Structure

Physi-Chem Properties

Molecular Weight:  361.88
Volume:  245.233
LogP:  5.026
LogD:  4.364
LogS:  -5.908
# 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:  0.441
Synthetic Accessibility Score:  4.405
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:  -4.409
MDCK Permeability:  1.8711929442360997e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.015
30% Bioavailability (F30%):  0.008

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.829
Plasma Protein Binding (PPB):  97.75093841552734%
Volume Distribution (VD):  3.563
Pgp-substrate:  3.893322229385376%

ADMET: Metabolism

CYP1A2-inhibitor:  0.885
CYP1A2-substrate:  0.883
CYP2C19-inhibitor:  0.778
CYP2C19-substrate:  0.822
CYP2C9-inhibitor:  0.919
CYP2C9-substrate:  0.286
CYP2D6-inhibitor:  0.042
CYP2D6-substrate:  0.426
CYP3A4-inhibitor:  0.321
CYP3A4-substrate:  0.617

ADMET: Excretion

Clearance (CL):  2.76
Half-life (T1/2):  0.085

ADMET: Toxicity

hERG Blockers:  0.004
Human Hepatotoxicity (H-HT):  0.817
Drug-inuced Liver Injury (DILI):  0.574
AMES Toxicity:  0.165
Rat Oral Acute Toxicity:  0.593
Maximum Recommended Daily Dose:  0.404
Skin Sensitization:  0.466
Carcinogencity:  0.617
Eye Corrosion:  0.971
Eye Irritation:  0.858
Respiratory Toxicity:  0.977

Download Data

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

  Natural Product: NPC474773

Natural Product ID:  NPC474773
Common Name*:   (Z)-6-Bromo-3-(Bromomethylene)-2,7-Dichloro-7-Methyloct-1-Ene
IUPAC Name:   (3Z)-6-bromo-3-(bromomethylidene)-2,7-dichloro-7-methyloct-1-ene
Synonyms:  
Standard InCHIKey:  AWTHGCZBYVEAJW-VURMDHGXSA-N
Standard InCHI:  InChI=1S/C10H14Br2Cl2/c1-7(13)8(6-11)4-5-9(12)10(2,3)14/h6,9H,1,4-5H2,2-3H3/b8-6-
SMILES:  CC(C)(C(CCC(=CBr)C(=C)Cl)Br)Cl
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL482224
PubChem CID:   11660589
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
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
NPT2752 Individual Protein DNA (cytosine-5)-methyltransferase 1 Homo sapiens Activity = 55.0 uM PMID[532919]

☑ 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 NPC474773 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
0.9 High Similarity NPC51086
0.8571 High Similarity NPC180409
0.8571 High Similarity NPC160588
0.8372 Intermediate Similarity NPC99746
0.7907 Intermediate Similarity NPC107849
0.7857 Intermediate Similarity NPC101811
0.75 Intermediate Similarity NPC259702
0.7442 Intermediate Similarity NPC55269
0.7111 Intermediate Similarity NPC469969
0.6977 Remote Similarity NPC201753
0.6863 Remote Similarity NPC469971
0.6852 Remote Similarity NPC469962
0.6545 Remote Similarity NPC469967
0.6316 Remote Similarity NPC183031
0.6271 Remote Similarity NPC110214
0.6167 Remote Similarity NPC52966
0.6 Remote Similarity NPC473533
0.5769 Remote Similarity NPC159420

  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 NPC474773 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