Structure

Physi-Chem Properties

Molecular Weight:  317.93
Volume:  241.16
LogP:  5.209
LogD:  3.526
LogS:  -5.408
# 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:  0.593
Synthetic Accessibility Score:  4.61
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:  -4.657
MDCK Permeability:  2.4262677470687777e-05
Pgp-inhibitor:  0.006
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.401
30% Bioavailability (F30%):  0.002

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.379
Plasma Protein Binding (PPB):  98.85394287109375%
Volume Distribution (VD):  5.215
Pgp-substrate:  2.5769436359405518%

ADMET: Metabolism

CYP1A2-inhibitor:  0.971
CYP1A2-substrate:  0.857
CYP2C19-inhibitor:  0.798
CYP2C19-substrate:  0.827
CYP2C9-inhibitor:  0.571
CYP2C9-substrate:  0.149
CYP2D6-inhibitor:  0.104
CYP2D6-substrate:  0.064
CYP3A4-inhibitor:  0.339
CYP3A4-substrate:  0.486

ADMET: Excretion

Clearance (CL):  8.955
Half-life (T1/2):  0.092

ADMET: Toxicity

hERG Blockers:  0.013
Human Hepatotoxicity (H-HT):  0.391
Drug-inuced Liver Injury (DILI):  0.797
AMES Toxicity:  0.643
Rat Oral Acute Toxicity:  0.209
Maximum Recommended Daily Dose:  0.235
Skin Sensitization:  0.427
Carcinogencity:  0.616
Eye Corrosion:  0.983
Eye Irritation:  0.968
Respiratory Toxicity:  0.973

Download Data

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

  Natural Product: NPC55269

Natural Product ID:  NPC55269
Common Name*:   (S)-3-Bromomethyl-2,3,6-Trichloro-7-Methyl-Octa-1,6-Diene
IUPAC Name:   (3S)-3-(bromomethyl)-2,3,6-trichloro-7-methylocta-1,6-diene
Synonyms:  
Standard InCHIKey:  IVWLPIDLFZKNHM-SNVBAGLBSA-N
Standard InCHI:  InChI=1S/C10H14BrCl3/c1-7(2)9(13)4-5-10(14,6-11)8(3)12/h3-6H2,1-2H3/t10-/m1/s1
SMILES:  CC(=C(CC[C@@](CBr)(C(=C)Cl)Cl)Cl)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL135141
PubChem CID:   10381365
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 = 741.0 nM PMID[508264]
NPT3804 Cell Line Human Tumor Cell lines TGI = 3390.0 nM PMID[508264]
NPT3804 Cell Line Human Tumor Cell lines LC50 = 17000.0 nM PMID[508264]

☑ 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 NPC55269 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 NPC107849
0.9474 High Similarity NPC259702
0.85 High Similarity NPC469969
0.8 Intermediate Similarity NPC101811
0.7949 Intermediate Similarity NPC201753
0.7805 Intermediate Similarity NPC51086
0.7442 Intermediate Similarity NPC180409
0.7442 Intermediate Similarity NPC474773
0.7111 Intermediate Similarity NPC473533
0.7045 Intermediate Similarity NPC160588
0.6889 Remote Similarity NPC99746
0.6604 Remote Similarity NPC469962
0.66 Remote Similarity NPC469971
0.6296 Remote Similarity NPC469967
0.6122 Remote Similarity NPC159420
0.6 Remote Similarity NPC477790
0.5854 Remote Similarity NPC206088
0.5714 Remote Similarity NPC213749

  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 NPC55269 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