Structure

Physi-Chem Properties

Molecular Weight:  227.84
Volume:  111.319
LogP:  1.588
LogD:  1.195
LogS:  -0.553
# Rotatable Bonds:  1
TPSA:  37.3
# H-Bond Aceptor:  2
# H-Bond Donor:  1
# Rings:  0
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.696
Synthetic Accessibility Score:  3.404
Fsp3:  0.0
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.978
MDCK Permeability:  3.723128975252621e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.326
20% Bioavailability (F20%):  0.883
30% Bioavailability (F30%):  0.996

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.33
Plasma Protein Binding (PPB):  68.73587799072266%
Volume Distribution (VD):  0.363
Pgp-substrate:  43.30477523803711%

ADMET: Metabolism

CYP1A2-inhibitor:  0.056
CYP1A2-substrate:  0.166
CYP2C19-inhibitor:  0.032
CYP2C19-substrate:  0.061
CYP2C9-inhibitor:  0.129
CYP2C9-substrate:  0.326
CYP2D6-inhibitor:  0.035
CYP2D6-substrate:  0.118
CYP3A4-inhibitor:  0.007
CYP3A4-substrate:  0.072

ADMET: Excretion

Clearance (CL):  0.689
Half-life (T1/2):  0.852

ADMET: Toxicity

hERG Blockers:  0.006
Human Hepatotoxicity (H-HT):  0.867
Drug-inuced Liver Injury (DILI):  0.729
AMES Toxicity:  0.967
Rat Oral Acute Toxicity:  0.774
Maximum Recommended Daily Dose:  0.013
Skin Sensitization:  0.961
Carcinogencity:  0.889
Eye Corrosion:  0.978
Eye Irritation:  0.992
Respiratory Toxicity:  0.916

Download Data

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

  Natural Product: NPC280312

Natural Product ID:  NPC280312
Common Name*:   3,3-Dibromoprop-2-Enoic Acid
IUPAC Name:   3,3-dibromoprop-2-enoic acid
Synonyms:  
Standard InCHIKey:  VWWPGQPTCCQNIO-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C3H2Br2O2/c4-2(5)1-3(6)7/h1H,(H,6,7)
SMILES:  BrC(=CC(=O)O)Br
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1521683
PubChem CID:   13250147
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000265] Carboxylic acids and derivatives
        • [CHEMONTID:0004450] Acrylic acids and derivatives

*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
NPT3 Individual Protein Thioredoxin glutathione reductase Schistosoma mansoni Potency = 50118.7 nM PMID[475256]
NPT56 Individual Protein Beta-lactamase AmpC Escherichia coli K-12 Potency = 44668.4 nM PMID[475256]
NPT2 Others Unspecified Potency = 163.6 nM PMID[475256]
NPT2 Others Unspecified Potency n.a. 35481.3 nM PMID[475256]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum Potency n.a. 11689.1 nM PMID[475256]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum Potency n.a. 32.9 nM PMID[475256]
NPT586 Organism Giardia Giardia Potency n.a. 818.0 nM PMID[475256]

☑ 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 NPC280312 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
0.7667 Intermediate Similarity NPC20903
0.6571 Remote Similarity NPC98098
0.6571 Remote Similarity NPC224651
0.6552 Remote Similarity NPC102686
0.6389 Remote Similarity NPC297363
0.6389 Remote Similarity NPC60675
0.6216 Remote Similarity NPC308418
0.6111 Remote Similarity NPC217161
0.6053 Remote Similarity NPC107877
0.5897 Remote Similarity NPC63598
0.5882 Remote Similarity NPC323552
0.575 Remote Similarity NPC298413
0.561 Remote Similarity NPC8270

  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 NPC280312 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
0.7667 Intermediate Similarity NPD8187 Phase 3
0.6571 Remote Similarity NPD8573 Approved

  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