Structure

Physi-Chem Properties

Molecular Weight:  84.09
Volume:  109.696
LogP:  3.278
LogD:  3.094
LogS:  -3.264
# Rotatable Bonds:  3
TPSA:  0.0
# H-Bond Aceptor:  0
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  0

MedChem Properties

QED Drug-Likeness Score:  0.364
Synthetic Accessibility Score:  2.084
Fsp3:  0.667
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
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:  -4.226
MDCK Permeability:  2.7078929633717053e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.249
30% Bioavailability (F30%):  0.863

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.999
Plasma Protein Binding (PPB):  84.04186248779297%
Volume Distribution (VD):  1.069
Pgp-substrate:  20.253286361694336%

ADMET: Metabolism

CYP1A2-inhibitor:  0.908
CYP1A2-substrate:  0.84
CYP2C19-inhibitor:  0.299
CYP2C19-substrate:  0.841
CYP2C9-inhibitor:  0.096
CYP2C9-substrate:  0.843
CYP2D6-inhibitor:  0.047
CYP2D6-substrate:  0.835
CYP3A4-inhibitor:  0.078
CYP3A4-substrate:  0.203

ADMET: Excretion

Clearance (CL):  9.016
Half-life (T1/2):  0.643

ADMET: Toxicity

hERG Blockers:  0.015
Human Hepatotoxicity (H-HT):  0.02
Drug-inuced Liver Injury (DILI):  0.026
AMES Toxicity:  0.023
Rat Oral Acute Toxicity:  0.094
Maximum Recommended Daily Dose:  0.025
Skin Sensitization:  0.868
Carcinogencity:  0.187
Eye Corrosion:  0.992
Eye Irritation:  0.993
Respiratory Toxicity:  0.292

Download Data

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

  Natural Product: NPC178306

Natural Product ID:  NPC178306
Common Name*:   1-Hexene
IUPAC Name:   hex-1-ene
Synonyms:   1-Hexene
Standard InCHIKey:  LIKMAJRDDDTEIG-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C6H12/c1-3-5-6-4-2/h3H,1,4-6H2,2H3
SMILES:  C=CCCCC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1548726
PubChem CID:   11597
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0002837] Hydrocarbons
      • [CHEMONTID:0004475] Unsaturated hydrocarbons
        • [CHEMONTID:0004476] Unsaturated aliphatic hydrocarbons

*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
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota Flowers n.a. n.a. DOI[10.1002/elan.200403102]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota Flowers n.a. n.a. DOI[10.1016/j.foodchem.2012.02.124]
NPO10339 Fragaria x ananassa Species Rosaceae Eukaryota Fruit n.a. n.a. DOI[10.1016/S0963-9969(99)00095-2]
NPO10339 Fragaria x ananassa Species Rosaceae Eukaryota Leaves (mother plant) Suwon, Korea 2011-Sep DOI[10.7235/HORT.2013.12200]
NPO10339 Fragaria x ananassa Species Rosaceae Eukaryota Roots (runner plant) Suwon, Korea 2011-Sep DOI[10.7235/HORT.2013.12200]
NPO10339 Fragaria x ananassa Species Rosaceae Eukaryota Fruits Suwon, Korea 2012-Nov DOI[10.7235/HORT.2013.12200]
NPO10339 Fragaria x ananassa Species Rosaceae Eukaryota Leaves Suwon, Korea DOI[10.7235/HORT.2013.12200]
NPO10339 Fragaria x ananassa Species Rosaceae Eukaryota Runners Suwon, Korea 2011-Sep DOI[10.7235/HORT.2013.12200]
NPO10339 Fragaria x ananassa Species Rosaceae Eukaryota Leaves (runner plant) Suwon, Korea 2011-Sep DOI[10.7235/HORT.2013.12200]
NPO10339 Fragaria x ananassa Species Rosaceae Eukaryota Roots (mother plant) Suwon, Korea 2011-Sep DOI[10.7235/HORT.2013.12200]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota Flowers n.a. n.a. PMID[11077184]
NPO6092 Symphyocladia latiuscula Species Rhodomelaceae Eukaryota n.a. n.a. n.a. PMID[11141124]
NPO3699 Acacia aulacocarpa Species Fabaceae Eukaryota n.a. leaf n.a. PMID[11735581]
NPO10339 Fragaria x ananassa Species Rosaceae Eukaryota n.a. n.a. n.a. PMID[1453178]
NPO10339 Fragaria x ananassa Species Rosaceae Eukaryota Fruits n.a. n.a. PMID[15568772]
NPO6092 Symphyocladia latiuscula Species Rhodomelaceae Eukaryota n.a. n.a. n.a. PMID[15844965]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota Flowers n.a. n.a. PMID[17328234]
NPO6092 Symphyocladia latiuscula Species Rhodomelaceae Eukaryota n.a. n.a. n.a. PMID[17602526]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota Flower buds n.a. n.a. PMID[18321056]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota n.a. flower n.a. PMID[21804227]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota flower buds Henan province, China 2005-MAY PMID[21942812]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota n.a. flower bud n.a. PMID[21942812]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota n.a. leaf n.a. PMID[23265495]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota Flower buds n.a. n.a. PMID[24279769]
NPO10339 Fragaria x ananassa Species Rosaceae Eukaryota Fruits n.a. Database[FooDB]
NPO10339 Fragaria x ananassa Species Rosaceae Eukaryota n.a. n.a. Database[FooDB]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3853 Aspidosperma subincanum Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4795.1 Prunus armeniaca var. ansu Varieties Rosaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10339 Fragaria x ananassa Species Rosaceae Eukaryota Fruits n.a. Database[Phenol-Explorer]
NPO4795.1 Prunus armeniaca var. ansu Varieties Rosaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10339 Fragaria x ananassa Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19948 Neolentinus lepideus Species Gloeophyllaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3853 Aspidosperma subincanum Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4823 Psiadia dentata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7569 Guatteria boliviana Species Annonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8418 Anemone flaccida Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO3699 Acacia aulacocarpa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO471 Ardisia neriifolia Species Primulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3853 Aspidosperma subincanum Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3597 Rheedia acuminata Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6729 Juniperus brevifolia Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6092 Symphyocladia latiuscula Species Rhodomelaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6237 Cryptocarya aschersoniana Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4823 Psiadia dentata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10339 Fragaria x ananassa Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19948 Neolentinus lepideus Species Gloeophyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8418 Anemone flaccida Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5155 Peritassa compta Species Celastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5196 Eupatorium argentinum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7569 Guatteria boliviana Species Annonaceae 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
NPO10339 NPC178306 n.a. Leaves (mother plant) 0.027 n.a. n.a. mg/m3 of FW DOI[10.7235/HORT.2013.12200]
NPO10339 NPC178306 n.a. Roots (runner plant) 0.014 n.a. n.a. mg/m3 of FW DOI[10.7235/HORT.2013.12200]

