NPASS Compound

Structure

NPC36673 OpenBabel06302215172D 40 42 0 0 1 0 0 0 0 0999 V2000 2.5981 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 1.0000 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 2 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 5.1962 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7942 1.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 7.8988 2.4945 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 7.1556 3.1637 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.8769 2.7024 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 9.3769 1.8364 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.7078 1.0933 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 8.9157 0.1151 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 8.1725 -0.5540 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.8667 -0.1939 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.6099 0.4752 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 9.2836 3.6160 0.0000 O 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 3.4641 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.7321 -0.0000 0.0000 O 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 -1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.0000 -2.0000 0.0000 C 0 0 2 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 -0.8660 -0.5000 0.0000 C 0 0 1 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 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 -1.7321 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -3.0000 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 5.1962 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 -3.5000 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 3 24 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 6 0 0 0 4 21 1 0 0 0 0 5 6 1 0 0 0 0 6 7 2 0 0 0 0 6 8 1 0 0 0 0 8 9 1 0 0 0 0 10 9 1 6 0 0 0 10 11 1 0 0 0 0 10 15 1 0 0 0 0 11 12 1 1 0 0 0 11 13 1 0 0 0 0 13 14 1 0 0 0 0 13 20 1 6 0 0 0 14 15 1 0 0 0 0 15 16 1 1 0 0 0 16 17 1 1 0 0 0 16 18 1 0 0 0 0 18 19 1 0 0 0 0 21 22 2 0 0 0 0 21 37 1 0 0 0 0 22 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 1 1 0 0 0 26 25 1 1 0 0 0 26 27 1 0 0 0 0 26 33 1 0 0 0 0 27 28 1 0 0 0 0 27 36 1 6 0 0 0 28 29 1 0 0 0 0 28 35 1 1 0 0 0 29 30 1 0 0 0 0 29 34 1 6 0 0 0 30 31 1 1 0 0 0 30 33 1 0 0 0 0 31 32 1 0 0 0 0 37 38 2 0 0 0 0 37 39 1 0 0 0 0 39 40 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	574.26
Volume:	553.606
LogP:	0.622
LogD:	0.923
LogS:	-1.482
# Rotatable Bonds:	12
TPSA:	201.67
# H-Bond Aceptor:	13
# H-Bond Donor:	6
# Rings:	3
# Heavy Atoms:	13

MedChem Properties

QED Drug-Likeness Score:	0.137
Synthetic Accessibility Score:	5.414
Fsp3:	0.778
Lipinski Rule-of-5:	Rejected
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:	-5.867
MDCK Permeability:	0.0002343973465031013
Pgp-inhibitor:	0.025
Pgp-substrate:	0.999
Human Intestinal Absorption (HIA):	0.953
20% Bioavailability (F20%):	0.005
30% Bioavailability (F30%):	0.995

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.225
Plasma Protein Binding (PPB):	37.170955657958984%
Volume Distribution (VD):	0.325
Pgp-substrate:	22.65160369873047%

ADMET: Metabolism

CYP1A2-inhibitor:	0.014
CYP1A2-substrate:	0.103
CYP2C19-inhibitor:	0.009
CYP2C19-substrate:	0.591
CYP2C9-inhibitor:	0.001
CYP2C9-substrate:	0.019
CYP2D6-inhibitor:	0.003
CYP2D6-substrate:	0.045
CYP3A4-inhibitor:	0.016
CYP3A4-substrate:	0.191

ADMET: Excretion

Clearance (CL):	2.214
Half-life (T1/2):	0.867

ADMET: Toxicity

hERG Blockers:	0.028
Human Hepatotoxicity (H-HT):	0.357
Drug-inuced Liver Injury (DILI):	0.941
AMES Toxicity:	0.517
Rat Oral Acute Toxicity:	0.509
Maximum Recommended Daily Dose:	0.742
Skin Sensitization:	0.203
Carcinogencity:	0.888
Eye Corrosion:	0.003
Eye Irritation:	0.014
Respiratory Toxicity:	0.949

Download Data

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

Natural Product: NPC36673

Natural Product ID:	NPC36673
*Common Name:**	XNIRCYGLGZSLPW-JMYXUZGCSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	XNIRCYGLGZSLPW-JMYXUZGCSA-N
Standard InCHI:	InChI=1S/C27H42O13/c1-5-14-16(7-21(31)37-10-17-13(3)19(30)6-15(17)12(2)8-28)18(25(35)36-4)11-38-26(14)40-27-24(34)23(33)22(32)20(9-29)39-27/h5,11-13,15-17,19-20,22-24,26-30,32-34H,6-10H2,1-4H3/b14-5+/t12-,13-,15+,16+,17-,19-,20-,22-,23+,24-,26+,27+/m1/s1
SMILES:	C/C=C/1[C@H](CC(=O)OC[C@@H]2[C@@H](C)[C@@H](C[C@H]2[C@H](C)CO)O)C(=CO[C@H]1O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)C(=O)OC
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:0002049] Terpene glycosides

*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
NPO1552	Euonymus japonicus	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1039/P19890001079]
NPO12062	Pseudoxandra cuspidata	Species	Annonaceae	Eukaryota	Bark	n.a.	n.a.	PMID[19299148]
NPO8614	Cinchona succirubra	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO1552	Euonymus japonicus	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO8614	Cinchona succirubra	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO1552	Euonymus japonicus	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO1552	Euonymus japonicus	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO1197	Panax trifoliatus	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10656	Rzedowskia tolantonguensis	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12298	Epilobium parviflorum	Species	Onagraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6240	Paliurus spina-christi	Species	Rhamnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8614	Cinchona succirubra	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11272	Plectranthus parviflorus	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3128	Solanum dasyphyllum	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9574	Trametes albida	Species	Coriolaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14343	Scapharca broughtonii	Species	Arcidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1552	Euonymus japonicus	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16173	Parmelia norcrambidiocarpa	Species	Parmeliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15096	Penicillium sclerotiorum	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10146	Bassia parkii	Species	Abylidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13363	Rumex aquaticus	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13239	Eudistoma toealensis	Species	Polycitoridae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11606	Anemoclema glaucifolium	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15423	Senecio ilicifolius	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14760	Eulophia ochreata	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2891	Montanelia tominii	Species	Parmeliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14219	Aconitum racemulosum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15910	Calea morii	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12062	Pseudoxandra cuspidata	Species	Annonaceae	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 NPC36673 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	199
0.1-0.2	1148
0.2-0.3	4348
0.3-0.4	8747
0.4-0.5	13158
0.5-0.6	7999
0.6-0.7	6019
0.7-0.8	1009
0.8-0.85	50
0.85-0.9	14
0.9-0.95	6
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 NPC36673 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	166
0.1-0.2	1498
0.2-0.3	3858
0.3-0.4	2429
0.4-0.5	731
0.5-0.6	296
0.6-0.7	154
0.7-0.8	18
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