Structure

Physi-Chem Properties

Molecular Weight:  254.06
Volume:  256.396
LogP:  2.776
LogD:  2.997
LogS:  -3.39
# Rotatable Bonds:  1
TPSA:  66.76
# H-Bond Aceptor:  4
# H-Bond Donor:  2
# Rings:  3
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.466
Synthetic Accessibility Score:  2.313
Fsp3:  0.0
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.988
MDCK Permeability:  1.6562349628657103e-05
Pgp-inhibitor:  0.011
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.008
20% Bioavailability (F20%):  0.694
30% Bioavailability (F30%):  0.054

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.064
Plasma Protein Binding (PPB):  96.43413543701172%
Volume Distribution (VD):  0.483
Pgp-substrate:  2.15580415725708%

ADMET: Metabolism

CYP1A2-inhibitor:  0.978
CYP1A2-substrate:  0.112
CYP2C19-inhibitor:  0.797
CYP2C19-substrate:  0.064
CYP2C9-inhibitor:  0.626
CYP2C9-substrate:  0.941
CYP2D6-inhibitor:  0.689
CYP2D6-substrate:  0.898
CYP3A4-inhibitor:  0.868
CYP3A4-substrate:  0.222

ADMET: Excretion

Clearance (CL):  13.316
Half-life (T1/2):  0.867

ADMET: Toxicity

hERG Blockers:  0.052
Human Hepatotoxicity (H-HT):  0.269
Drug-inuced Liver Injury (DILI):  0.526
AMES Toxicity:  0.22
Rat Oral Acute Toxicity:  0.917
Maximum Recommended Daily Dose:  0.751
Skin Sensitization:  0.754
Carcinogencity:  0.761
Eye Corrosion:  0.004
Eye Irritation:  0.814
Respiratory Toxicity:  0.299

Download Data

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

  Natural Product: NPC100370

Natural Product ID:  NPC100370
Common Name*:   DJGNNZVFOBIPMK-NTUHNPAUSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  DJGNNZVFOBIPMK-NTUHNPAUSA-N
Standard InCHI:  InChI=1S/C15H10O4/c16-10-3-1-9(2-4-10)7-13-12-6-5-11(17)8-14(12)19-15(13)18/h1-8,16-17H/b13-7+
SMILES:  c1cc(ccc1/C=C/1c2ccc(cc2OC1=O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   9837937
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000301] Benzofurans

*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
NPO20097 Thermobifida alba Species 0cardiopsaceae Bacteria n.a. n.a. n.a. PMID[11430001]
NPO20097 Thermobifida alba Species 0cardiopsaceae Bacteria 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
NPT143 Individual Protein DNA topoisomerase I Homo sapiens IC50 = 307000.0 nM PMID[15808469]
NPT1044 Individual Protein DNA topoisomerase II alpha Homo sapiens IC50 > 400000.0 nM PMID[15808469]
NPT4476 Individual Protein DNA topoisomerase Bos taurus IC50 = 307000.0 nM PMID[11430001]
NPT4451 Individual Protein DNA topoisomerase I Mus musculus IC50 > 400000.0 nM PMID[11430001]
NPT4477 Individual Protein DNA topoisomerase 1 Chlorocebus aethiops IC50 > 400000.0 nM PMID[11430001]
NPT143 Individual Protein DNA topoisomerase I Homo sapiens IC50 > 400000.0 nM PMID[11430001]
NPT1044 Individual Protein DNA topoisomerase II alpha Homo sapiens IC50 > 400000.0 nM PMID[11430001]
NPT4478 Individual Protein Deoxyribonuclease-1 Bos taurus IC50 > 400000.0 nM PMID[11430001]
NPT4479 Individual Protein Deoxyribonuclease-2-alpha Sus scrofa IC50 > 400000.0 nM PMID[11430001]
NPT4480 Individual Protein DNA ligase Enterobacteria phage T4 IC50 > 400000.0 nM PMID[11430001]
NPT4481 Individual Protein Type-2 restriction enzyme BamHI Bacillus amyloliquefaciens IC50 > 400000.0 nM PMID[11430001]
NPT4482 Individual Protein Type-2 restriction enzyme EcoRI Escherichia coli IC50 > 400000.0 nM PMID[11430001]
NPT4483 Individual Protein Type-2 restriction enzyme HindIII Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) IC50 > 400000.0 nM PMID[11430001]
NPT4484 Individual Protein Type-2 restriction enzyme PstI Providencia stuartii IC50 > 400000.0 nM PMID[11430001]
NPT4485 Individual Protein Type-2 restriction enzyme ScaI Streptomyces caespitosus IC50 > 400000.0 nM PMID[11430001]
NPT144 Individual Protein Telomerase reverse transcriptase Homo sapiens IC50 > 400000.0 nM PMID[11430001]
NPT2 Others Unspecified IC50 = 67000.0 nM PMID[11430001]
NPT908 Individual Protein Ribonuclease pancreatic Bos taurus IC50 > 400000.0 nM PMID[11430001]
NPT2 Others Unspecified IC50 > 400000.0 nM PMID[11430001]
NPT21657 SINGLE PROTEIN DNA topoisomerase I Bos taurus IC50 = 307000.0 nM PMID[30739824]
NPT2 Others Unspecified IC50 = 67000.0 nM PMID[30739824]

☑ 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 NPC100370 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 NPC100370 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