Structure

Physi-Chem Properties

Molecular Weight:  100.05
Volume:  101.424
LogP:  -0.085
LogD:  -0.543
LogS:  0.579
# Rotatable Bonds:  0
TPSA:  26.3
# H-Bond Aceptor:  2
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.439
Synthetic Accessibility Score:  3.567
Fsp3:  0.8
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.25
MDCK Permeability:  2.9556438676081598e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.004
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.003
30% Bioavailability (F30%):  0.005

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.745
Plasma Protein Binding (PPB):  16.97863006591797%
Volume Distribution (VD):  1.09
Pgp-substrate:  83.96133422851562%

ADMET: Metabolism

CYP1A2-inhibitor:  0.051
CYP1A2-substrate:  0.647
CYP2C19-inhibitor:  0.026
CYP2C19-substrate:  0.698
CYP2C9-inhibitor:  0.006
CYP2C9-substrate:  0.265
CYP2D6-inhibitor:  0.006
CYP2D6-substrate:  0.481
CYP3A4-inhibitor:  0.005
CYP3A4-substrate:  0.231

ADMET: Excretion

Clearance (CL):  6.265
Half-life (T1/2):  0.896

ADMET: Toxicity

hERG Blockers:  0.015
Human Hepatotoxicity (H-HT):  0.209
Drug-inuced Liver Injury (DILI):  0.464
AMES Toxicity:  0.677
Rat Oral Acute Toxicity:  0.318
Maximum Recommended Daily Dose:  0.023
Skin Sensitization:  0.36
Carcinogencity:  0.308
Eye Corrosion:  0.809
Eye Irritation:  0.958
Respiratory Toxicity:  0.042

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

  Natural Product: NPC233231

Natural Product ID:  NPC233231
Common Name*:   2-Methyloxolan-3-One
IUPAC Name:   2-methyloxolan-3-one
Synonyms:  
Standard InCHIKey:  FCWYQRVIQDNGBI-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C5H8O2/c1-4-5(6)2-3-7-4/h4H,2-3H2,1H3
SMILES:  O=C1CCOC1C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3188615
PubChem CID:   18522
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0001983] Dihydrofurans
        • [CHEMONTID:0001982] Furanones

*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
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota Flowers Tantempango, Hidalgo, Mexico 2019-May DOI[10.1007/s11130-020-00822-2]
NPO17755 Inula helenium Species Asteraceae Eukaryota n.a. root n.a. PMID[10364842]
NPO17755 Inula helenium Species Asteraceae Eukaryota n.a. root n.a. PMID[12392098]
NPO17823 Lycium chinense Species Solanaceae Eukaryota fruits n.a. n.a. PMID[12467621]
NPO17823 Lycium chinense Species Solanaceae Eukaryota n.a. root n.a. PMID[16212233]
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. PMID[16297615]
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota n.a. whole plant n.a. PMID[18543151]
NPO17823 Lycium chinense Species Solanaceae Eukaryota root bark n.a. n.a. PMID[23282106]
NPO17755 Inula helenium Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[23501116]
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. PMID[24358188]
NPO17755 Inula helenium Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[24996657]
NPO17755 Inula helenium Species Asteraceae Eukaryota n.a. root n.a. PMID[25767328]
NPO17823 Lycium chinense Species Solanaceae Eukaryota Root Bark n.a. n.a. PMID[26982999]
NPO23429 Lycium barbarum Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[31397570]
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. PMID[8778246]
NPO17823 Lycium chinense Species Solanaceae Eukaryota fruits n.a. n.a. PMID[9090870]
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17823 Lycium chinense Species Solanaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23429 Lycium barbarum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17755 Inula helenium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14763 Aloe ferox Species Asphodelaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17823 Lycium chinense Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23429 Lycium barbarum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17755 Inula helenium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14763 Aloe ferox Species Asphodelaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO23429 Lycium barbarum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO14763 Aloe ferox Species Asphodelaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO17823 Lycium chinense Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO17755 Inula helenium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO14763 Aloe ferox Species Asphodelaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO2837 Aloe spicata Species Asphodelaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO2997 Aloe africana Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO23429 Lycium barbarum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO17823 Lycium chinense Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO14763 Aloe ferox Species Asphodelaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17755 Inula helenium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2997 Aloe africana Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17823 Lycium chinense Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23429 Lycium barbarum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11578 Aloe vera Species Xanthorrhoeaceae 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
NPT106 Individual Protein Peroxisome proliferator-activated receptor delta Homo sapiens Potency n.a. 21872.4 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 1949.4 nM PubChem BioAssay data set

☑ 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 NPC233231 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.56 or Top200).

Similarity Score Similarity Level Natural Product ID
0.6944 Remote Similarity NPC5934
0.6923 Remote Similarity NPC321699
0.6667 Remote Similarity NPC320331
0.6429 Remote Similarity NPC94368
0.6316 Remote Similarity NPC228727
0.6216 Remote Similarity NPC270334
0.6154 Remote Similarity NPC217218
0.6111 Remote Similarity NPC248233
0.6053 Remote Similarity NPC302611
0.6 Remote Similarity NPC259982
0.6 Remote Similarity NPC176500
0.6 Remote Similarity NPC228782
0.6 Remote Similarity NPC313565
0.5897 Remote Similarity NPC12904
0.5833 Remote Similarity NPC127134
0.5833 Remote Similarity NPC166804
0.575 Remote Similarity NPC286695
0.575 Remote Similarity NPC322892
0.5745 Remote Similarity NPC273545
0.5714 Remote Similarity NPC103612
0.5714 Remote Similarity NPC24967
0.5676 Remote Similarity NPC143211
0.5641 Remote Similarity NPC265882
0.5625 Remote Similarity NPC63182
0.5625 Remote Similarity NPC105329
0.5625 Remote Similarity NPC52700
0.5625 Remote Similarity NPC145045
0.561 Remote Similarity NPC154396
0.561 Remote Similarity NPC227267
0.561 Remote Similarity NPC140229
0.561 Remote Similarity NPC127142
0.56 Remote Similarity NPC46254

  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 NPC233231 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

Similarity Score Similarity Level Drug ID Developmental Stage
0.6944 Remote Similarity NPD8856 Phase 2
0.5952 Remote Similarity NPD9131 Discovery
0.5833 Remote Similarity NPD8989 Approved

  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