Structure

Physi-Chem Properties

Molecular Weight:  361.88
Volume:  245.233
LogP:  5.302
LogD:  3.725
LogS:  -5.548
# Rotatable Bonds:  5
TPSA:  0.0
# H-Bond Aceptor:  0
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.558
Synthetic Accessibility Score:  4.714
Fsp3:  0.6
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:  -4.64
MDCK Permeability:  2.6432700906298123e-05
Pgp-inhibitor:  0.002
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.01
20% Bioavailability (F20%):  0.64
30% Bioavailability (F30%):  0.024

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.544
Plasma Protein Binding (PPB):  98.42716217041016%
Volume Distribution (VD):  3.465
Pgp-substrate:  3.633021116256714%

ADMET: Metabolism

CYP1A2-inhibitor:  0.977
CYP1A2-substrate:  0.732
CYP2C19-inhibitor:  0.857
CYP2C19-substrate:  0.828
CYP2C9-inhibitor:  0.636
CYP2C9-substrate:  0.15
CYP2D6-inhibitor:  0.058
CYP2D6-substrate:  0.071
CYP3A4-inhibitor:  0.304
CYP3A4-substrate:  0.364

ADMET: Excretion

Clearance (CL):  5.447
Half-life (T1/2):  0.062

ADMET: Toxicity

hERG Blockers:  0.017
Human Hepatotoxicity (H-HT):  0.338
Drug-inuced Liver Injury (DILI):  0.838
AMES Toxicity:  0.529
Rat Oral Acute Toxicity:  0.192
Maximum Recommended Daily Dose:  0.212
Skin Sensitization:  0.59
Carcinogencity:  0.578
Eye Corrosion:  0.987
Eye Irritation:  0.975
Respiratory Toxicity:  0.975

Download Data

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

  Natural Product: NPC107849

Natural Product ID:  NPC107849
Common Name*:   (S)-6-Bromo-3-Bromomethyl-2,3-Dichloro-7-Methyl-Octa-1,6-Diene
IUPAC Name:   (3S)-6-bromo-3-(bromomethyl)-2,3-dichloro-7-methylocta-1,6-diene
Synonyms:  
Standard InCHIKey:  QOZBNRJYHFRDPQ-SNVBAGLBSA-N
Standard InCHI:  InChI=1S/C10H14Br2Cl2/c1-7(2)9(12)4-5-10(14,6-11)8(3)13/h3-6H2,1-2H3/t10-/m1/s1
SMILES:  CC(=C(CC[C@@](CBr)(C(=C)Cl)Cl)Br)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL343316
PubChem CID:   10044349
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001549] Monoterpenoids
          • [CHEMONTID:0001127] Acyclic monoterpenoids

*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
NPO32563 portieria hornemannii Species Rhizophyllidaceae Eukaryota n.a. Madagascar n.a. PMID[16643029]
NPO32563 portieria hornemannii Species Rhizophyllidaceae Eukaryota n.a. n.a. n.a. PMID[7996553]

☑ 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
NPT3804 Cell Line Human Tumor Cell lines GI50 = 691.0 nM PMID[564041]
NPT3804 Cell Line Human Tumor Cell lines TGI = 3020.0 nM PMID[564041]
NPT3804 Cell Line Human Tumor Cell lines LC50 = 13500.0 nM PMID[564041]

☑ 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 NPC107849 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
0.9474 High Similarity NPC55269
0.9 High Similarity NPC259702
0.85 High Similarity NPC101811
0.8293 Intermediate Similarity NPC51086
0.8095 Intermediate Similarity NPC469969
0.7907 Intermediate Similarity NPC474773
0.7907 Intermediate Similarity NPC180409
0.7561 Intermediate Similarity NPC201753
0.75 Intermediate Similarity NPC160588
0.7333 Intermediate Similarity NPC99746
0.7 Intermediate Similarity NPC469971
0.6809 Remote Similarity NPC473533
0.6667 Remote Similarity NPC469962
0.6364 Remote Similarity NPC469967
0.5882 Remote Similarity NPC159420
0.5789 Remote Similarity NPC477790

  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 NPC107849 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