Structure

Physi-Chem Properties

Molecular Weight:  383.84
Volume:  268.946
LogP:  4.71
LogD:  3.023
LogS:  -5.728
# Rotatable Bonds:  5
TPSA:  0.0
# H-Bond Aceptor:  0
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.402
Synthetic Accessibility Score:  5.455
Fsp3:  0.4
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  2
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.709
MDCK Permeability:  0.00015496656124014407
Pgp-inhibitor:  0.0
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.005
20% Bioavailability (F20%):  0.004
30% Bioavailability (F30%):  0.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.056
Plasma Protein Binding (PPB):  100.05586242675781%
Volume Distribution (VD):  3.142
Pgp-substrate:  1.6056329011917114%

ADMET: Metabolism

CYP1A2-inhibitor:  0.683
CYP1A2-substrate:  0.869
CYP2C19-inhibitor:  0.471
CYP2C19-substrate:  0.878
CYP2C9-inhibitor:  0.065
CYP2C9-substrate:  0.172
CYP2D6-inhibitor:  0.915
CYP2D6-substrate:  0.218
CYP3A4-inhibitor:  0.912
CYP3A4-substrate:  0.347

ADMET: Excretion

Clearance (CL):  1.674
Half-life (T1/2):  0.349

ADMET: Toxicity

hERG Blockers:  0.003
Human Hepatotoxicity (H-HT):  0.046
Drug-inuced Liver Injury (DILI):  0.062
AMES Toxicity:  0.87
Rat Oral Acute Toxicity:  0.34
Maximum Recommended Daily Dose:  0.769
Skin Sensitization:  0.806
Carcinogencity:  0.691
Eye Corrosion:  0.995
Eye Irritation:  0.97
Respiratory Toxicity:  0.984

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General Info & Identifiers & Properties  
Structure MOL file  
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Biological Activities  
Similar NPs/Drugs  

  Natural Product: NPC473533

Natural Product ID:  NPC473533
Common Name*:   (1E,3E,5S,6S,7E)-8-Bromo-1,5,6-Trichloro-2-(Dichloromethyl)-6-Methylocta-1,3,7-Triene
IUPAC Name:   (1E,3E,5S,6S,7E)-8-bromo-1,5,6-trichloro-2-(dichloromethyl)-6-methylocta-1,3,7-triene
Synonyms:  
Standard InCHIKey:  WSTOEGOKMOGOKF-ZFPCQVTASA-N
Standard InCHI:  InChI=1S/C10H10BrCl5/c1-10(16,4-5-11)8(13)3-2-7(6-12)9(14)15/h2-6,8-9H,1H3/b3-2+,5-4+,7-6+/t8-,10-/m0/s1
SMILES:  CC(C=CBr)(C(C=CC(=CCl)C(Cl)Cl)Cl)Cl
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL444765
PubChem CID:   44583705
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000267] Organohalogen compounds
      • [CHEMONTID:0002868] Vinyl halides
        • [CHEMONTID:0002863] Vinyl chlorides

*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
NPO18850 Aplysia dactylomela Species Aplysiidae Eukaryota n.a. tenerife n.a. PMID[10924166]
NPO18850 Aplysia dactylomela Species Aplysiidae Eukaryota n.a. n.a. n.a. PMID[16309323]
NPO18850 Aplysia dactylomela Species Aplysiidae Eukaryota n.a. n.a. n.a. PMID[22220686]
NPO18850 Aplysia dactylomela Species Aplysiidae Eukaryota n.a. n.a. n.a. PMID[24279991]
NPO18850 Aplysia dactylomela Species Aplysiidae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18850 Aplysia dactylomela Species Aplysiidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18850 Aplysia dactylomela Species Aplysiidae 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
NPT65 Cell Line HepG2 Homo sapiens IC50 = 1.0 ug.mL-1 PMID[450097]
NPT83 Cell Line MCF7 Homo sapiens IC50 = 1.5 ug.mL-1 PMID[450097]
NPT1034 Cell Line Lu1 Homo sapiens IC50 > 25.0 ug.mL-1 PMID[450097]
NPT91 Cell Line KB Homo sapiens IC50 > 25.0 ug.mL-1 PMID[450097]
NPT133 Cell Line ZR-75-1 Homo sapiens IC50 > 25.0 ug.mL-1 PMID[450097]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. IC50 = 1.1 ug.mL-1 PMID[450097]
NPT1230 Organism Bacillus megaterium Bacillus megaterium IZ = 2.0 mm PMID[450097]
NPT1234 Organism Chlorella fusca Chlorella fusca IZ = 1.0 mm PMID[450097]

☑ 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 NPC473533 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
0.7556 Intermediate Similarity NPC259702
0.7442 Intermediate Similarity NPC201753
0.7222 Intermediate Similarity NPC477790
0.7174 Intermediate Similarity NPC469969
0.7111 Intermediate Similarity NPC55269
0.6809 Remote Similarity NPC107849
0.68 Remote Similarity NPC159420
0.6739 Remote Similarity NPC101811
0.6607 Remote Similarity NPC469967
0.62 Remote Similarity NPC99746
0.6047 Remote Similarity NPC60288
0.6034 Remote Similarity NPC469962
0.6 Remote Similarity NPC180409
0.6 Remote Similarity NPC474773
0.5952 Remote Similarity NPC288991
0.5952 Remote Similarity NPC262789
0.5952 Remote Similarity NPC64176
0.5814 Remote Similarity NPC138113
0.5745 Remote Similarity NPC282119
0.5686 Remote Similarity NPC160588
0.5652 Remote Similarity NPC173592
0.5652 Remote Similarity NPC305759
0.5652 Remote Similarity NPC99088
0.56 Remote Similarity NPC51086

  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 NPC473533 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