Structure

Physi-Chem Properties

Molecular Weight:  282.16
Volume:  319.193
LogP:  3.441
LogD:  3.6
LogS:  -3.83
# Rotatable Bonds:  7
TPSA:  40.46
# H-Bond Aceptor:  2
# H-Bond Donor:  2
# Rings:  2
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.799
Synthetic Accessibility Score:  2.482
Fsp3:  0.263
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
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:  -4.819
MDCK Permeability:  1.3736679647990968e-05
Pgp-inhibitor:  0.053
Pgp-substrate:  0.382
Human Intestinal Absorption (HIA):  0.015
20% Bioavailability (F20%):  1.0
30% Bioavailability (F30%):  0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.189
Plasma Protein Binding (PPB):  97.06815338134766%
Volume Distribution (VD):  0.595
Pgp-substrate:  1.4113898277282715%

ADMET: Metabolism

CYP1A2-inhibitor:  0.973
CYP1A2-substrate:  0.303
CYP2C19-inhibitor:  0.961
CYP2C19-substrate:  0.201
CYP2C9-inhibitor:  0.837
CYP2C9-substrate:  0.964
CYP2D6-inhibitor:  0.797
CYP2D6-substrate:  0.871
CYP3A4-inhibitor:  0.398
CYP3A4-substrate:  0.388

ADMET: Excretion

Clearance (CL):  11.957
Half-life (T1/2):  0.821

ADMET: Toxicity

hERG Blockers:  0.372
Human Hepatotoxicity (H-HT):  0.065
Drug-inuced Liver Injury (DILI):  0.015
AMES Toxicity:  0.105
Rat Oral Acute Toxicity:  0.032
Maximum Recommended Daily Dose:  0.827
Skin Sensitization:  0.949
Carcinogencity:  0.645
Eye Corrosion:  0.418
Eye Irritation:  0.985
Respiratory Toxicity:  0.257

Download Data

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

  Natural Product: NPC51329

Natural Product ID:  NPC51329
Common Name*:   Oxiran-2-Ylmethyl 2-Methylprop-2-Enoate
IUPAC Name:   oxiran-2-ylmethyl 2-methylprop-2-enoate
Synonyms:  
Standard InCHIKey:  VOZRXNHHFUQHIL-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C7H10O3/c1-5(2)7(8)10-4-6-3-9-6/h6H,1,3-4H2,2H3
SMILES:  CC(=C)C(=O)OCC1CO1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1333073
PubChem CID:   7837
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000265] Carboxylic acids and derivatives
        • [CHEMONTID:0001093] Carboxylic acid derivatives
          • [CHEMONTID:0001238] Carboxylic acid esters
            • [CHEMONTID:0003628] Alpha,beta-unsaturated carboxylic esters
              • [CHEMONTID:0003626] Enoate esters

*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
NPO26327 Chaenomeles sinensis Species Rosaceae Eukaryota n.a. n.a. n.a. PMID[14600382]
NPO2392 Hansenia weberbaueriana Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[25333853]
NPO26327 Chaenomeles sinensis Species Rosaceae Eukaryota Twigs n.a. n.a. PMID[25894905]
NPO26327 Chaenomeles sinensis Species Rosaceae Eukaryota Twigs n.a. n.a. PMID[28358502]
NPO26327 Chaenomeles sinensis Species Rosaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26327 Chaenomeles sinensis Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2392 Hansenia weberbaueriana Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24644 Hansenia forbesii Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2953 Ostericum grosseserratum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO2392 Hansenia weberbaueriana Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO26327 Chaenomeles sinensis Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO24644 Hansenia forbesii Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO24644 Hansenia forbesii Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2953 Ostericum grosseserratum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26327 Chaenomeles sinensis Species Rosaceae 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
NPT162 Individual Protein Heat shock protein beta-1 Homo sapiens Potency n.a. 61004.3 nM PubChem BioAssay data set
NPT94 Individual Protein Aldehyde dehydrogenase 1A1 Homo sapiens Potency = 31622.8 nM PMID[551573]
NPT2 Others Unspecified Potency n.a. 61652.4 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 3029.5 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 76098.7 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 21645.1 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 1911.5 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 6100.4 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 53873.8 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 NPC51329 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
0.8372 Intermediate Similarity NPC159773
0.7083 Intermediate Similarity NPC312547
0.6818 Remote Similarity NPC65353
0.6744 Remote Similarity NPC63354
0.6667 Remote Similarity NPC68577
0.6596 Remote Similarity NPC203382
0.6538 Remote Similarity NPC223675
0.6531 Remote Similarity NPC40805
0.6415 Remote Similarity NPC15789
0.6415 Remote Similarity NPC236338
0.6341 Remote Similarity NPC88135
0.6279 Remote Similarity NPC281883
0.625 Remote Similarity NPC281043
0.6129 Remote Similarity NPC308457
0.6129 Remote Similarity NPC470808
0.6111 Remote Similarity NPC275316
0.6087 Remote Similarity NPC9290
0.6071 Remote Similarity NPC327103
0.6042 Remote Similarity NPC147824
0.6032 Remote Similarity NPC273600
0.6 Remote Similarity NPC41409
0.6 Remote Similarity NPC190649
0.6 Remote Similarity NPC217161
0.5962 Remote Similarity NPC47946
0.5962 Remote Similarity NPC26600
0.5938 Remote Similarity NPC475675
0.5938 Remote Similarity NPC475555
0.5938 Remote Similarity NPC124586
0.5926 Remote Similarity NPC135698
0.5926 Remote Similarity NPC126184
0.5918 Remote Similarity NPC297608
0.5893 Remote Similarity NPC191643
0.5854 Remote Similarity NPC127134
0.5849 Remote Similarity NPC197467
0.5806 Remote Similarity NPC151648
0.5781 Remote Similarity NPC476589
0.5763 Remote Similarity NPC230296
0.5763 Remote Similarity NPC150717
0.5745 Remote Similarity NPC103612
0.5745 Remote Similarity NPC24967
0.5738 Remote Similarity NPC286189
0.5738 Remote Similarity NPC302564
0.5714 Remote Similarity NPC44343
0.5714 Remote Similarity NPC2328
0.5714 Remote Similarity NPC179087
0.5714 Remote Similarity NPC210303
0.5714 Remote Similarity NPC217940
0.5714 Remote Similarity NPC473737
0.5686 Remote Similarity NPC57923
0.5667 Remote Similarity NPC293437
0.5667 Remote Similarity NPC135863
0.5667 Remote Similarity NPC249850
0.566 Remote Similarity NPC172042
0.566 Remote Similarity NPC270706
0.5652 Remote Similarity NPC477311
0.5652 Remote Similarity NPC477303
0.5645 Remote Similarity NPC26223
0.5645 Remote Similarity NPC130953
0.5645 Remote Similarity NPC79756
0.5636 Remote Similarity NPC234084
0.5625 Remote Similarity NPC148233
0.5625 Remote Similarity NPC25747
0.561 Remote Similarity NPC41485
0.561 Remote Similarity NPC32280
0.56 Remote Similarity NPC250954

  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 NPC51329 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
0.66 Remote Similarity NPD9378 Approved
0.6415 Remote Similarity NPD9437 Clinical (unspecified phase)
0.6279 Remote Similarity NPD9636 Phase 2
0.625 Remote Similarity NPD8839 Phase 3
0.5957 Remote Similarity NPD9115 Approved
0.5854 Remote Similarity NPD8989 Approved
0.5714 Remote Similarity NPD6927 Phase 3

  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