Structure

Physi-Chem Properties

Molecular Weight:  405.83
Volume:  243.385
LogP:  4.832
LogD:  4.32
LogS:  -6.217
# Rotatable Bonds:  2
TPSA:  0.0
# H-Bond Aceptor:  0
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.549
Synthetic Accessibility Score:  4.7
Fsp3:  0.8
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:  -4.49
MDCK Permeability:  1.9313161828904413e-05
Pgp-inhibitor:  0.002
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.044
20% Bioavailability (F20%):  0.189
30% Bioavailability (F30%):  0.031

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.756
Plasma Protein Binding (PPB):  98.04659271240234%
Volume Distribution (VD):  2.712
Pgp-substrate:  3.4677834510803223%

ADMET: Metabolism

CYP1A2-inhibitor:  0.879
CYP1A2-substrate:  0.925
CYP2C19-inhibitor:  0.8
CYP2C19-substrate:  0.902
CYP2C9-inhibitor:  0.926
CYP2C9-substrate:  0.953
CYP2D6-inhibitor:  0.008
CYP2D6-substrate:  0.894
CYP3A4-inhibitor:  0.14
CYP3A4-substrate:  0.613

ADMET: Excretion

Clearance (CL):  2.029
Half-life (T1/2):  0.029

ADMET: Toxicity

hERG Blockers:  0.003
Human Hepatotoxicity (H-HT):  0.237
Drug-inuced Liver Injury (DILI):  0.823
AMES Toxicity:  0.249
Rat Oral Acute Toxicity:  0.748
Maximum Recommended Daily Dose:  0.869
Skin Sensitization:  0.368
Carcinogencity:  0.767
Eye Corrosion:  0.967
Eye Irritation:  0.861
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: NPC469971

Natural Product ID:  NPC469971
Common Name*:   2,4-Dibromo-1-(2-Bromo-1-Chloroethyl)-3,3-Dimethylcyclohexene
IUPAC Name:   2,4-dibromo-1-(2-bromo-1-chloroethyl)-3,3-dimethylcyclohexene
Synonyms:  
Standard InCHIKey:  CYZCHHADPFRZIU-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C10H14Br3Cl/c1-10(2)8(12)4-3-6(9(10)13)7(14)5-11/h7-8H,3-5H2,1-2H3
SMILES:  BrCC(C1=C(Br)C(C(CC1)Br)(C)C)Cl
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL140233
PubChem CID:   10476601
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000267] Organohalogen compounds
      • [CHEMONTID:0002868] Vinyl halides
        • [CHEMONTID:0002864] Vinyl bromides

*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 = 21900.0 nM PMID[534834]
NPT3804 Cell Line Human Tumor Cell lines TGI = 45700.0 nM PMID[534834]
NPT3804 Cell Line Human Tumor Cell lines LC50 = 93300.0 nM PMID[534834]

☑ 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 NPC469971 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
0.7679 Intermediate Similarity NPC469962
0.7679 Intermediate Similarity NPC469967
0.72 Intermediate Similarity NPC180409
0.7059 Intermediate Similarity NPC99746
0.7 Intermediate Similarity NPC107849
0.6863 Remote Similarity NPC474773
0.68 Remote Similarity NPC51086
0.6774 Remote Similarity NPC110214
0.66 Remote Similarity NPC101811
0.66 Remote Similarity NPC55269
0.6557 Remote Similarity NPC183031
0.6538 Remote Similarity NPC160588
0.6364 Remote Similarity NPC159420
0.6346 Remote Similarity NPC259702
0.6346 Remote Similarity NPC469969
0.5909 Remote Similarity NPC52966
0.5882 Remote Similarity NPC201753

  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 NPC469971 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