Structure

Physi-Chem Properties

Molecular Weight:  248.0
Volume:  208.102
LogP:  4.965
LogD:  4.278
LogS:  -4.937
# Rotatable Bonds:  4
TPSA:  0.0
# H-Bond Aceptor:  0
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.497
Synthetic Accessibility Score:  3.568
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:  -4.465
MDCK Permeability:  2.2694084691465832e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.002
20% Bioavailability (F20%):  0.18
30% Bioavailability (F30%):  0.183

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.825
Plasma Protein Binding (PPB):  97.9410171508789%
Volume Distribution (VD):  5.191
Pgp-substrate:  3.040611505508423%

ADMET: Metabolism

CYP1A2-inhibitor:  0.904
CYP1A2-substrate:  0.318
CYP2C19-inhibitor:  0.347
CYP2C19-substrate:  0.765
CYP2C9-inhibitor:  0.22
CYP2C9-substrate:  0.15
CYP2D6-inhibitor:  0.175
CYP2D6-substrate:  0.188
CYP3A4-inhibitor:  0.132
CYP3A4-substrate:  0.234

ADMET: Excretion

Clearance (CL):  7.96
Half-life (T1/2):  0.125

ADMET: Toxicity

hERG Blockers:  0.005
Human Hepatotoxicity (H-HT):  0.925
Drug-inuced Liver Injury (DILI):  0.357
AMES Toxicity:  0.315
Rat Oral Acute Toxicity:  0.803
Maximum Recommended Daily Dose:  0.085
Skin Sensitization:  0.663
Carcinogencity:  0.68
Eye Corrosion:  0.932
Eye Irritation:  0.968
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: NPC201753

Natural Product ID:  NPC201753
Common Name*:   (3Z)-3-(Bromomethylidene)-2-Chloro-7-Methylocta-1,6-Diene
IUPAC Name:   (3Z)-3-(bromomethylidene)-2-chloro-7-methylocta-1,6-diene
Synonyms:  
Standard InCHIKey:  DZHVYBHDGBQWNN-YFHOEESVSA-N
Standard InCHI:  InChI=1S/C10H14BrCl/c1-8(2)5-4-6-10(7-11)9(3)12/h5,7H,3-4,6H2,1-2H3/b10-7-
SMILES:  CC(=CCC/C(=C/Br)/C(=C)Cl)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL342015
PubChem CID:   5469803
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 = 19500.0 nM PMID[505560]
NPT3804 Cell Line Human Tumor Cell lines TGI = 44700.0 nM PMID[505560]
NPT3804 Cell Line Human Tumor Cell lines LC50 > 100000.0 nM PMID[505560]

☑ 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 NPC201753 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 NPC101811
0.8462 Intermediate Similarity NPC469969
0.8462 Intermediate Similarity NPC259702
0.7949 Intermediate Similarity NPC55269
0.7561 Intermediate Similarity NPC107849
0.7442 Intermediate Similarity NPC473533
0.6977 Remote Similarity NPC474773
0.6944 Remote Similarity NPC138113
0.6757 Remote Similarity NPC60288
0.6538 Remote Similarity NPC469967
0.6486 Remote Similarity NPC123965
0.6486 Remote Similarity NPC115959
0.6383 Remote Similarity NPC159420
0.625 Remote Similarity NPC173592
0.625 Remote Similarity NPC99088
0.625 Remote Similarity NPC305759
0.6226 Remote Similarity NPC469962
0.6222 Remote Similarity NPC160588
0.6216 Remote Similarity NPC288991
0.6216 Remote Similarity NPC262789
0.6216 Remote Similarity NPC64176
0.6154 Remote Similarity NPC3649
0.6154 Remote Similarity NPC471327
0.6154 Remote Similarity NPC206088
0.6154 Remote Similarity NPC100879
0.6154 Remote Similarity NPC66577
0.6136 Remote Similarity NPC51086
0.6087 Remote Similarity NPC99746
0.6 Remote Similarity NPC13217
0.6 Remote Similarity NPC213749
0.5952 Remote Similarity NPC282119
0.5926 Remote Similarity NPC477790
0.5882 Remote Similarity NPC469971
0.587 Remote Similarity NPC180409
0.5789 Remote Similarity NPC138325
0.5682 Remote Similarity NPC45727
0.5682 Remote Similarity NPC239039
0.5682 Remote Similarity NPC48638
0.5682 Remote Similarity NPC266298
0.5641 Remote Similarity NPC34671

  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 NPC201753 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