Structure

Physi-Chem Properties

Molecular Weight:  334.21
Volume:  367.898
LogP:  6.224
LogD:  4.34
LogS:  -6.513
# Rotatable Bonds:  14
TPSA:  52.6
# H-Bond Aceptor:  4
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.391
Synthetic Accessibility Score:  1.865
Fsp3:  0.6
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:  -4.673
MDCK Permeability:  2.446789039822761e-05
Pgp-inhibitor:  0.954
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.001
20% Bioavailability (F20%):  0.999
30% Bioavailability (F30%):  0.997

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.027
Plasma Protein Binding (PPB):  97.88397979736328%
Volume Distribution (VD):  1.367
Pgp-substrate:  1.607798457145691%

ADMET: Metabolism

CYP1A2-inhibitor:  0.735
CYP1A2-substrate:  0.205
CYP2C19-inhibitor:  0.782
CYP2C19-substrate:  0.058
CYP2C9-inhibitor:  0.407
CYP2C9-substrate:  0.711
CYP2D6-inhibitor:  0.564
CYP2D6-substrate:  0.073
CYP3A4-inhibitor:  0.527
CYP3A4-substrate:  0.079

ADMET: Excretion

Clearance (CL):  10.377
Half-life (T1/2):  0.123

ADMET: Toxicity

hERG Blockers:  0.233
Human Hepatotoxicity (H-HT):  0.004
Drug-inuced Liver Injury (DILI):  0.289
AMES Toxicity:  0.005
Rat Oral Acute Toxicity:  0.002
Maximum Recommended Daily Dose:  0.005
Skin Sensitization:  0.912
Carcinogencity:  0.242
Eye Corrosion:  0.034
Eye Irritation:  0.987
Respiratory Toxicity:  0.041

Download Data

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

  Natural Product: NPC53406

Natural Product ID:  NPC53406
Common Name*:   UOGBMDMLDZZHGP-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  UOGBMDMLDZZHGP-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C8H18O4/c1-4-10-8(7-9,11-5-2)12-6-3/h9H,4-7H2,1-3H3
SMILES:  CCOC(CO)(OCC)OCC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   5322034
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0002926] Ortho esters

*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
NPO21891 Panax notoginseng Species Araliaceae Eukaryota Flower buds n.a. n.a. PMID[12880307]
NPO21891 Panax notoginseng Species Araliaceae Eukaryota Stems n.a. n.a. PMID[17663584]
NPO21891 Panax notoginseng Species Araliaceae Eukaryota Roots n.a. n.a. PMID[18186611]
NPO12773 Stephania tetrandra Species Menispermaceae Eukaryota n.a. root n.a. PMID[20030508]
NPO21891 Panax notoginseng Species Araliaceae Eukaryota Steamed Roots n.a. n.a. PMID[26200131]
NPO12773 Stephania tetrandra Species Menispermaceae Eukaryota n.a. n.a. n.a. PMID[3728032]
NPO12773 Stephania tetrandra Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[Article]
NPO14105.2 Panax pseudo-ginseng var. notoginseng Varieties Araliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12773 Stephania tetrandra Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14105.2 Panax pseudo-ginseng var. notoginseng Varieties Araliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12773 Stephania tetrandra Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21891 Panax notoginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO12773 Stephania tetrandra Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO21891 Panax notoginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO12773 Stephania tetrandra Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO21891 Panax notoginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12773 Stephania tetrandra Species Menispermaceae 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 NPC53406 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 NPC53406 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