin Sensitization:	0.111
Carcinogencity:	0.248
Eye Corrosion:	0.239
Eye Irritation:	0.293
Respiratory Toxicity:	0.185

Download Data

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

Natural Product: NPC211872

Natural Product ID:	NPC211872
*Common Name:**	RTZXXBPATUWPKS-DKNBSHDWSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	RTZXXBPATUWPKS-DKNBSHDWSA-N
Standard InCHI:	InChI=1S/C17H22O5/c1-8-7-12-14(9(2)16(20)22-12)15(21-10(3)18)17(4)11(8)5-6-13(17)19/h5,8-9,12,14-15H,6-7H2,1-4H3/t8-,9-,12-,14-,15+,17+/m1/s1
SMILES:	C[C@@H]1C[C@@H]2[C@@H]([C@@H](C)C(=O)O2)[C@@H]([C@@]2(C)C1=CCC2=O)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

*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
NPO10732	Erysimum allionii	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28309	Artocarpus nitidus	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11615	Kopsia deverrei	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17192	Licaria macrophylla	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16848	Nasutitermes nigriceps	Species	Termitoidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18577	Lathyrus roseus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18249	Eucalyptus deglupta	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19131	Callilepis salicifolia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15631	Baccharis neaei	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15114	Oxalis pes-caprae	Species	Oxalidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9681	Toxicodendron diversilobum	Species	Anacardiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17502	Senecio jacquemontianus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21499	Halimeda tuna	Species	Halimedaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8509	Senecio discolor	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16482	Hypoestes forskalei	Species	Acanthaceae	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 NPC211872 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	221
0.1-0.2	1567
0.2-0.3	6829
0.3-0.4	15201
0.4-0.5	8338
0.5-0.6	7057
0.6-0.7	3050
0.7-0.8	383
0.8-0.85	29
0.85-0.9	14
0.9-0.95	8
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 NPC211872 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	208
0.1-0.2	2256
0.2-0.3	4048
0.3-0.4	1802
0.4-0.5	473
0.5-0.6	264
0.6-0.7	87
0.7-0.8	11
0.8-0.85	0
0.85-0.9	1
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