Structure

Physi-Chem Properties

Molecular Weight:  216.17
Volume:  239.843
LogP:  3.56
LogD:  1.964
LogS:  -2.909
# Rotatable Bonds:  10
TPSA:  57.53
# H-Bond Aceptor:  3
# H-Bond Donor:  2
# Rings:  0
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.552
Synthetic Accessibility Score:  2.329
Fsp3:  0.917
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.943
MDCK Permeability:  3.611069041653536e-05
Pgp-inhibitor:  0.013
Pgp-substrate:  0.606
Human Intestinal Absorption (HIA):  0.012
20% Bioavailability (F20%):  0.984
30% Bioavailability (F30%):  0.985

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.829
Plasma Protein Binding (PPB):  91.9234619140625%
Volume Distribution (VD):  0.279
Pgp-substrate:  9.601480484008789%

ADMET: Metabolism

CYP1A2-inhibitor:  0.038
CYP1A2-substrate:  0.249
CYP2C19-inhibitor:  0.025
CYP2C19-substrate:  0.704
CYP2C9-inhibitor:  0.11
CYP2C9-substrate:  0.972
CYP2D6-inhibitor:  0.007
CYP2D6-substrate:  0.083
CYP3A4-inhibitor:  0.007
CYP3A4-substrate:  0.04

ADMET: Excretion

Clearance (CL):  8.754
Half-life (T1/2):  0.817

ADMET: Toxicity

hERG Blockers:  0.023
Human Hepatotoxicity (H-HT):  0.056
Drug-inuced Liver Injury (DILI):  0.019
AMES Toxicity:  0.007
Rat Oral Acute Toxicity:  0.016
Maximum Recommended Daily Dose:  0.472
Skin Sensitization:  0.591
Carcinogencity:  0.198
Eye Corrosion:  0.986
Eye Irritation:  0.991
Respiratory Toxicity:  0.516

Download Data

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

  Natural Product: NPC236473

Natural Product ID:  NPC236473
Common Name*:   MUCMKTPAZLSKTL-NSHDSACASA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  MUCMKTPAZLSKTL-NSHDSACASA-N
Standard InCHI:  InChI=1S/C12H24O3/c1-2-3-4-5-6-7-8-9-11(13)10-12(14)15/h11,13H,2-10H2,1H3,(H,14,15)/t11-/m0/s1
SMILES:  CCCCCCCCC[C@@H](CC(=O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   5312805
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000472] Hydroxy acids and derivatives
        • [CHEMONTID:0000299] Medium-chain hydroxy acids and derivatives

*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]
NPO19188 Phaseolus lunatus Species Fabaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO19188 Phaseolus lunatus Species Fabaceae Eukaryota Leaf Diffusate n.a. n.a. Database[FooDB]
NPO19188 Phaseolus lunatus Species Fabaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO19188 Phaseolus lunatus Species Fabaceae Eukaryota Sprout Seedling n.a. n.a. Database[FooDB]
NPO19188 Phaseolus lunatus Species Fabaceae Eukaryota n.a. n.a. Database[FooDB]
NPO28295 Foeniculum vulgare Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19188 Phaseolus lunatus Species Fabaceae Eukaryota Seeds n.a. Database[Phenol-Explorer]
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]
NPO18635 Ulva rigid Species Ulvaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19188 Phaseolus lunatus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12808 Berberis sieboldii Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1318 Lepidium bonariense Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
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

☑ 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 NPC236473 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

  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 NPC236473 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

  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