NPASS Compound

Structure

NPC33129 OpenBabel06302215412D 27 30 0 0 1 0 0 0 0 0999 V2000 -5.3007 1.9945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4347 1.4945 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.4347 2.4945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5686 2.9945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7026 2.4945 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.8366 2.9945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8366 3.9945 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.9706 2.4945 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.9706 1.4945 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.8366 0.9945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7026 1.4945 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.7026 0.4945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5686 0.9945 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.5686 -0.0055 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4347 -0.5055 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.3007 -0.0055 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.3007 0.9945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.1667 1.4945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.1667 2.4945 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.0327 0.9945 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.8988 1.4945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4347 -1.5055 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.1045 0.9945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8090 1.4013 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4781 0.6581 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9781 -0.2079 0.0000 O 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 2 1 1 1 0 0 0 2 17 1 0 0 0 0 2 3 1 0 0 0 0 2 13 1 0 0 0 0 3 4 1 0 0 0 0 5 4 1 6 0 0 0 5 6 1 0 0 0 0 5 11 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 9 10 1 0 0 0 0 9 23 1 1 0 0 0 10 11 1 0 0 0 0 11 12 1 6 0 0 0 11 13 1 0 0 0 0 13 14 1 6 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 15 22 1 6 0 0 0 16 17 2 0 0 0 0 17 18 1 0 0 0 0 18 19 2 0 0 0 0 18 20 1 0 0 0 0 20 21 1 0 0 0 0 23 27 2 0 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 25 26 1 0 0 0 0 26 27 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	374.17
Volume:	377.105
LogP:	2.554
LogD:	2.443
LogS:	-3.912
# Rotatable Bonds:	3
TPSA:	82.81
# H-Bond Aceptor:	6
# H-Bond Donor:	0
# Rings:	4
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.737
Synthetic Accessibility Score:	4.59
Fsp3:	0.667
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:	-4.963
MDCK Permeability:	2.151575063180644e-05
Pgp-inhibitor:	0.91
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.005
20% Bioavailability (F20%):	0.038
30% Bioavailability (F30%):	0.908

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.828
Plasma Protein Binding (PPB):	62.42780303955078%
Volume Distribution (VD):	0.985
Pgp-substrate:	40.46419143676758%

ADMET: Metabolism

CYP1A2-inhibitor:	0.044
CYP1A2-substrate:	0.542
CYP2C19-inhibitor:	0.781
CYP2C19-substrate:	0.598
CYP2C9-inhibitor:	0.43
CYP2C9-substrate:	0.07
CYP2D6-inhibitor:	0.014
CYP2D6-substrate:	0.328
CYP3A4-inhibitor:	0.836
CYP3A4-substrate:	0.34

ADMET: Excretion

Clearance (CL):	7.648
Half-life (T1/2):	0.457

ADMET: Toxicity

hERG Blockers:	0.027
Human Hepatotoxicity (H-HT):	0.356
Drug-inuced Liver Injury (DILI):	0.275
AMES Toxicity:	0.028
Rat Oral Acute Toxicity:	0.897
Maximum Recommended Daily Dose:	0.903
Skin Sensitization:	0.109
Carcinogencity:	0.147
Eye Corrosion:	0.006
Eye Irritation:	0.045
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: NPC33129

Natural Product ID:	NPC33129
*Common Name:**	OEIVLTVYSSPDHE-CLHXGTDGSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	OEIVLTVYSSPDHE-CLHXGTDGSA-N
Standard InCHI:	InChI=1S/C21H26O6/c1-20-6-4-14-19(24)27-16(12-5-7-26-11-12)10-21(14,2)17(20)9-13(22)8-15(20)18(23)25-3/h5,7-8,11,13-14,16-17,22H,4,6,9-10H2,1-3H3/t13-,14-,16-,17-,20+,21-/m1/s1
SMILES:	C[C@]12CC[C@@H]3C(=O)O[C@H](C[C@@]3(C)[C@@H]2C[C@@H](C=C1C(=O)OC)O)c1ccoc1
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:0001538] Diterpene 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
NPO28478	Magnolia ovata	Species	Magnoliaceae	Eukaryota	n.a.	leaf	n.a.	PMID[19658431]
NPO28478	Magnolia ovata	Species	Magnoliaceae	Eukaryota	n.a.	fruit	n.a.	PMID[23157012]
NPO28194	Stevia rebaudiana	Species	Asteraceae	Eukaryota	Leaves	n.a.	n.a.	PMID[24758242]
NPO28243	Canarium schweinfurthii	Species	Burseraceae	Eukaryota	Fruits	Edem-ani community of Nsukka local government area (LGA), Enugu State, South-east of Nigeria	n.a.	PMID[35717414]
NPO27082	Citrus yuko	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO27082	Citrus yuko	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27809	Stereocaulon japonicum	Species	Stereocaulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28068	Mostuea brunonis	Species	Loganiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27082	Citrus yuko	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28194	Stevia rebaudiana	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28278	Axinella verrucosa	Species	Axinellidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4118	Jacobaea incana	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28243	Canarium schweinfurthii	Species	Burseraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28459	Bipolaris bicolor	Species	Pleosporaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23215	Ilyocoris cimicoides	Species	Naucoridae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28478	Magnolia ovata	Species	Magnoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28402	Solanum tomatillo	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28140	Herrania albiflora	Species	Malvaceae	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 NPC33129 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	288
0.1-0.2	1140
0.2-0.3	2603
0.3-0.4	5198
0.4-0.5	10397
0.5-0.6	11123
0.6-0.7	9641
0.7-0.8	1869
0.8-0.85	280
0.85-0.9	134
0.9-0.95	22
0.95-1	2

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 NPC33129 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	248
0.1-0.2	849
0.2-0.3	1828
0.3-0.4	2578
0.4-0.5	2106
0.5-0.6	1173
0.6-0.7	327
0.7-0.8	39
0.8-0.85	2
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