Structure

Physi-Chem Properties

Molecular Weight:  234.98
Volume:  195.612
LogP:  0.099
LogD:  -0.085
LogS:  -1.275
# Rotatable Bonds:  2
TPSA:  80.39
# H-Bond Aceptor:  4
# H-Bond Donor:  3
# Rings:  1
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.729
Synthetic Accessibility Score:  3.496
Fsp3:  0.25
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.446
MDCK Permeability:  0.0001499284408055246
Pgp-inhibitor:  0.004
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.002
30% Bioavailability (F30%):  0.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.559
Plasma Protein Binding (PPB):  51.61247253417969%
Volume Distribution (VD):  0.751
Pgp-substrate:  53.78300094604492%

ADMET: Metabolism

CYP1A2-inhibitor:  0.21
CYP1A2-substrate:  0.504
CYP2C19-inhibitor:  0.16
CYP2C19-substrate:  0.072
CYP2C9-inhibitor:  0.043
CYP2C9-substrate:  0.464
CYP2D6-inhibitor:  0.047
CYP2D6-substrate:  0.284
CYP3A4-inhibitor:  0.01
CYP3A4-substrate:  0.218

ADMET: Excretion

Clearance (CL):  6.185
Half-life (T1/2):  0.321

ADMET: Toxicity

hERG Blockers:  0.021
Human Hepatotoxicity (H-HT):  0.769
Drug-inuced Liver Injury (DILI):  0.141
AMES Toxicity:  0.975
Rat Oral Acute Toxicity:  0.948
Maximum Recommended Daily Dose:  0.179
Skin Sensitization:  0.729
Carcinogencity:  0.97
Eye Corrosion:  0.004
Eye Irritation:  0.171
Respiratory Toxicity:  0.982

Download Data

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

  Natural Product: NPC82674

Natural Product ID:  NPC82674
Common Name*:   Dichloroverongiaquinol
IUPAC Name:   2-(3,5-dichloro-1-hydroxy-4-oxocyclohexa-2,5-dien-1-yl)acetamide
Synonyms:   Dichloroverongiaquinol
Standard InCHIKey:  JYWPCJDFYIJMEM-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C8H7Cl2NO3/c9-4-1-8(14,3-6(11)12)2-5(10)7(4)13/h1-2,14H,3H2,(H2,11,12)
SMILES:  C1=C(C(=O)C(=CC1(CC(=N)O)O)Cl)Cl
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1813813
PubChem CID:   14726963
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000129] Alcohols and polyols
          • [CHEMONTID:0001670] Tertiary alcohols

*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
NPO29034 Suberea mollis Species Aplysinellidae Eukaryota n.a. red sea n.a. PMID[18656986]
NPO29034 Suberea mollis Species Aplysinellidae Eukaryota n.a. Red Sea n.a. PMID[21542602]
NPO29034 Suberea mollis Species Aplysinellidae Eukaryota n.a. n.a. n.a. PMID[21542602]
NPO29034 Suberea mollis Species Aplysinellidae 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
NPT165 Cell Line HeLa Homo sapiens IC50 = 13000.0 nM PMID[536339]
NPT19 Organism Escherichia coli Escherichia coli IZ = 15.0 mm PMID[536339]

☑ 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 NPC82674 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
0.7969 Intermediate Similarity NPC247769
0.625 Remote Similarity NPC313911
0.625 Remote Similarity NPC314854
0.6 Remote Similarity NPC86789
0.5833 Remote Similarity NPC263732
0.5714 Remote Similarity NPC245650
0.5714 Remote Similarity NPC472613
0.5714 Remote Similarity NPC471022
0.5652 Remote Similarity NPC116930

  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 NPC82674 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
NPD

  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