Structure

Physi-Chem Properties

Molecular Weight:  248.21
Volume:  277.153
LogP:  4.514
LogD:  3.951
LogS:  -5.79
# Rotatable Bonds:  0
TPSA:  20.23
# H-Bond Aceptor:  1
# H-Bond Donor:  1
# Rings:  4
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.687
Synthetic Accessibility Score:  3.953
Fsp3:  1.0
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.748
MDCK Permeability:  0.00012893260281998664
Pgp-inhibitor:  0.008
Pgp-substrate:  0.002
Human Intestinal Absorption (HIA):  0.016
20% Bioavailability (F20%):  0.017
30% Bioavailability (F30%):  0.14

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.272
Plasma Protein Binding (PPB):  96.13667297363281%
Volume Distribution (VD):  1.493
Pgp-substrate:  1.5196325778961182%

ADMET: Metabolism

CYP1A2-inhibitor:  0.375
CYP1A2-substrate:  0.733
CYP2C19-inhibitor:  0.149
CYP2C19-substrate:  0.796
CYP2C9-inhibitor:  0.38
CYP2C9-substrate:  0.636
CYP2D6-inhibitor:  0.002
CYP2D6-substrate:  0.814
CYP3A4-inhibitor:  0.209
CYP3A4-substrate:  0.627

ADMET: Excretion

Clearance (CL):  17.341
Half-life (T1/2):  0.085

ADMET: Toxicity

hERG Blockers:  0.095
Human Hepatotoxicity (H-HT):  0.329
Drug-inuced Liver Injury (DILI):  0.611
AMES Toxicity:  0.056
Rat Oral Acute Toxicity:  0.007
Maximum Recommended Daily Dose:  0.454
Skin Sensitization:  0.955
Carcinogencity:  0.046
Eye Corrosion:  0.095
Eye Irritation:  0.579
Respiratory Toxicity:  0.531

Download Data

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

  Natural Product: NPC461221

Natural Product ID:  NPC461221
Common Name*:   Sterols
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  FPXSXMFOYWRHDX-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C17H28O/c18-13-6-9-15-12(10-13)5-8-16-14-3-1-2-11(14)4-7-17(15)16/h11-18H,1-10H2
SMILES:  OC1CCC2C(CCC3C4CCCC4CCC23)C1
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:0000258] Steroids and steroid derivatives
        • [CHEMONTID:0001295] Hydroxysteroids
          • [CHEMONTID:0003027] 3-hydroxysteroids

*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
NPO24778 Sesamum orientale Species Pedaliaceae Eukaryota n.a. seed n.a. PMID[11540412]
NPO10449 Arctium lappa Species Asteraceae Eukaryota n.a. fruit n.a. PMID[22396124]
NPO10449 Arctium lappa Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[23501116]
NPO24778 Sesamum orientale Species Pedaliaceae Eukaryota n.a. n.a. Database[FooDB]
NPO10449 Arctium lappa Species Asteraceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO24778 Sesamum orientale Species Pedaliaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO10449 Arctium lappa Species Asteraceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO10449 Arctium lappa Species Asteraceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO24778 Sesamum orientale Species Pedaliaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO10449 Arctium lappa Species Asteraceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO10449 Arctium lappa Species Asteraceae Eukaryota n.a. n.a. Database[FooDB]
NPO24778 Sesamum orientale Species Pedaliaceae Eukaryota n.a. n.a. Database[FooDB]
NPO10449 Arctium lappa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24778 Sesamum orientale Species Pedaliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10449 Arctium lappa Species Asteraceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO24778 Sesamum orientale Species Pedaliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10449 Arctium lappa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10449 Arctium lappa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO24778 Sesamum orientale Species Pedaliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO24778 Sesamum orientale Species Pedaliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO10449 Arctium lappa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO10449 Arctium lappa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24778 Sesamum orientale Species Pedaliaceae 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
NPO10449 NPC461221 Other (raw) Root 20 20 20 mg/100g Database [DUKE]
NPO24778 NPC461221 Other Seed 188.3 65.6 311 mg/100g Database [DUKE]

☑ 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 NPC461221 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 NPC461221 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