Structure

Physi-Chem Properties

Molecular Weight:  81.06
Volume:  98.124
LogP:  1.446
LogD:  0.602
LogS:  -1.604
# 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:  -4.182
MDCK Permeability:  3.1664261769037694e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.004
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.002
30% Bioavailability (F30%):  0.003

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.996
Plasma Protein Binding (PPB):  61.61487579345703%
Volume Distribution (VD):  1.216
Pgp-substrate:  32.54088592529297%

ADMET: Metabolism

CYP1A2-inhibitor:  0.922
CYP1A2-substrate:  0.721
CYP2C19-inhibitor:  0.575
CYP2C19-substrate:  0.798
CYP2C9-inhibitor:  0.227
CYP2C9-substrate:  0.614
CYP2D6-inhibitor:  0.416
CYP2D6-substrate:  0.397
CYP3A4-inhibitor:  0.144
CYP3A4-substrate:  0.331

ADMET: Excretion

Clearance (CL):  7.251
Half-life (T1/2):  0.838

ADMET: Toxicity

hERG Blockers:  0.016
Human Hepatotoxicity (H-HT):  0.463
Drug-inuced Liver Injury (DILI):  0.04
AMES Toxicity:  0.142
Rat Oral Acute Toxicity:  0.902
Maximum Recommended Daily Dose:  0.618
Skin Sensitization:  0.923
Carcinogencity:  0.827
Eye Corrosion:  0.983
Eye Irritation:  0.993
Respiratory Toxicity:  0.944

Download Data

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

  Natural Product: NPC51067

Natural Product ID:  NPC51067
Common Name*:   Pent-2-Enenitrile
IUPAC Name:   pent-2-enenitrile
Synonyms:  
Standard InCHIKey:  ISBHMJZRKAFTGE-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C5H7N/c1-2-3-4-5-6/h3-4H,2H2,1H3
SMILES:  CCC=CC#N
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3185046
PubChem CID:   25833
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]

*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]
NPO18046 Mosla chinensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
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[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
NPT2 Others Unspecified Potency n.a. 1685.2 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 9393.7 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 30 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 52824.7 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 475 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 939.4 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 NPC51067 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 NPC19070
1.0 High Similarity NPC225191
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 NPC51067 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