Structure

Physi-Chem Properties

Molecular Weight:  134.11
Volume:  170.97
LogP:  3.482
LogD:  3.234
LogS:  -3.604
# 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:  0.52
Synthetic Accessibility Score:  3.471
Fsp3:  0.2
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.32
MDCK Permeability:  2.8536171157611534e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.004
30% Bioavailability (F30%):  0.001

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.941
Plasma Protein Binding (PPB):  84.68106842041016%
Volume Distribution (VD):  1.523
Pgp-substrate:  12.921209335327148%

ADMET: Metabolism

CYP1A2-inhibitor:  0.911
CYP1A2-substrate:  0.527
CYP2C19-inhibitor:  0.25
CYP2C19-substrate:  0.852
CYP2C9-inhibitor:  0.056
CYP2C9-substrate:  0.676
CYP2D6-inhibitor:  0.269
CYP2D6-substrate:  0.854
CYP3A4-inhibitor:  0.183
CYP3A4-substrate:  0.228

ADMET: Excretion

Clearance (CL):  9.451
Half-life (T1/2):  0.612

ADMET: Toxicity

hERG Blockers:  0.01
Human Hepatotoxicity (H-HT):  0.879
Drug-inuced Liver Injury (DILI):  0.349
AMES Toxicity:  0.709
Rat Oral Acute Toxicity:  0.93
Maximum Recommended Daily Dose:  0.914
Skin Sensitization:  0.917
Carcinogencity:  0.872
Eye Corrosion:  0.962
Eye Irritation:  0.99
Respiratory Toxicity:  0.962

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

  Natural Product: NPC305094

Natural Product ID:  NPC305094
Common Name*:   2,6-Dimethyl-1,3,5,7-Octatetraene
IUPAC Name:   (3E,5Z)-2,6-dimethylocta-1,3,5,7-tetraene
Synonyms:  
Standard InCHIKey:  HPZWSJQQCJZBBG-QDJLDCPTSA-N
Standard InCHI:  InChI=1S/C10H14/c1-5-10(4)8-6-7-9(2)3/h5-8H,1-2H2,3-4H3/b7-6+,10-8-
SMILES:  CC(=C)/C=C/C=C(/C)C=C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   12304092
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0002837] Hydrocarbons
      • [CHEMONTID:0004475] Unsaturated hydrocarbons
        • [CHEMONTID:0002838] Olefins
          • [CHEMONTID:0002839] Acyclic olefins
            • [CHEMONTID:0002842] Alkatetraenes

*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
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]
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]
NPO10339 Fragaria x ananassa Species Rosaceae Eukaryota n.a. n.a. Database[FooDB]
NPO10339 Fragaria x ananassa Species Rosaceae Eukaryota Fruits n.a. Database[FooDB]
NPO10339 Fragaria x ananassa Species Rosaceae Eukaryota Fruits n.a. Database[Phenol-Explorer]
NPO10339 Fragaria x ananassa Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10339 Fragaria x ananassa 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
NPO10339 NPC305094 n.a. Roots (runner plant) 0.018 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

☑ 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 NPC305094 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

  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 NPC305094 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

  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