Structure

Physi-Chem Properties

Molecular Weight:  218.94
Volume:  175.896
LogP:  4.181
LogD:  3.599
LogS:  -5.254
# Rotatable Bonds:  0
TPSA:  15.79
# H-Bond Aceptor:  1
# H-Bond Donor:  1
# Rings:  2
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.687
Synthetic Accessibility Score:  2.552
Fsp3:  0.0
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:  -4.715
MDCK Permeability:  1.558021904202178e-05
Pgp-inhibitor:  0.003
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.005
20% Bioavailability (F20%):  0.007
30% Bioavailability (F30%):  0.89

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.277
Plasma Protein Binding (PPB):  99.33428192138672%
Volume Distribution (VD):  4.703
Pgp-substrate:  1.2002053260803223%

ADMET: Metabolism

CYP1A2-inhibitor:  0.991
CYP1A2-substrate:  0.871
CYP2C19-inhibitor:  0.848
CYP2C19-substrate:  0.164
CYP2C9-inhibitor:  0.884
CYP2C9-substrate:  0.837
CYP2D6-inhibitor:  0.679
CYP2D6-substrate:  0.497
CYP3A4-inhibitor:  0.312
CYP3A4-substrate:  0.554

ADMET: Excretion

Clearance (CL):  6.521
Half-life (T1/2):  0.287

ADMET: Toxicity

hERG Blockers:  0.022
Human Hepatotoxicity (H-HT):  0.14
Drug-inuced Liver Injury (DILI):  0.905
AMES Toxicity:  0.082
Rat Oral Acute Toxicity:  0.557
Maximum Recommended Daily Dose:  0.893
Skin Sensitization:  0.566
Carcinogencity:  0.561
Eye Corrosion:  0.917
Eye Irritation:  0.987
Respiratory Toxicity:  0.949

Download Data

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

  Natural Product: NPC296205

Natural Product ID:  NPC296205
Common Name*:   YVMFEDFGLONICM-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  YVMFEDFGLONICM-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C8H4Cl3N/c9-5-3-1-2-4-6(10)8(11)12-7(4)5/h1-3,12H
SMILES:  c1cc2c(c(Cl)[nH]c2c(c1)Cl)Cl
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   12706661
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000211] Indoles and derivatives
        • [CHEMONTID:0002497] Indoles

*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
NPO8705 Rhodophyllis membranacea Species Cystocloniaceae Eukaryota n.a. n.a. n.a. PMID[26756908]
NPO505 Agathosma ciliaris Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3320 Sesbania aegyptiaca Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2920 Tagetes elliptica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6765 Illicium micranthum Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8162 Digitalis thapsi Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8705 Rhodophyllis membranacea Species Cystocloniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2716 Anemone cylindrica Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5321 Anacamptis morio Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25634 Echinothrix calamaris Species Diadematidae 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 NPC296205 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 NPC296205 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