Structure

Physi-Chem Properties

Molecular Weight:  171.85
Volume:  64.42
LogP:  1.72
LogD:  1.524
LogS:  -1.269
# Rotatable Bonds:  0
TPSA:  0.0
# H-Bond Aceptor:  0
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.49
Synthetic Accessibility Score:  3.48
Fsp3:  1.0
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.322
MDCK Permeability:  2.655126081663184e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.04
20% Bioavailability (F20%):  0.022
30% Bioavailability (F30%):  0.784

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.963
Plasma Protein Binding (PPB):  52.954410552978516%
Volume Distribution (VD):  1.652
Pgp-substrate:  61.79180908203125%

ADMET: Metabolism

CYP1A2-inhibitor:  0.563
CYP1A2-substrate:  0.763
CYP2C19-inhibitor:  0.094
CYP2C19-substrate:  0.894
CYP2C9-inhibitor:  0.019
CYP2C9-substrate:  0.689
CYP2D6-inhibitor:  0.009
CYP2D6-substrate:  0.591
CYP3A4-inhibitor:  0.021
CYP3A4-substrate:  0.269

ADMET: Excretion

Clearance (CL):  1.368
Half-life (T1/2):  0.732

ADMET: Toxicity

hERG Blockers:  0.021
Human Hepatotoxicity (H-HT):  0.193
Drug-inuced Liver Injury (DILI):  0.952
AMES Toxicity:  0.906
Rat Oral Acute Toxicity:  0.193
Maximum Recommended Daily Dose:  0.039
Skin Sensitization:  0.913
Carcinogencity:  0.894
Eye Corrosion:  0.961
Eye Irritation:  0.994
Respiratory Toxicity:  0.982

Download Data

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

  Natural Product: NPC100002

Natural Product ID:  NPC100002
Common Name*:   Dibromomethane
IUPAC Name:   dibromomethane
Synonyms:  
Standard InCHIKey:  FJBFPHVGVWTDIP-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/CH2Br2/c2-1-3/h1H2
SMILES:  C(Br)Br
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1229889
PubChem CID:   3024
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000267] Organohalogen compounds
      • [CHEMONTID:0002867] Alkyl halides
        • [CHEMONTID:0004157] Halomethanes

*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
NPO17890 Platycarphella carlinoides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13323 Uncaria quadrangularis Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14808 Ainsliaea dissecta Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16800 Pulicaria dysenterica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]

☑ 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
NPT2 Others Unspecified Potency n.a. 12680 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 56639.3 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 28.1 nM PubChem BioAssay data set

☑ 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 NPC100002 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
1.0 High Similarity NPC78825
0.625 Remote Similarity NPC119914

  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 NPC100002 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