Structure

Physi-Chem Properties

Molecular Weight:  240.25
Volume:  285.526
LogP:  6.795
LogD:  4.319
LogS:  -6.526
# Rotatable Bonds:  13
TPSA:  12.53
# H-Bond Aceptor:  1
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.307
Synthetic Accessibility Score:  2.356
Fsp3:  1.0
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  2
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.735
MDCK Permeability:  1.6982268789433874e-05
Pgp-inhibitor:  0.006
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.002
20% Bioavailability (F20%):  0.281
30% Bioavailability (F30%):  0.959

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.133
Plasma Protein Binding (PPB):  97.66229248046875%
Volume Distribution (VD):  1.62
Pgp-substrate:  1.687476396560669%

ADMET: Metabolism

CYP1A2-inhibitor:  0.34
CYP1A2-substrate:  0.221
CYP2C19-inhibitor:  0.348
CYP2C19-substrate:  0.077
CYP2C9-inhibitor:  0.115
CYP2C9-substrate:  0.793
CYP2D6-inhibitor:  0.094
CYP2D6-substrate:  0.084
CYP3A4-inhibitor:  0.187
CYP3A4-substrate:  0.064

ADMET: Excretion

Clearance (CL):  4.314
Half-life (T1/2):  0.098

ADMET: Toxicity

hERG Blockers:  0.263
Human Hepatotoxicity (H-HT):  0.037
Drug-inuced Liver Injury (DILI):  0.279
AMES Toxicity:  0.019
Rat Oral Acute Toxicity:  0.023
Maximum Recommended Daily Dose:  0.052
Skin Sensitization:  0.964
Carcinogencity:  0.095
Eye Corrosion:  0.99
Eye Irritation:  0.991
Respiratory Toxicity:  0.716

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

  Natural Product: NPC139569

Natural Product ID:  NPC139569
Common Name*:   2-Tetradecyloxirane
IUPAC Name:   2-tetradecyloxirane
Synonyms:  
Standard InCHIKey:  DSZTYVZOIUIIGA-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C16H32O/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-16-15-17-16/h16H,2-15H2,1H3
SMILES:  CCCCCCCCCCCCCCC1OC1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1606644
PubChem CID:   23741
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000159] Epoxides

*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
NPO28295 Foeniculum vulgare Species Apiaceae Eukaryota n.a. leaf n.a. DOI[10.1016/S0031-9422(00)94055-X]
NPO28295 Foeniculum vulgare Species Apiaceae Eukaryota n.a. flower n.a. DOI[10.3390/70200245]
NPO11438 Angelica gigas Species Apiaceae Eukaryota n.a. root n.a. PMID[11374978]
NPO11438 Angelica gigas Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[15679317]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota roots purchased from Kiu Shun Trading Ltd., Vancouver, Canada 2000 PMID[16643021]
NPO11438 Angelica gigas Species Apiaceae Eukaryota n.a. root n.a. PMID[17997069]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. leaf n.a. PMID[18409045]
NPO29141 Panax ginseng Species Araliaceae Eukaryota flower buds n.a. n.a. PMID[19926279]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. root n.a. PMID[2092947]
NPO29141 Panax ginseng Species Araliaceae Eukaryota berry n.a. n.a. PMID[21216145]
NPO29141 Panax ginseng Species Araliaceae Eukaryota leaves n.a. n.a. PMID[24290061]
NPO28295 Foeniculum vulgare Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[24617303]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. PMID[24968750]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. PMID[25152999]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[25538068]
NPO29141 Panax ginseng Species Araliaceae Eukaryota stems-leaves n.a. n.a. PMID[26420067]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[27400088]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. stem n.a. PMID[27914541]
NPO29141 Panax ginseng Species Araliaceae Eukaryota Flower Buds n.a. n.a. PMID[28345906]
NPO1436 Houttuynia cordata Species Saururaceae Eukaryota n.a. n.a. n.a. PMID[29099182]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. PMID[32129622]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11438 Angelica gigas Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2921 Angelica acutiloba Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1436 Houttuynia cordata Species Saururaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28295 Foeniculum vulgare Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1320 Thalictrum ichangense Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[MetaboLights]
NPO1436 Houttuynia cordata Species Saururaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28295 Foeniculum vulgare Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2921 Angelica acutiloba Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1320 Thalictrum ichangense Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11438 Angelica gigas Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO1436 Houttuynia cordata Species Saururaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO2921 Angelica acutiloba Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO11438 Angelica gigas Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28295 Foeniculum vulgare Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO1436 Houttuynia cordata Species Saururaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO2921 Angelica acutiloba Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO11438 Angelica gigas Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO28295 Foeniculum vulgare Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO1320 Thalictrum ichangense Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28295 Foeniculum vulgare Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2921 Angelica acutiloba Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11438 Angelica gigas Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29141 Panax ginseng Species Araliaceae 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
NPT152 Individual Protein Nuclear factor erythroid 2-related factor 2 Homo sapiens Potency n.a. 74978.0 nM PMID[537160]
NPT2 Others Unspecified Potency n.a. 976.6 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency = 6309.6 nM PMID[537160]

