Structure

Physi-Chem Properties

Molecular Weight:  56.03
Volume:  63.962
LogP:  -0.289
LogD:  -0.047
LogS:  0.745
# Rotatable Bonds:  0
TPSA:  20.23
# H-Bond Aceptor:  1
# H-Bond Donor:  1
# Rings:  0
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.375
Synthetic Accessibility Score:  3.352
Fsp3:  0.333
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:  -4.177
MDCK Permeability:  6.671119626844302e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.005
20% Bioavailability (F20%):  0.47
30% Bioavailability (F30%):  0.656

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.998
Plasma Protein Binding (PPB):  36.81865692138672%
Volume Distribution (VD):  0.698
Pgp-substrate:  58.4225959777832%

ADMET: Metabolism

CYP1A2-inhibitor:  0.253
CYP1A2-substrate:  0.68
CYP2C19-inhibitor:  0.034
CYP2C19-substrate:  0.672
CYP2C9-inhibitor:  0.007
CYP2C9-substrate:  0.596
CYP2D6-inhibitor:  0.01
CYP2D6-substrate:  0.239
CYP3A4-inhibitor:  0.007
CYP3A4-substrate:  0.184

ADMET: Excretion

Clearance (CL):  6.201
Half-life (T1/2):  0.881

ADMET: Toxicity

hERG Blockers:  0.006
Human Hepatotoxicity (H-HT):  0.09
Drug-inuced Liver Injury (DILI):  0.166
AMES Toxicity:  0.515
Rat Oral Acute Toxicity:  0.963
Maximum Recommended Daily Dose:  0.165
Skin Sensitization:  0.89
Carcinogencity:  0.246
Eye Corrosion:  0.983
Eye Irritation:  0.996
Respiratory Toxicity:  0.895

Download Data

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

  Natural Product: NPC34153

Natural Product ID:  NPC34153
Common Name*:   Prop-2-Yn-1-Ol
IUPAC Name:   prop-2-yn-1-ol
Synonyms:  
Standard InCHIKey:  TVDSBUOJIPERQY-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C3H4O/c1-2-3-4/h1,4H,3H2
SMILES:  C#CCO
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1563026
PubChem CID:   7859
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004478] Acetylides

*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
NPO28295 Foeniculum vulgare Species Apiaceae Eukaryota n.a. leaf n.a. DOI[10.1016/S0031-9422(00)94055-X]
NPO28295 Foeniculum vulgare Species Apiaceae Eukaryota n.a. flower n.a. DOI[10.3390/70200245]
NPO28295 Foeniculum vulgare Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[24617303]
NPO28295 Foeniculum vulgare Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28295 Foeniculum vulgare Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28295 Foeniculum vulgare Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28295 Foeniculum vulgare Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO28295 Foeniculum vulgare Species Apiaceae 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
NPT152 Individual Protein Nuclear factor erythroid 2-related factor 2 Homo sapiens Potency n.a. 26603.2 nM PMID[471003]
NPT94 Individual Protein Aldehyde dehydrogenase 1A1 Homo sapiens Potency = 22387.2 nM PMID[471003]
NPT2 Others Unspecified Potency n.a. 197 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 NPC34153 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
0.7222 Intermediate Similarity NPC2724
0.7 Intermediate Similarity NPC311000
0.6667 Remote Similarity NPC163707
0.6667 Remote Similarity NPC236761
0.65 Remote Similarity NPC149567
0.6364 Remote Similarity NPC294703
0.619 Remote Similarity NPC322425
0.6087 Remote Similarity NPC110344
0.6087 Remote Similarity NPC219266
0.6087 Remote Similarity NPC88839
0.6087 Remote Similarity NPC299484
0.5926 Remote Similarity NPC65940
0.5926 Remote Similarity NPC223195
0.5833 Remote Similarity NPC39977
0.5833 Remote Similarity NPC52403
0.5652 Remote Similarity NPC85721
0.56 Remote Similarity NPC306009
0.56 Remote Similarity NPC87529
0.56 Remote Similarity NPC114270
0.56 Remote Similarity NPC256186
0.56 Remote Similarity NPC23071
0.56 Remote Similarity NPC94144
0.56 Remote Similarity NPC157340
0.56 Remote Similarity NPC199270
0.56 Remote Similarity NPC245688

  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 NPC34153 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
0.7 Intermediate Similarity NPD8223 Approved
0.6667 Remote Similarity NPD8224 Approved
0.65 Remote Similarity NPD7374 Approved
0.6087 Remote Similarity NPD8196 Approved
0.56 Remote Similarity NPD8225 Phase 3
0.56 Remote Similarity NPD8226 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