Structure

Physi-Chem Properties

Molecular Weight:  112.03
Volume:  106.769
LogP:  -0.837
LogD:  -0.605
LogS:  0.163
# Rotatable Bonds:  0
TPSA:  86.18
# H-Bond Aceptor:  4
# H-Bond Donor:  4
# Rings:  0
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.354
Synthetic Accessibility Score:  3.606
Fsp3:  0.0
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
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:  -4.942
MDCK Permeability:  0.00045978595153428614
Pgp-inhibitor:  0.001
Pgp-substrate:  0.919
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.003
30% Bioavailability (F30%):  0.008

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.787
Plasma Protein Binding (PPB):  39.06184387207031%
Volume Distribution (VD):  0.521
Pgp-substrate:  53.61949157714844%

ADMET: Metabolism

CYP1A2-inhibitor:  0.036
CYP1A2-substrate:  0.211
CYP2C19-inhibitor:  0.045
CYP2C19-substrate:  0.053
CYP2C9-inhibitor:  0.084
CYP2C9-substrate:  0.194
CYP2D6-inhibitor:  0.01
CYP2D6-substrate:  0.154
CYP3A4-inhibitor:  0.005
CYP3A4-substrate:  0.078

ADMET: Excretion

Clearance (CL):  5.635
Half-life (T1/2):  0.136

ADMET: Toxicity

hERG Blockers:  0.028
Human Hepatotoxicity (H-HT):  0.075
Drug-inuced Liver Injury (DILI):  0.892
AMES Toxicity:  0.255
Rat Oral Acute Toxicity:  0.545
Maximum Recommended Daily Dose:  0.011
Skin Sensitization:  0.872
Carcinogencity:  0.695
Eye Corrosion:  0.052
Eye Irritation:  0.941
Respiratory Toxicity:  0.959

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

  Natural Product: NPC138865

Natural Product ID:  NPC138865
Common Name*:   5-Isothiocyanatopent-1-Ene
IUPAC Name:   5-isothiocyanatopent-1-ene
Synonyms:  
Standard InCHIKey:  DBISBKDNOKIADM-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C6H9NS/c1-2-3-4-5-7-6-8/h2H,1,3-5H2
SMILES:  C=CCCCN=C=S
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3593943
PubChem CID:   87436
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000004] Organosulfur compounds
      • [CHEMONTID:0001234] Isothiocyanates

*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
NPO16755 Saposhnikovia divaricata Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[17703773]
NPO29007 Brassica juncea Species Brassicaceae Eukaryota n.a. n.a. n.a. PMID[25700090]
NPO29007 Brassica juncea Species Brassicaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO29007 Brassica juncea Species Brassicaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO29007 Brassica juncea Species Brassicaceae Eukaryota n.a. n.a. Database[FooDB]
NPO29007 Brassica juncea Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16755 Saposhnikovia divaricata Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16755 Saposhnikovia divaricata Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29007 Brassica juncea Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9047.1 Brassica rapa subsp. oleifera Subspecies Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29007 Brassica juncea Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO29007 Brassica juncea Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO9047.1 Brassica rapa subsp. oleifera Subspecies Brassicaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO16755 Saposhnikovia divaricata Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO9047.1 Brassica rapa subsp. oleifera Subspecies Brassicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29007 Brassica juncea Species Brassicaceae 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
NPT346 Individual Protein Transient receptor potential cation channel subfamily A member 1 Homo sapiens EC50 = 540.0 nM PMID[575285]
NPT346 Individual Protein Transient receptor potential cation channel subfamily A member 1 Homo sapiens max activation = 90.0 % PMID[575285]

☑ 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 NPC138865 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
0.8966 High Similarity NPC27723
0.8 Intermediate Similarity NPC144939
0.7105 Intermediate Similarity NPC205586
0.6667 Remote Similarity NPC245814
0.625 Remote Similarity NPC106203
0.6 Remote Similarity NPC51917
0.5938 Remote Similarity NPC133836
0.5862 Remote Similarity NPC33192
0.5667 Remote Similarity NPC225855
0.5625 Remote Similarity NPC266347

  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 NPC138865 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
0.8 Intermediate Similarity NPD8580 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