Structure

Physi-Chem Properties

Molecular Weight:  140.16
Volume:  178.88
LogP:  5.223
LogD:  4.099
LogS:  -5.242
# Rotatable Bonds:  7
TPSA:  0.0
# H-Bond Aceptor:  0
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  0

MedChem Properties

QED Drug-Likeness Score:  0.371
Synthetic Accessibility Score:  1.829
Fsp3:  0.8
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:  -4.436
MDCK Permeability:  1.7205553376697935e-05
Pgp-inhibitor:  0.009
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.315
30% Bioavailability (F30%):  0.617

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.991
Plasma Protein Binding (PPB):  95.64999389648438%
Volume Distribution (VD):  1.196
Pgp-substrate:  5.027693748474121%

ADMET: Metabolism

CYP1A2-inhibitor:  0.951
CYP1A2-substrate:  0.52
CYP2C19-inhibitor:  0.611
CYP2C19-substrate:  0.457
CYP2C9-inhibitor:  0.384
CYP2C9-substrate:  0.899
CYP2D6-inhibitor:  0.095
CYP2D6-substrate:  0.656
CYP3A4-inhibitor:  0.401
CYP3A4-substrate:  0.132

ADMET: Excretion

Clearance (CL):  5.688
Half-life (T1/2):  0.279

ADMET: Toxicity

hERG Blockers:  0.036
Human Hepatotoxicity (H-HT):  0.014
Drug-inuced Liver Injury (DILI):  0.034
AMES Toxicity:  0.015
Rat Oral Acute Toxicity:  0.043
Maximum Recommended Daily Dose:  0.028
Skin Sensitization:  0.946
Carcinogencity:  0.13
Eye Corrosion:  0.993
Eye Irritation:  0.988
Respiratory Toxicity:  0.355

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

  Natural Product: NPC31891

Natural Product ID:  NPC31891
Common Name*:   Dec-1-Ene
IUPAC Name:   dec-1-ene
Synonyms:  
Standard InCHIKey:  AFFLGGQVNFXPEV-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C10H20/c1-3-5-7-9-10-8-6-4-2/h3H,1,4-10H2,2H3
SMILES:  C=CCCCCCCCC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3187990
PubChem CID:   13381
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
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. Nigeria(latitude 80°N and longitude 4°E) 2005; 2006 DOI[10.1002/ejlt.201000080]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. DOI[10.1007/s11306-010-0259-y]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. DOI[10.1007/s11306-014-0638-x]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. DOI[10.1007/s11746-997-0093-1]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.phytol.2008.07.007]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota Seeds Plovdiv, Plovdiv region in South Bulgaria DOI[10.1051/CTV/20163101031]
NPO17755 Inula helenium Species Asteraceae Eukaryota n.a. root n.a. PMID[10364842]
NPO523 Tussilago farfara Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[10543912]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. PMID[11170689]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. leaf n.a. PMID[11312782]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. fruit n.a. PMID[11312782]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. PMID[11408943]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. fruit n.a. PMID[12105962]
NPO17755 Inula helenium Species Asteraceae Eukaryota n.a. root n.a. PMID[12392098]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. Esuela Tecnica Superior de Ingenieros Agrónomos de Albacete 2007 PMID[19256538]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. PMID[20826702]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. PMID[22537213]
NPO17755 Inula helenium Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[23501116]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. PMID[23759170]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota Stalks n.a. n.a. PMID[24521157]
NPO17755 Inula helenium Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[24996657]
NPO17755 Inula helenium Species Asteraceae Eukaryota n.a. root n.a. PMID[25767328]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota Seeds Benedictine Pannonhalma Archabbey, Hungary PMID[29803478]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. PMID[31433178]
NPO523 Tussilago farfara Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[32881525]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota Stem n.a. n.a. Database[FooDB]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. Database[FooDB]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota Fruits n.a. Database[FooDB]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota Leaf Essent. Oil n.a. n.a. Database[FooDB]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO17755 Inula helenium 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]
NPO523 Tussilago farfara Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. Database[MetaboLights]
NPO523 Tussilago farfara Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7642 Cleome gynandra Species Cleomaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17755 Inula helenium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO523 Tussilago farfara Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO17755 Inula helenium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO523 Tussilago farfara Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO17755 Inula helenium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO523 Tussilago farfara 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]

