Structure

Physi-Chem Properties

Molecular Weight:  488.35
Volume:  517.412
LogP:  3.809
LogD:  3.021
LogS:  -4.738
# Rotatable Bonds:  2
TPSA:  90.15
# H-Bond Aceptor:  5
# H-Bond Donor:  4
# Rings:  7
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.44
Synthetic Accessibility Score:  6.891
Fsp3:  0.933
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
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:  -5.387
MDCK Permeability:  8.589607205067296e-06
Pgp-inhibitor:  0.012
Pgp-substrate:  0.515
Human Intestinal Absorption (HIA):  0.012
20% Bioavailability (F20%):  0.048
30% Bioavailability (F30%):  0.998

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.445
Plasma Protein Binding (PPB):  80.48344421386719%
Volume Distribution (VD):  0.8
Pgp-substrate:  14.279190063476562%

ADMET: Metabolism

CYP1A2-inhibitor:  0.007
CYP1A2-substrate:  0.401
CYP2C19-inhibitor:  0.013
CYP2C19-substrate:  0.609
CYP2C9-inhibitor:  0.057
CYP2C9-substrate:  0.026
CYP2D6-inhibitor:  0.004
CYP2D6-substrate:  0.082
CYP3A4-inhibitor:  0.886
CYP3A4-substrate:  0.345

ADMET: Excretion

Clearance (CL):  6.15
Half-life (T1/2):  0.113

ADMET: Toxicity

hERG Blockers:  0.035
Human Hepatotoxicity (H-HT):  0.691
Drug-inuced Liver Injury (DILI):  0.006
AMES Toxicity:  0.018
Rat Oral Acute Toxicity:  0.509
Maximum Recommended Daily Dose:  0.938
Skin Sensitization:  0.151
Carcinogencity:  0.674
Eye Corrosion:  0.011
Eye Irritation:  0.032
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: NPC53939

Natural Product ID:  NPC53939
Common Name*:   GTAXFXIOLOZIPX-XSHWOCSPSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  GTAXFXIOLOZIPX-XSHWOCSPSA-N
Standard InCHI:  InChI=1S/C15H17Br2ClO2/c1-10-15-14(17)7-6-13(20-15)9-11(18)4-5-12(19-10)3-2-8-16/h3-6,8,10-12,14-15H,7,9H2,1H3/b5-4+/t2-,10+,11+,12-,14+,15-/m1/s1
SMILES:  C[C@H]1[C@@H]2[C@H](CC=C(C[C@H](/C=C/[C@@H](C=C=CBr)O1)Cl)O2)Br
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   n.a.
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000267] Organohalogen compounds
      • [CHEMONTID:0002868] Vinyl halides
        • [CHEMONTID:0002864] Vinyl bromides

*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
NPO8821 Delphinium dictyocarpum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2491 Laurencia obtusa Species Rhodomelaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8821 Delphinium dictyocarpum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13493 Mauremys reevesii Species Geoemydidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2329 Scutellaria glabra Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1221 Juniperus serawschanica Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO666 Cymbidium aloifolium Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5527 Ligularia atroviolacea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10341 Pseudogymnoascus pannorum Species Pseudeurotiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2491 Laurencia obtusa Species Rhodomelaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8821 Delphinium dictyocarpum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1054 Peucedanum graveolens Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18938 Ladeania juncea Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15600 Trifolium pannonicum Species Fabaceae 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 NPC53939 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 NPC53939 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