Structure

Physi-Chem Properties

Molecular Weight:  112.13
Volume:  144.288
LogP:  4.24
LogD:  3.701
LogS:  -4.253
# Rotatable Bonds:  5
TPSA:  0.0
# H-Bond Aceptor:  0
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  0

MedChem Properties

QED Drug-Likeness Score:  0.378
Synthetic Accessibility Score:  1.875
Fsp3:  0.75
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.332
MDCK Permeability:  2.0880746887996793e-05
Pgp-inhibitor:  0.002
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.369
30% Bioavailability (F30%):  0.743

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.998
Plasma Protein Binding (PPB):  91.3211669921875%
Volume Distribution (VD):  1.138
Pgp-substrate:  10.926480293273926%

ADMET: Metabolism

CYP1A2-inhibitor:  0.945
CYP1A2-substrate:  0.744
CYP2C19-inhibitor:  0.503
CYP2C19-substrate:  0.697
CYP2C9-inhibitor:  0.28
CYP2C9-substrate:  0.871
CYP2D6-inhibitor:  0.063
CYP2D6-substrate:  0.769
CYP3A4-inhibitor:  0.194
CYP3A4-substrate:  0.166

ADMET: Excretion

Clearance (CL):  7.303
Half-life (T1/2):  0.444

ADMET: Toxicity

hERG Blockers:  0.023
Human Hepatotoxicity (H-HT):  0.017
Drug-inuced Liver Injury (DILI):  0.029
AMES Toxicity:  0.019
Rat Oral Acute Toxicity:  0.057
Maximum Recommended Daily Dose:  0.026
Skin Sensitization:  0.933
Carcinogencity:  0.18
Eye Corrosion:  0.993
Eye Irritation:  0.991
Respiratory Toxicity:  0.343

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

  Natural Product: NPC88325

Natural Product ID:  NPC88325
Common Name*:   Oct-1-Ene
IUPAC Name:   oct-1-ene
Synonyms:  
Standard InCHIKey:  KWKAKUADMBZCLK-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C8H16/c1-3-5-7-8-6-4-2/h3H,1,4-8H2,2H3
SMILES:  CCCCCCC=C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1376677
PubChem CID:   8125
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
NPO20440 Chrysanthemum x morifolium Species Asteraceae Eukaryota Flowers n.a. n.a. DOI[10.1016/j.foodchem.2009.03.042]
NPO28276 Artemisia argyi Species Asteraceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.jep.2005.01.054]
NPO20440 Chrysanthemum x morifolium Species Asteraceae Eukaryota Flowers n.a. n.a. DOI[10.3136/fstr.15.499]
NPO20440 Chrysanthemum x morifolium Species Asteraceae Eukaryota Flowers n.a. n.a. DOI[10.5897/AJB10.140]
NPO20440 Chrysanthemum x morifolium Species Asteraceae Eukaryota Flowers n.a. n.a. DOI[10.5897/AJB2010.000-3252]
NPO25094 Artemisia princeps Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[17996677]
NPO20440 Chrysanthemum x morifolium Species Asteraceae Eukaryota Flowers Tongxiang, China n.a. PMID[24621197]
NPO20440 Chrysanthemum x morifolium Species Asteraceae Eukaryota Flowers n.a. n.a. PMID[28248102]
NPO28276 Artemisia argyi Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[31181920]
NPO28276 Artemisia argyi Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[31418264]
NPO19048 Pinellia ternata Species Araceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25094 Artemisia princeps Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7642 Cleome gynandra Species Cleomaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28276 Artemisia argyi Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19048 Pinellia ternata Species Araceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7642 Cleome gynandra Species Cleomaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28276 Artemisia argyi Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20440 Chrysanthemum x morifolium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25094 Artemisia princeps Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19048 Pinellia ternata Species Araceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28276 Artemisia argyi Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO25094 Artemisia princeps Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO19048 Pinellia ternata Species Araceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO20440 Chrysanthemum x morifolium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO28276 Artemisia argyi Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO10492 Artemisia montana Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO28276 Artemisia argyi Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7642 Cleome gynandra Species Cleomaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20440 Chrysanthemum x morifolium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25094 Artemisia princeps Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10492 Artemisia montana Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19048 Pinellia ternata Species Araceae 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. 59381.6 nM PubChem BioAssay data set
NPT210 Individual Protein Thyroid stimulating hormone receptor Homo sapiens Potency = 5011.9 nM PMID[449638]
NPT347 Cell Line Lymphoblastoid cells Homo sapiens Potency = 1258.9 nM PMID[449638]
NPT108 Individual Protein Estrogen receptor alpha Homo sapiens Potency n.a. 12589.3 nM PMID[449638]
NPT152 Individual Protein Nuclear factor erythroid 2-related factor 2 Homo sapiens Potency n.a. 47307.9 nM PMID[449638]
NPT2 Others Unspecified Potency n.a. 11848.2 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 66086.3 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 58899.4 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 23640.3 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 59381.6 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 52923.9 nM PubChem BioAssay data set
NPT74 Individual Protein Proto-oncogene c-JUN Homo sapiens Potency n.a. 59381.6 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 104739.7 nM PubChem BioAssay data set
NPT35 Others n.a. LogP = 4.57 n.a. PMID[449639]
NPT35 Others n.a. Solubility = 3.0 ug.mL-1 PMID[449639]

