Structure

Physi-Chem Properties

Molecular Weight:  390.28
Volume:  431.162
LogP:  5.011
LogD:  4.191
LogS:  -5.479
# Rotatable Bonds:  8
TPSA:  52.6
# H-Bond Aceptor:  4
# H-Bond Donor:  0
# Rings:  2
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.436
Synthetic Accessibility Score:  4.273
Fsp3:  0.75
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:  -4.637
MDCK Permeability:  2.033801683865022e-05
Pgp-inhibitor:  0.994
Pgp-substrate:  0.003
Human Intestinal Absorption (HIA):  0.009
20% Bioavailability (F20%):  0.69
30% Bioavailability (F30%):  0.804

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.459
Plasma Protein Binding (PPB):  88.05674743652344%
Volume Distribution (VD):  1.402
Pgp-substrate:  19.229415893554688%

ADMET: Metabolism

CYP1A2-inhibitor:  0.164
CYP1A2-substrate:  0.08
CYP2C19-inhibitor:  0.186
CYP2C19-substrate:  0.467
CYP2C9-inhibitor:  0.413
CYP2C9-substrate:  0.106
CYP2D6-inhibitor:  0.062
CYP2D6-substrate:  0.134
CYP3A4-inhibitor:  0.567
CYP3A4-substrate:  0.277

ADMET: Excretion

Clearance (CL):  3.866
Half-life (T1/2):  0.157

ADMET: Toxicity

hERG Blockers:  0.038
Human Hepatotoxicity (H-HT):  0.365
Drug-inuced Liver Injury (DILI):  0.72
AMES Toxicity:  0.005
Rat Oral Acute Toxicity:  0.072
Maximum Recommended Daily Dose:  0.536
Skin Sensitization:  0.369
Carcinogencity:  0.1
Eye Corrosion:  0.5
Eye Irritation:  0.73
Respiratory Toxicity:  0.903

Download Data

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

  Natural Product: NPC305078

Natural Product ID:  NPC305078
Common Name*:   TXDYVSBYMBLCOL-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  TXDYVSBYMBLCOL-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C6H12O/c1-2-3-4-5-6-7/h1-6H2
SMILES:  [CH2+]CCCCC[O-]
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   53627517
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0003940] Organic oxides

*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
NPO16755 Saposhnikovia divaricata Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[17703773]
NPO18176 Ephedra sinica Species Ephedraceae Eukaryota n.a. root n.a. PMID[18975262]
NPO18176 Ephedra sinica Species Ephedraceae Eukaryota n.a. n.a. n.a. PMID[24333010]
NPO30125 0topterygium forbesii n.a. n.a. n.a. n.a. n.a. n.a. Database[HerDing]
NPO21343 Eupatorium fortunei Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4795.1 Prunus armeniaca var. ansu Varieties Rosaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18176 Ephedra sinica Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21620 Thlaspi arvense Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10597 Fructus syzygii n.a. n.a. n.a. n.a. n.a. n.a. Database[HerDing]
NPO16755 Saposhnikovia divaricata Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10597 Fructus syzygii n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO21343 Eupatorium fortunei Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4795.1 Prunus armeniaca var. ansu Varieties Rosaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16755 Saposhnikovia divaricata Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18176 Ephedra sinica Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24644 Hansenia forbesii Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21620 Thlaspi arvense Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18176 Ephedra sinica Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO21620 Thlaspi arvense Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO30125 0topterygium forbesii n.a. n.a. n.a. n.a. n.a. n.a. Database[TCM_Taiwan]
NPO21343 Eupatorium fortunei Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO24644 Hansenia forbesii Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO21620 Thlaspi arvense Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO16755 Saposhnikovia divaricata Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO18176 Ephedra sinica Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO24644 Hansenia forbesii Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21343 Eupatorium fortunei Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21620 Thlaspi arvense Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18176 Ephedra sinica Species Ephedraceae 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 NPC305078 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 NPC305078 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