Structure

Physi-Chem Properties

Molecular Weight:  81.06
Volume:  98.124
LogP:  0.621
LogD:  0.796
LogS:  -0.904
# Rotatable Bonds:  1
TPSA:  23.79
# H-Bond Aceptor:  1
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.438
Synthetic Accessibility Score:  3.564
Fsp3:  0.4
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
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:  -4.242
MDCK Permeability:  0.00013195951760280877
Pgp-inhibitor:  0.0
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.007
20% Bioavailability (F20%):  0.004
30% Bioavailability (F30%):  0.005

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.989
Plasma Protein Binding (PPB):  61.52452087402344%
Volume Distribution (VD):  1.03
Pgp-substrate:  43.39535903930664%

ADMET: Metabolism

CYP1A2-inhibitor:  0.659
CYP1A2-substrate:  0.55
CYP2C19-inhibitor:  0.049
CYP2C19-substrate:  0.062
CYP2C9-inhibitor:  0.011
CYP2C9-substrate:  0.746
CYP2D6-inhibitor:  0.016
CYP2D6-substrate:  0.184
CYP3A4-inhibitor:  0.015
CYP3A4-substrate:  0.197

ADMET: Excretion

Clearance (CL):  8.073
Half-life (T1/2):  0.866

ADMET: Toxicity

hERG Blockers:  0.007
Human Hepatotoxicity (H-HT):  0.292
Drug-inuced Liver Injury (DILI):  0.276
AMES Toxicity:  0.028
Rat Oral Acute Toxicity:  0.026
Maximum Recommended Daily Dose:  0.718
Skin Sensitization:  0.807
Carcinogencity:  0.91
Eye Corrosion:  0.991
Eye Irritation:  0.996
Respiratory Toxicity:  0.966

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General Info & Identifiers & Properties  
Structure MOL file  
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Similar NPs/Drugs  

  Natural Product: NPC179860

Natural Product ID:  NPC179860
Common Name*:   (E)-Pent-3-Enenitrile
IUPAC Name:   (E)-pent-3-enenitrile
Synonyms:  
Standard InCHIKey:  UVKXJAUUKPDDNW-NSCUHMNNSA-N
Standard InCHI:  InChI=1S/C5H7N/c1-2-3-4-5-6/h2-3H,4H2,1H3/b3-2+
SMILES:  C/C=C/CC#N
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1322495
PubChem CID:   5324707
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004707] Organic nitrogen compounds
      • [CHEMONTID:0000278] Organonitrogen compounds
        • [CHEMONTID:0004504] Organic cyanides
          • [CHEMONTID:0000362] Nitriles

*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
NPO784 Sinapis alba Species Brassicaceae Eukaryota n.a. seed n.a. DOI[10.1007/s11418-005-0009-z]
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]
NPO784 Sinapis alba Species Brassicaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO29007 Brassica juncea Species Brassicaceae Eukaryota n.a. n.a. Database[FooDB]
NPO784 Sinapis alba Species Brassicaceae Eukaryota n.a. n.a. Database[FooDB]
NPO784 Sinapis alba Species Brassicaceae Eukaryota n.a. n.a. Database[FooDB]
NPO29007 Brassica juncea Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO784 Sinapis alba Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO784 Sinapis alba Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29007 Brassica juncea Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO784 Sinapis alba 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[TCM_Taiwan]
NPO29007 Brassica juncea Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO784 Sinapis alba Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO29007 Brassica juncea Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO784 Sinapis alba 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
NPT210 Individual Protein Thyroid stimulating hormone receptor Homo sapiens Potency = 39810.7 nM PMID[454846]
NPT443 Individual Protein Histone acetyltransferase GCN5 Homo sapiens Potency n.a. 35481.3 nM PMID[454847]
NPT135 Individual Protein Chromobox protein homolog 1 Homo sapiens Potency n.a. 89125.1 nM PMID[454847]
NPT152 Individual Protein Nuclear factor erythroid 2-related factor 2 Homo sapiens Potency n.a. 37578.0 nM PMID[454846]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum Potency n.a. 13115.4 nM PMID[454847]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum Potency n.a. 4653.5 nM PMID[454847]

☑ 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 NPC179860 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
0.9231 High Similarity NPC19070
0.9231 High Similarity NPC51067
0.9231 High Similarity NPC225191
0.7188 Intermediate Similarity NPC13217
0.5938 Remote Similarity NPC288991
0.5938 Remote Similarity NPC262789
0.5938 Remote Similarity NPC64176
0.5938 Remote Similarity NPC138325
0.5926 Remote Similarity NPC225855
0.5758 Remote Similarity NPC138113
0.5758 Remote Similarity NPC34671
0.5714 Remote Similarity NPC178306

  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 NPC179860 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
0.6207 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