☑ 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 NPC88325 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
0.9583 High Similarity NPC287191
0.9583 High Similarity NPC266539
0.9583 High Similarity NPC31891
0.9583 High Similarity NPC266144
0.9167 High Similarity NPC38513
0.8846 High Similarity NPC76765
0.8846 High Similarity NPC179103
0.8261 Intermediate Similarity NPC178306
0.7931 Intermediate Similarity NPC151719
0.7857 Intermediate Similarity NPC34671
0.7826 Intermediate Similarity NPC225855
0.7586 Intermediate Similarity NPC16561
0.75 Intermediate Similarity NPC138325
0.7391 Intermediate Similarity NPC33192
0.7333 Intermediate Similarity NPC471327
0.7333 Intermediate Similarity NPC3649
0.7333 Intermediate Similarity NPC100879
0.7241 Intermediate Similarity NPC138113
0.7188 Intermediate Similarity NPC182392
0.7 Intermediate Similarity NPC60288
0.6875 Remote Similarity NPC62779
0.6774 Remote Similarity NPC196831
0.6774 Remote Similarity NPC206088
0.6774 Remote Similarity NPC66577
0.6667 Remote Similarity NPC123965
0.6667 Remote Similarity NPC115959
0.6552 Remote Similarity NPC10183
0.6538 Remote Similarity NPC96619
0.6471 Remote Similarity NPC213767
0.6471 Remote Similarity NPC92224
0.6471 Remote Similarity NPC282119
0.6389 Remote Similarity NPC217923
0.6364 Remote Similarity NPC173592
0.6364 Remote Similarity NPC305759
0.6364 Remote Similarity NPC99088
0.6333 Remote Similarity NPC262789
0.6333 Remote Similarity NPC64176
0.6333 Remote Similarity NPC288991
0.6286 Remote Similarity NPC34764
0.6286 Remote Similarity NPC76145
0.6286 Remote Similarity NPC216416
0.6286 Remote Similarity NPC190810
0.6216 Remote Similarity NPC183670
0.6111 Remote Similarity NPC239039
0.6111 Remote Similarity NPC92863
0.6111 Remote Similarity NPC155880
0.6111 Remote Similarity NPC229262
0.6111 Remote Similarity NPC297643
0.6111 Remote Similarity NPC139717
0.6111 Remote Similarity NPC266298
0.6061 Remote Similarity NPC213749
0.6053 Remote Similarity NPC218918
0.6053 Remote Similarity NPC144023
0.6053 Remote Similarity NPC120926
0.6053 Remote Similarity NPC33489
0.5946 Remote Similarity NPC15934
0.5897 Remote Similarity NPC249801
0.5897 Remote Similarity NPC67920
0.5897 Remote Similarity NPC298710
0.5897 Remote Similarity NPC46248
0.5897 Remote Similarity NPC190232
0.5897 Remote Similarity NPC287397
0.5897 Remote Similarity NPC105246
0.5897 Remote Similarity NPC177470
0.5833 Remote Similarity NPC273385
0.5833 Remote Similarity NPC278711
0.5833 Remote Similarity NPC302327
0.5833 Remote Similarity NPC220061
0.5833 Remote Similarity NPC82648
0.5833 Remote Similarity NPC136996
0.5833 Remote Similarity NPC64370
0.5833 Remote Similarity NPC227986
0.5789 Remote Similarity NPC48930
0.575 Remote Similarity NPC15162
0.575 Remote Similarity NPC252978
0.5676 Remote Similarity NPC48638
0.5676 Remote Similarity NPC34873
0.5676 Remote Similarity NPC45727
0.5676 Remote Similarity NPC40434
0.5652 Remote Similarity NPC98925
0.561 Remote Similarity NPC108195
0.561 Remote Similarity NPC145755
0.561 Remote Similarity NPC267514
0.56 Remote Similarity NPC89422

  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 NPC88325 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
0.6286 Remote Similarity NPD319 Phase 1
0.5897 Remote Similarity NPD1799 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