Structure

Physi-Chem Properties

Molecular Weight:  204.19
Volume:  245.61
LogP:  5.914
LogD:  4.335
LogS:  -5.419
# Rotatable Bonds:  0
TPSA:  0.0
# H-Bond Aceptor:  0
# H-Bond Donor:  0
# Rings:  2
# Heavy Atoms:  0

MedChem Properties

QED Drug-Likeness Score:  0.501
Synthetic Accessibility Score:  3.908
Fsp3:  0.733
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:  -4.518
MDCK Permeability:  1.5269573850673623e-05
Pgp-inhibitor:  0.587
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.002
20% Bioavailability (F20%):  0.991
30% Bioavailability (F30%):  0.321

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.426
Plasma Protein Binding (PPB):  94.49264526367188%
Volume Distribution (VD):  3.726
Pgp-substrate:  6.380018711090088%

ADMET: Metabolism

CYP1A2-inhibitor:  0.689
CYP1A2-substrate:  0.564
CYP2C19-inhibitor:  0.583
CYP2C19-substrate:  0.854
CYP2C9-inhibitor:  0.539
CYP2C9-substrate:  0.782
CYP2D6-inhibitor:  0.083
CYP2D6-substrate:  0.56
CYP3A4-inhibitor:  0.307
CYP3A4-substrate:  0.294

ADMET: Excretion

Clearance (CL):  7.628
Half-life (T1/2):  0.041

ADMET: Toxicity

hERG Blockers:  0.045
Human Hepatotoxicity (H-HT):  0.342
Drug-inuced Liver Injury (DILI):  0.535
AMES Toxicity:  0.013
Rat Oral Acute Toxicity:  0.498
Maximum Recommended Daily Dose:  0.536
Skin Sensitization:  0.231
Carcinogencity:  0.75
Eye Corrosion:  0.314
Eye Irritation:  0.728
Respiratory Toxicity:  0.763

Download Data

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

  Natural Product: NPC233039

Natural Product ID:  NPC233039
Common Name*:   BJRNKVDFDLYUGJ-SVNGYHJRSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  BJRNKVDFDLYUGJ-SVNGYHJRSA-N
Standard InCHI:  InChI=1S/C12H16O7/c13-5-8-9(15)10(16)11(17)12(19-8)18-7-3-1-6(14)2-4-7/h1-4,8-17H,5H2/t8-,9-,10+,11-,12-/m0/s1
SMILES:  c1cc(ccc1O)O[C@@H]1[C@H]([C@@H]([C@H]([C@H](CO)O1)O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   667463
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates
          • [CHEMONTID:0002105] Glycosyl compounds
            • [CHEMONTID:0004165] Phenolic glycosides

*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
NPO9164 Catunaregam spinosa Species Rubiaceae Eukaryota stem bark n.a. n.a. PMID[21861991]
NPO8343 Centaurea corcubionensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1189 Aspergillus giganteus Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10444 Dendrophthoe falcata Species Loranthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9164 Catunaregam spinosa Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12044 Dorstenia barteri Species Moraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15245 Paenibacillus macerans Species Paenibacillaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO16866 Rhododendron luteum Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10919 Salvia cyanescens Species Lamiaceae 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 NPC233039 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 NPC233039 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