☑ 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 NPC139569 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
0.8 Intermediate Similarity NPC97967
0.7778 Intermediate Similarity NPC474914
0.7778 Intermediate Similarity NPC474392
0.7429 Intermediate Similarity NPC139131
0.7429 Intermediate Similarity NPC272998
0.7429 Intermediate Similarity NPC193062
0.7429 Intermediate Similarity NPC185538
0.7429 Intermediate Similarity NPC291158
0.7429 Intermediate Similarity NPC181516
0.7429 Intermediate Similarity NPC205141
0.7429 Intermediate Similarity NPC66124
0.7429 Intermediate Similarity NPC319034
0.7429 Intermediate Similarity NPC72324
0.7429 Intermediate Similarity NPC1748
0.7222 Intermediate Similarity NPC474120
0.7222 Intermediate Similarity NPC474089
0.7143 Intermediate Similarity NPC126915
0.7143 Intermediate Similarity NPC122962
0.7143 Intermediate Similarity NPC267243
0.7105 Intermediate Similarity NPC128996
0.6944 Remote Similarity NPC152759
0.6944 Remote Similarity NPC12231
0.6923 Remote Similarity NPC197039
0.6857 Remote Similarity NPC112242
0.6857 Remote Similarity NPC24506
0.6857 Remote Similarity NPC163556
0.6857 Remote Similarity NPC185041
0.6857 Remote Similarity NPC147096
0.6857 Remote Similarity NPC236797
0.6857 Remote Similarity NPC225783
0.6818 Remote Similarity NPC8597
0.675 Remote Similarity NPC471282
0.6744 Remote Similarity NPC47363
0.6744 Remote Similarity NPC287231
0.6667 Remote Similarity NPC272426
0.6667 Remote Similarity NPC74352
0.6585 Remote Similarity NPC152008
0.6579 Remote Similarity NPC223374
0.6579 Remote Similarity NPC196442
0.6579 Remote Similarity NPC301398
0.6579 Remote Similarity NPC86545
0.6571 Remote Similarity NPC110884
0.6486 Remote Similarity NPC147054
0.6364 Remote Similarity NPC215358
0.6364 Remote Similarity NPC469781
0.6364 Remote Similarity NPC62014
0.6341 Remote Similarity NPC221022
0.6316 Remote Similarity NPC286498
0.6304 Remote Similarity NPC106872
0.6286 Remote Similarity NPC159845
0.6286 Remote Similarity NPC279895
0.6279 Remote Similarity NPC203531
0.6279 Remote Similarity NPC236579
0.6222 Remote Similarity NPC473914
0.619 Remote Similarity NPC28598
0.619 Remote Similarity NPC161097
0.6087 Remote Similarity NPC324004
0.6087 Remote Similarity NPC328497
0.6078 Remote Similarity NPC223604
0.6042 Remote Similarity NPC55678
0.6 Remote Similarity NPC80641
0.5918 Remote Similarity NPC474331
0.5918 Remote Similarity NPC287811
0.5909 Remote Similarity NPC474125
0.5909 Remote Similarity NPC474126
0.587 Remote Similarity NPC52700
0.587 Remote Similarity NPC30195
0.587 Remote Similarity NPC12438
0.587 Remote Similarity NPC63182
0.587 Remote Similarity NPC105329
0.587 Remote Similarity NPC145045
0.5854 Remote Similarity NPC177022
0.5814 Remote Similarity NPC149299
0.5814 Remote Similarity NPC40597
0.5814 Remote Similarity NPC12156
0.5814 Remote Similarity NPC160261
0.5814 Remote Similarity NPC250028
0.5814 Remote Similarity NPC165533
0.5814 Remote Similarity NPC256163
0.5814 Remote Similarity NPC469759
0.5789 Remote Similarity NPC40965
0.5778 Remote Similarity NPC317128
0.5745 Remote Similarity NPC326957
0.5714 Remote Similarity NPC305660
0.5714 Remote Similarity NPC201622
0.5714 Remote Similarity NPC54980
0.5714 Remote Similarity NPC560
0.5714 Remote Similarity NPC22903
0.5714 Remote Similarity NPC90904
0.5682 Remote Similarity NPC53541
0.5652 Remote Similarity NPC273545
0.5641 Remote Similarity NPC322892
0.5625 Remote Similarity NPC61373

  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 NPC139569 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
0.7429 Intermediate Similarity NPD5383 Approved
0.7429 Intermediate Similarity NPD2272 Approved
0.6744 Remote Similarity NPD2699 Approved
0.6667 Remote Similarity NPD1461 Approved
0.6667 Remote Similarity NPD907 Approved
0.6667 Remote Similarity NPD908 Approved
0.6585 Remote Similarity NPD7536 Approved
0.6341 Remote Similarity NPD5799 Discontinued
0.619 Remote Similarity NPD1460 Approved
0.6 Remote Similarity NPD370 Phase 3
0.5957 Remote Similarity NPD6125 Clinical (unspecified phase)
0.5909 Remote Similarity NPD1462 Approved
0.5714 Remote Similarity NPD3214 Discontinued
0.5714 Remote Similarity NPD3206 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