Structure

Physi-Chem Properties

Molecular Weight:  256.09
Volume:  249.747
LogP:  0.803
LogD:  1.081
LogS:  -1.562
# Rotatable Bonds:  5
TPSA:  78.9
# H-Bond Aceptor:  6
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.414
Synthetic Accessibility Score:  3.774
Fsp3:  0.583
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.57
MDCK Permeability:  4.7608478780603036e-05
Pgp-inhibitor:  0.999
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.011
20% Bioavailability (F20%):  0.948
30% Bioavailability (F30%):  0.995

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.984
Plasma Protein Binding (PPB):  25.926719665527344%
Volume Distribution (VD):  0.427
Pgp-substrate:  79.4573745727539%

ADMET: Metabolism

CYP1A2-inhibitor:  0.241
CYP1A2-substrate:  0.524
CYP2C19-inhibitor:  0.288
CYP2C19-substrate:  0.768
CYP2C9-inhibitor:  0.047
CYP2C9-substrate:  0.062
CYP2D6-inhibitor:  0.006
CYP2D6-substrate:  0.142
CYP3A4-inhibitor:  0.086
CYP3A4-substrate:  0.47

ADMET: Excretion

Clearance (CL):  9.684
Half-life (T1/2):  0.94

ADMET: Toxicity

hERG Blockers:  0.016
Human Hepatotoxicity (H-HT):  0.73
Drug-inuced Liver Injury (DILI):  0.446
AMES Toxicity:  0.17
Rat Oral Acute Toxicity:  0.134
Maximum Recommended Daily Dose:  0.511
Skin Sensitization:  0.892
Carcinogencity:  0.386
Eye Corrosion:  0.79
Eye Irritation:  0.714
Respiratory Toxicity:  0.116

Download Data

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

  Natural Product: NPC140366

Natural Product ID:  NPC140366
Common Name*:   SKLFBVDVHXYCOT-LSRCEVBISA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  SKLFBVDVHXYCOT-LSRCEVBISA-N
Standard InCHI:  InChI=1S/C12H16O6/c1-4-7-8(5-10(13)16-2)9(11(14)17-3)6-18-12(7)15/h4,8-9H,5-6H2,1-3H3/b7-4-/t8-,9-/m0/s1
SMILES:  C/C=C1/[C@H](CC(=O)OC)[C@H](COC1=O)C(=O)OC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   n.a.
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001283] Terpene lactones

*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
NPO27821 Pochonia chlamydosporia Species Clavicipitaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.tetlet.2008.10.099]
NPO14484 Echinacea purpurea Species Asteraceae Eukaryota root n.a. n.a. PMID[15921428]
NPO14484 Echinacea purpurea Species Asteraceae Eukaryota flowers n.a. n.a. PMID[19374389]
NPO27821 Pochonia chlamydosporia Species Clavicipitaceae Eukaryota Roots n.a. n.a. PMID[20000774]
NPO7507 Portulaca grandiflora Species Portulacaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16321 Cratoxylum prunifolium Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14484 Echinacea purpurea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18715 Ephedra minuta Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12532 Amomum muricarpum Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14484 Echinacea purpurea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18715 Ephedra minuta Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16321 Cratoxylum prunifolium Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7507 Portulaca grandiflora Species Portulacaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18715 Ephedra minuta Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO16321 Cratoxylum prunifolium Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18715 Ephedra minuta Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27821 Pochonia chlamydosporia Species Clavicipitaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12532 Amomum muricarpum Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14484 Echinacea purpurea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7507 Portulaca grandiflora Species Portulacaceae 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 NPC140366 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 NPC140366 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