Structure

Physi-Chem Properties

Molecular Weight:  193.11
Volume:  196.447
LogP:  1.732
LogD:  1.73
LogS:  -2.285
# Rotatable Bonds:  1
TPSA:  29.54
# H-Bond Aceptor:  3
# H-Bond Donor:  0
# Rings:  3
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.633
Synthetic Accessibility Score:  3.584
Fsp3:  0.727
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:  -4.476
MDCK Permeability:  3.4165248507633805e-05
Pgp-inhibitor:  0.049
Pgp-substrate:  0.004
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.004
30% Bioavailability (F30%):  0.016

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.968
Plasma Protein Binding (PPB):  58.520782470703125%
Volume Distribution (VD):  0.716
Pgp-substrate:  51.657901763916016%

ADMET: Metabolism

CYP1A2-inhibitor:  0.051
CYP1A2-substrate:  0.158
CYP2C19-inhibitor:  0.117
CYP2C19-substrate:  0.804
CYP2C9-inhibitor:  0.022
CYP2C9-substrate:  0.258
CYP2D6-inhibitor:  0.054
CYP2D6-substrate:  0.306
CYP3A4-inhibitor:  0.065
CYP3A4-substrate:  0.351

ADMET: Excretion

Clearance (CL):  4.636
Half-life (T1/2):  0.334

ADMET: Toxicity

hERG Blockers:  0.015
Human Hepatotoxicity (H-HT):  0.739
Drug-inuced Liver Injury (DILI):  0.286
AMES Toxicity:  0.016
Rat Oral Acute Toxicity:  0.055
Maximum Recommended Daily Dose:  0.157
Skin Sensitization:  0.682
Carcinogencity:  0.46
Eye Corrosion:  0.011
Eye Irritation:  0.131
Respiratory Toxicity:  0.036

Download Data

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

  Natural Product: NPC477688

Natural Product ID:  NPC477688
Common Name*:   2-Cyclopropyl-3-methyl-6,7,8,8a-tetrahydro-4H-pyrrolo[2,1-b][1,3]oxazine-4-one
IUPAC Name:   2-cyclopropyl-3-methyl-6,7,8,8a-tetrahydropyrrolo[2,1-b][1,3]oxazin-4-one
Synonyms:  
Standard InCHIKey:  ILJXACFPEYTPJK-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C11H15NO2/c1-7-10(8-4-5-8)14-9-3-2-6-12(9)11(7)13/h8-9H,2-6H2,1H3
SMILES:  CC1=C(OC2CCCN2C1=O)C3CC3
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   10655410
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000218] Pyrrolidines

*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
NPO33542 Penicilliun brevicompactum Species n.a. n.a. n.a. n.a. n.a. PMID[10956170]

☑ 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
NPT1262 Organism Aspergillus parasiticus Aspergillus parasiticus GI = 11.3 % PMID[10956170]
NPT4814 Organism Penicillium italicum Penicillium italicum GI = 23.6 % PMID[10956170]
NPT2567 Organism Trichoderma viride Hypocrea rufa GI = 0 % PMID[10956170]
NPT2793 Organism Phytophthora citrophthora Phytophthora citrophthora GI = 37.5 % PMID[10956170]
NPT1503 Organism Verticillium dahliae Verticillium dahliae GI = 65.4 % PMID[10956170]
NPT2646 Organism Alternaria tenuis Alternaria tenuis GI = 23.9 % PMID[10956170]
NPT6882 Organism Trichothecium roseum Trichothecium roseum GI = 0 % PMID[10956170]
NPT3518 Organism Colletotrichum coccodes Colletotrichum coccodes GI = 37.8 % PMID[10956170]
NPT562 Organism Colletotrichum gloeosporioides Colletotrichum gloeosporioides GI = 11.8 % PMID[10956170]
NPT3594 Organism Galactomyces geotrichum Galactomyces geotrichum GI = 0 % PMID[10956170]
NPT5164 Organism Fusarium oxysporum f. sp. niveum Fusarium oxysporum f. sp. niveum GI = 26.2 % PMID[10956170]
NPT6887 Organism Fusarium oxysporum f. sp. gladioli Fusarium oxysporum f. sp. gladioli GI = 24.1 % PMID[10956170]
NPT1278 Organism Fusarium culmorum Fusarium culmorum GI = 38.9 % PMID[10956170]

☑ 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 NPC477688 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
0.6118 Remote Similarity NPC471768
0.6076 Remote Similarity NPC96272
0.6071 Remote Similarity NPC46268
0.5977 Remote Similarity NPC226982
0.5977 Remote Similarity NPC277341
0.5946 Remote Similarity NPC385
0.5909 Remote Similarity NPC473810
0.5867 Remote Similarity NPC133923
0.5783 Remote Similarity NPC252503
0.5745 Remote Similarity NPC53240
0.5714 Remote Similarity NPC2640
0.5714 Remote Similarity NPC319913
0.5714 Remote Similarity NPC296589
0.5714 Remote Similarity NPC14437
0.5714 Remote Similarity NPC252684
0.5714 Remote Similarity NPC270412
0.5652 Remote Similarity NPC322672
0.5638 Remote Similarity NPC81195
0.5625 Remote Similarity NPC78625
0.561 Remote Similarity NPC90782
0.5604 Remote Similarity NPC475975

  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 NPC477688 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
0.5714 Remote Similarity NPD9418 Clinical (unspecified phase)

  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