☑ 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
NPT210 Individual Protein Thyroid stimulating hormone receptor Homo sapiens Potency = 25118.9 nM PMID[554010]
NPT249 Individual Protein Glucocorticoid receptor Homo sapiens Potency n.a. 281.8 nM PMID[554010]
NPT94 Individual Protein Aldehyde dehydrogenase 1A1 Homo sapiens Potency = 14125.4 nM PMID[554010]
NPT35 Others n.a. LogP = 3.324 n.a. PMID[554011]

☑ 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 NPC178306 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
0.9474 High Similarity NPC225855
0.8947 High Similarity NPC33192
0.8261 Intermediate Similarity NPC88325
0.7917 Intermediate Similarity NPC31891
0.7917 Intermediate Similarity NPC266539
0.7917 Intermediate Similarity NPC287191
0.7917 Intermediate Similarity NPC266144
0.7727 Intermediate Similarity NPC96619
0.75 Intermediate Similarity NPC38513
0.7308 Intermediate Similarity NPC179103
0.7308 Intermediate Similarity NPC76765
0.7308 Intermediate Similarity NPC138325
0.7037 Intermediate Similarity NPC34671
0.7037 Intermediate Similarity NPC138113
0.6786 Remote Similarity NPC60288
0.6552 Remote Similarity NPC151719
0.6552 Remote Similarity NPC206088
0.6552 Remote Similarity NPC66577
0.6429 Remote Similarity NPC123965
0.6429 Remote Similarity NPC115959
0.6296 Remote Similarity NPC10183
0.6207 Remote Similarity NPC16561
0.6129 Remote Similarity NPC305759
0.6129 Remote Similarity NPC173592
0.6129 Remote Similarity NPC99088
0.6071 Remote Similarity NPC262789
0.6071 Remote Similarity NPC288991
0.6071 Remote Similarity NPC64176
0.6 Remote Similarity NPC3649
0.6 Remote Similarity NPC471327
0.6 Remote Similarity NPC100879
0.6 Remote Similarity NPC196831
0.6 Remote Similarity NPC142438
0.5938 Remote Similarity NPC182392
0.5862 Remote Similarity NPC155900
0.5806 Remote Similarity NPC13217
0.5806 Remote Similarity NPC213749
0.5758 Remote Similarity NPC282119
0.5758 Remote Similarity NPC79544
0.5714 Remote Similarity NPC19070
0.5714 Remote Similarity NPC51067
0.5714 Remote Similarity NPC179860
0.5714 Remote Similarity NPC225191
0.5625 Remote Similarity NPC62779
0.5625 Remote Similarity NPC81989
0.56 Remote Similarity NPC184203
0.56 Remote Similarity NPC220140

  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 NPC178306 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
0.5769 Remote Similarity NPD8834 Discontinued

  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