Structure

Physi-Chem Properties

Molecular Weight:  81.06
Volume:  98.124
LogP:  1.489
LogD:  0.847
LogS:  -1.736
# 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:  3.273
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:  -4.042
MDCK Permeability:  3.101844777120277e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.003
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.002
30% Bioavailability (F30%):  0.336

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.963
Plasma Protein Binding (PPB):  55.248050689697266%
Volume Distribution (VD):  1.493
Pgp-substrate:  37.093292236328125%

ADMET: Metabolism

CYP1A2-inhibitor:  0.939
CYP1A2-substrate:  0.724
CYP2C19-inhibitor:  0.518
CYP2C19-substrate:  0.789
CYP2C9-inhibitor:  0.128
CYP2C9-substrate:  0.079
CYP2D6-inhibitor:  0.149
CYP2D6-substrate:  0.16
CYP3A4-inhibitor:  0.176
CYP3A4-substrate:  0.304

ADMET: Excretion

Clearance (CL):  8.533
Half-life (T1/2):  0.862

ADMET: Toxicity

hERG Blockers:  0.01
Human Hepatotoxicity (H-HT):  0.421
Drug-inuced Liver Injury (DILI):  0.174
AMES Toxicity:  0.124
Rat Oral Acute Toxicity:  0.923
Maximum Recommended Daily Dose:  0.104
Skin Sensitization:  0.461
Carcinogencity:  0.818
Eye Corrosion:  0.979
Eye Irritation:  0.997
Respiratory Toxicity:  0.898

Download Data

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

  Natural Product: NPC19070

Natural Product ID:  NPC19070
Common Name*:   (Z)-Pent-2-Enenitrile
IUPAC Name:   (Z)-pent-2-enenitrile
Synonyms:  
Standard InCHIKey:  ISBHMJZRKAFTGE-ARJAWSKDSA-N
Standard InCHI:  InChI=1S/C5H7N/c1-2-3-4-5-6/h3-4H,2H2,1H3/b4-3-
SMILES:  CC/C=CC#N
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3185899
PubChem CID:   6433944
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
NPO21355 Elsholtzia ciliata Species Lamiaceae Eukaryota Aerial Parts n.a. n.a. PMID[32991171]
NPO21355 Elsholtzia ciliata Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18046 Mosla chinensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18046 Mosla chinensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21355 Elsholtzia ciliata Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21355 Elsholtzia ciliata Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO18046 Mosla chinensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO18046 Mosla chinensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO21355 Elsholtzia ciliata Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO18046 Mosla chinensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21355 Elsholtzia ciliata Species Lamiaceae 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
NPT153 Individual Protein Androgen Receptor Homo sapiens Potency n.a. 2187.2 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 61644.8 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 54482.7 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 NPC19070 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 NPC225191
1.0 High Similarity NPC51067
0.9231 High Similarity NPC179860
0.7742 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 NPC34671
0.5758 Remote Similarity NPC138113
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 NPC19070 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