Structure

Physi-Chem Properties

Molecular Weight:  325.91
Volume:  227.385
LogP:  5.001
LogD:  4.38
LogS:  -5.081
# Rotatable Bonds:  4
TPSA:  0.0
# H-Bond Aceptor:  0
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.599
Synthetic Accessibility Score:  4.153
Fsp3:  0.4
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
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:  -4.447
MDCK Permeability:  2.5329434720333666e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.528
30% Bioavailability (F30%):  0.025

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.896
Plasma Protein Binding (PPB):  98.59014129638672%
Volume Distribution (VD):  4.445
Pgp-substrate:  3.747853994369507%

ADMET: Metabolism

CYP1A2-inhibitor:  0.938
CYP1A2-substrate:  0.493
CYP2C19-inhibitor:  0.663
CYP2C19-substrate:  0.763
CYP2C9-inhibitor:  0.62
CYP2C9-substrate:  0.185
CYP2D6-inhibitor:  0.066
CYP2D6-substrate:  0.185
CYP3A4-inhibitor:  0.115
CYP3A4-substrate:  0.264

ADMET: Excretion

Clearance (CL):  4.048
Half-life (T1/2):  0.074

ADMET: Toxicity

hERG Blockers:  0.004
Human Hepatotoxicity (H-HT):  0.791
Drug-inuced Liver Injury (DILI):  0.576
AMES Toxicity:  0.471
Rat Oral Acute Toxicity:  0.732
Maximum Recommended Daily Dose:  0.148
Skin Sensitization:  0.514
Carcinogencity:  0.741
Eye Corrosion:  0.948
Eye Irritation:  0.96
Respiratory Toxicity:  0.976

Download Data

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

  Natural Product: NPC101811

Natural Product ID:  NPC101811
Common Name*:   (Z)-6-Bromo-3-(Bromomethylene)-2-Chloro-7-Methylocta-1,6-Diene
IUPAC Name:   (3Z)-6-bromo-3-(bromomethylidene)-2-chloro-7-methylocta-1,6-diene
Synonyms:  
Standard InCHIKey:  HADZLPWHSAKXHN-TWGQIWQCSA-N
Standard InCHI:  InChI=1S/C10H13Br2Cl/c1-7(2)10(12)5-4-9(6-11)8(3)13/h6H,3-5H2,1-2H3/b9-6-
SMILES:  Br/C=C(C(=C)Cl)/CCC(=C(C)C)Br
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL455474
PubChem CID:   11493622
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
NPT2752 Individual Protein DNA (cytosine-5)-methyltransferase 1 Homo sapiens Activity = 1.65 uM PMID[456083]

☑ 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 NPC101811 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
0.8919 High Similarity NPC201753
0.85 High Similarity NPC107849
0.8049 Intermediate Similarity NPC469969
0.8049 Intermediate Similarity NPC259702
0.8 Intermediate Similarity NPC55269
0.7857 Intermediate Similarity NPC474773
0.6977 Remote Similarity NPC51086
0.6739 Remote Similarity NPC473533
0.6667 Remote Similarity NPC180409
0.6667 Remote Similarity NPC160588
0.6604 Remote Similarity NPC469967
0.66 Remote Similarity NPC469971
0.6522 Remote Similarity NPC99746
0.6296 Remote Similarity NPC469962
0.6154 Remote Similarity NPC138113
0.6 Remote Similarity NPC60288
0.5882 Remote Similarity NPC477789
0.58 Remote Similarity NPC159420
0.575 Remote Similarity NPC123965
0.575 Remote Similarity NPC115959
0.5714 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 NPC101811 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