☑ 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
NPT2 Others Unspecified Potency n.a. 77.4 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 55317.6 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 NPC31891 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
1.0 High Similarity NPC266144
1.0 High Similarity NPC266539
1.0 High Similarity NPC287191
0.9583 High Similarity NPC88325
0.9583 High Similarity NPC38513
0.9231 High Similarity NPC76765
0.9231 High Similarity NPC179103
0.8276 Intermediate Similarity NPC151719
0.7931 Intermediate Similarity NPC16561
0.7917 Intermediate Similarity NPC178306
0.7586 Intermediate Similarity NPC34671
0.75 Intermediate Similarity NPC182392
0.75 Intermediate Similarity NPC225855
0.7241 Intermediate Similarity NPC138325
0.7188 Intermediate Similarity NPC62779
0.7097 Intermediate Similarity NPC3649
0.7097 Intermediate Similarity NPC471327
0.7097 Intermediate Similarity NPC100879
0.7083 Intermediate Similarity NPC33192
0.7 Intermediate Similarity NPC138113
0.6774 Remote Similarity NPC60288
0.6571 Remote Similarity NPC216416
0.6562 Remote Similarity NPC196831
0.6562 Remote Similarity NPC66577
0.6562 Remote Similarity NPC206088
0.6452 Remote Similarity NPC115959
0.6452 Remote Similarity NPC123965
0.6389 Remote Similarity NPC297643
0.6389 Remote Similarity NPC229262
0.6389 Remote Similarity NPC139717
0.6333 Remote Similarity NPC10183
0.6296 Remote Similarity NPC96619
0.6286 Remote Similarity NPC213767
0.6286 Remote Similarity NPC282119
0.6286 Remote Similarity NPC92224
0.625 Remote Similarity NPC136996
0.625 Remote Similarity NPC302327
0.625 Remote Similarity NPC278711
0.625 Remote Similarity NPC273385
0.625 Remote Similarity NPC82648
0.625 Remote Similarity NPC64370
0.625 Remote Similarity NPC227986
0.6216 Remote Similarity NPC217923
0.6176 Remote Similarity NPC305759
0.6176 Remote Similarity NPC173592
0.6176 Remote Similarity NPC99088
0.6154 Remote Similarity NPC287397
0.6154 Remote Similarity NPC177470
0.6154 Remote Similarity NPC190232
0.6154 Remote Similarity NPC67920
0.6154 Remote Similarity NPC298710
0.6154 Remote Similarity NPC105246
0.6129 Remote Similarity NPC288991
0.6129 Remote Similarity NPC262789
0.6129 Remote Similarity NPC64176
0.6111 Remote Similarity NPC34764
0.6111 Remote Similarity NPC76145
0.6111 Remote Similarity NPC190810
0.6053 Remote Similarity NPC48930
0.6053 Remote Similarity NPC183670
0.6 Remote Similarity NPC89422
0.6 Remote Similarity NPC252978
0.5946 Remote Similarity NPC92863
0.5946 Remote Similarity NPC155880
0.5946 Remote Similarity NPC266298
0.5946 Remote Similarity NPC239039
0.5897 Remote Similarity NPC144023
0.5897 Remote Similarity NPC33489
0.5897 Remote Similarity NPC120926
0.5897 Remote Similarity NPC218918
0.5882 Remote Similarity NPC213749
0.5854 Remote Similarity NPC145755
0.5854 Remote Similarity NPC108195
0.5854 Remote Similarity NPC267514
0.5833 Remote Similarity NPC224874
0.5789 Remote Similarity NPC15934
0.5769 Remote Similarity NPC77249
0.5769 Remote Similarity NPC26974
0.5769 Remote Similarity NPC26229
0.5769 Remote Similarity NPC154477
0.5769 Remote Similarity NPC239406
0.575 Remote Similarity NPC473912
0.575 Remote Similarity NPC249801
0.575 Remote Similarity NPC46248
0.575 Remote Similarity NPC149668
0.5714 Remote Similarity NPC269074
0.5714 Remote Similarity NPC239754
0.5714 Remote Similarity NPC76976
0.5676 Remote Similarity NPC220061
0.5641 Remote Similarity NPC227632
0.5641 Remote Similarity NPC246165
0.5641 Remote Similarity NPC62086
0.5641 Remote Similarity NPC78551
0.561 Remote Similarity NPC60556
0.561 Remote Similarity NPC15162
0.561 Remote Similarity NPC86538
0.561 Remote Similarity NPC109813

  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 NPC31891 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
0.6154 Remote Similarity NPD1799 Clinical (unspecified phase)
0.6111 Remote Similarity NPD319 Phase 1

  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