Structure

Physi-Chem Properties

Molecular Weight:  342.07
Volume:  326.098
LogP:  2.872
LogD:  2.716
LogS:  -4.601
# Rotatable Bonds:  3
TPSA:  87.36
# H-Bond Aceptor:  7
# H-Bond Donor:  1
# Rings:  4
# Heavy Atoms:  7

MedChem Properties

QED Drug-Likeness Score:  0.783
Synthetic Accessibility Score:  2.426
Fsp3:  0.167
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:  -4.799
MDCK Permeability:  4.4930540752829984e-05
Pgp-inhibitor:  0.085
Pgp-substrate:  0.004
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.003
30% Bioavailability (F30%):  0.01

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.036
Plasma Protein Binding (PPB):  89.15935516357422%
Volume Distribution (VD):  0.61
Pgp-substrate:  9.659162521362305%

ADMET: Metabolism

CYP1A2-inhibitor:  0.872
CYP1A2-substrate:  0.846
CYP2C19-inhibitor:  0.912
CYP2C19-substrate:  0.101
CYP2C9-inhibitor:  0.766
CYP2C9-substrate:  0.873
CYP2D6-inhibitor:  0.867
CYP2D6-substrate:  0.908
CYP3A4-inhibitor:  0.905
CYP3A4-substrate:  0.191

ADMET: Excretion

Clearance (CL):  9.705
Half-life (T1/2):  0.512

ADMET: Toxicity

hERG Blockers:  0.062
Human Hepatotoxicity (H-HT):  0.213
Drug-inuced Liver Injury (DILI):  0.722
AMES Toxicity:  0.031
Rat Oral Acute Toxicity:  0.139
Maximum Recommended Daily Dose:  0.344
Skin Sensitization:  0.803
Carcinogencity:  0.704
Eye Corrosion:  0.004
Eye Irritation:  0.233
Respiratory Toxicity:  0.466

Download Data

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

  Natural Product: NPC298113

Natural Product ID:  NPC298113
Common Name*:   OJZMBJPPHULSCR-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  OJZMBJPPHULSCR-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C18H14O7/c1-21-15-3-9(4-16(22-2)18(15)20)11-7-23-12-6-14-13(24-8-25-14)5-10(12)17(11)19/h3-7,20H,8H2,1-2H3
SMILES:  COc1cc(cc(c1O)OC)c1coc2cc3c(cc2c1=O)OCO3
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   15290941
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0002506] Isoflavonoids
        • [CHEMONTID:0002586] O-methylated isoflavonoids
          • [CHEMONTID:0002605] 3'-O-methylated isoflavonoids
            • [CHEMONTID:0002690] 3'-O-methylisoflavones

*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
NPO28689 Armillaria mellea Species Physalacriaceae Eukaryota n.a. n.a. n.a. PMID[19795841]
NPO28689 Armillaria mellea Species Physalacriaceae Eukaryota n.a. n.a. n.a. PMID[4040154]
NPO28689 Armillaria mellea Species Physalacriaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28647 Fleischmannia deborabellae Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28624 Canthium gilfillanii Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28328 Cortispongilla barroisi Species Malawispongiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28672 Ficus cunia Species Ficidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22882 Biancaea millettii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29071 Anacardium giganteum Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28689 Armillaria mellea Species Physalacriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28761 Tricholoma populinum Species Tricholomataceae 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 NPC298113 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 NPC298113 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