Structure

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Physi-Chem Properties

Molecular Weight:  388.15
Volume:  383.259
LogP:  2.072
LogD:  2.677
LogS:  -4.461
# Rotatable Bonds:  5
TPSA:  86.61
# H-Bond Aceptor:  7
# H-Bond Donor:  2
# Rings:  4
# Heavy Atoms:  7

MedChem Properties

QED Drug-Likeness Score:  0.813
Synthetic Accessibility Score:  3.742
Fsp3:  0.429
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  1
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.774
MDCK Permeability:  2.7249408958596177e-05
Pgp-inhibitor:  0.019
Pgp-substrate:  0.12
Human Intestinal Absorption (HIA):  0.01
20% Bioavailability (F20%):  0.009
30% Bioavailability (F30%):  0.031

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.056
Plasma Protein Binding (PPB):  92.65935516357422%
Volume Distribution (VD):  0.788
Pgp-substrate:  7.054266452789307%

ADMET: Metabolism

CYP1A2-inhibitor:  0.028
CYP1A2-substrate:  0.945
CYP2C19-inhibitor:  0.048
CYP2C19-substrate:  0.843
CYP2C9-inhibitor:  0.221
CYP2C9-substrate:  0.732
CYP2D6-inhibitor:  0.164
CYP2D6-substrate:  0.877
CYP3A4-inhibitor:  0.351
CYP3A4-substrate:  0.616

ADMET: Excretion

Clearance (CL):  6.716
Half-life (T1/2):  0.515

ADMET: Toxicity

hERG Blockers:  0.088
Human Hepatotoxicity (H-HT):  0.177
Drug-inuced Liver Injury (DILI):  0.187
AMES Toxicity:  0.126
Rat Oral Acute Toxicity:  0.184
Maximum Recommended Daily Dose:  0.507
Skin Sensitization:  0.852
Carcinogencity:  0.135
Eye Corrosion:  0.003
Eye Irritation:  0.264
Respiratory Toxicity:  0.492

Download Data

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

  Natural Product: NPC252126

Natural Product ID:  NPC252126
Common Name*:   VJOBNGRIBLNUKN-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  VJOBNGRIBLNUKN-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C21H24O7/c1-24-16-6-11(4-5-15(16)22)20-13-9-28-21(14(13)10-27-20)12-7-17(25-2)19(23)18(8-12)26-3/h4-8,13-14,20-23H,9-10H2,1-3H3
SMILES:  COc1cc(ccc1O)C1C2COC(c3cc(c(c(c3)OC)O)OC)C2CO1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   4546425
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0001392] Lignans, neolignans and related compounds
      • [CHEMONTID:0003686] Furanoid lignans

*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

☑ 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

☑ 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

☑ 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 NPC252126 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.56 or Top200).

  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 NPC252126 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

  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