Structure

Physi-Chem Properties

Molecular Weight:  78.01
Volume:  64.16
LogP:  -0.713
LogD:  -0.801
LogS:  0.85
# Rotatable Bonds:  1
TPSA:  37.3
# H-Bond Aceptor:  2
# H-Bond Donor:  1
# Rings:  0
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.48
Synthetic Accessibility Score:  2.467
Fsp3:  0.5
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:  -5.417
MDCK Permeability:  0.00016854330897331238
Pgp-inhibitor:  0.001
Pgp-substrate:  0.002
Human Intestinal Absorption (HIA):  0.017
20% Bioavailability (F20%):  0.014
30% Bioavailability (F30%):  0.933

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.854
Plasma Protein Binding (PPB):  23.592742919921875%
Volume Distribution (VD):  0.259
Pgp-substrate:  73.15321350097656%

ADMET: Metabolism

CYP1A2-inhibitor:  0.018
CYP1A2-substrate:  0.097
CYP2C19-inhibitor:  0.03
CYP2C19-substrate:  0.065
CYP2C9-inhibitor:  0.008
CYP2C9-substrate:  0.886
CYP2D6-inhibitor:  0.012
CYP2D6-substrate:  0.262
CYP3A4-inhibitor:  0.009
CYP3A4-substrate:  0.047

ADMET: Excretion

Clearance (CL):  5.72
Half-life (T1/2):  0.755

ADMET: Toxicity

hERG Blockers:  0.005
Human Hepatotoxicity (H-HT):  0.62
Drug-inuced Liver Injury (DILI):  0.166
AMES Toxicity:  0.865
Rat Oral Acute Toxicity:  0.989
Maximum Recommended Daily Dose:  0.092
Skin Sensitization:  0.782
Carcinogencity:  0.953
Eye Corrosion:  0.985
Eye Irritation:  0.991
Respiratory Toxicity:  0.992

Download Data

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

  Natural Product: NPC7922

Natural Product ID:  NPC7922
Common Name*:   Fluoroacetate
IUPAC Name:   2-fluoroacetic acid
Synonyms:   2-Fluoroacetic Acid; Fluoroacetate
Standard InCHIKey:  QEWYKACRFQMRMB-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C2H3FO2/c3-1-2(4)5/h1H2,(H,4,5)
SMILES:  C(C(=O)O)F
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL509273
PubChem CID:   5237
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000265] Carboxylic acids and derivatives
        • [CHEMONTID:0001548] Alpha-halocarboxylic acids and derivatives
          • [CHEMONTID:0003000] Alpha-halocarboxylic acids

*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
NPO8852 Croton jatrophoides Species Euphorbiaceae Eukaryota n.a. n.a. n.a. PMID[15730253]
NPO8852 Croton jatrophoides Species Euphorbiaceae Eukaryota n.a. n.a. n.a. PMID[16792423]
NPO20987 Penicillium janthinellum Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[17555349]
NPO20987 Penicillium janthinellum Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[31668073]
NPO5116 Fagara nitida n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO12706 Dichapetalum cymosum Species Dichapetalaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6767 Bursa pastoris Species Bursidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8852 Croton jatrophoides Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8219 Kielmeyera speciosa Species Calophyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20987 Penicillium janthinellum Species Aspergillaceae 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
NPT106 Individual Protein Peroxisome proliferator-activated receptor delta Homo sapiens Potency n.a. 61682.5 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 68589.6 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 48557.7 nM PubChem BioAssay data set
NPT35 Others n.a. pKa = 2.66 n.a. PMID[477570]
NPT32 Organism Mus musculus Mus musculus LD50 = 100.0 umol.kg-1 PMID[477572]
NPT27 Others Unspecified LD = 2.0 mg kg-1 PMID[477573]
NPT27 Others Unspecified LD = 0.1 mg kg-1 PMID[477573]
NPT27 Others Unspecified LD = 0.05 mg kg-1 PMID[477573]
NPT2 Others Unspecified K = 172.0 nmol/min PMID[477573]
NPT2 Others Unspecified K = 210.0 nmol/min PMID[477573]
NPT25383 SINGLE PROTEIN Maleylacetoacetate isomerase Rattus norvegicus Activity = 3.0 % PMID[477573]

☑ 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 NPC7922 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
0.7895 Intermediate Similarity NPC68873
0.7 Intermediate Similarity NPC283245
0.6818 Remote Similarity NPC181153
0.6522 Remote Similarity NPC102686
0.6522 Remote Similarity NPC307812
0.625 Remote Similarity NPC158994
0.619 Remote Similarity NPC137050
0.6 Remote Similarity NPC165122
0.5909 Remote Similarity NPC37493
0.5909 Remote Similarity NPC301950
0.5769 Remote Similarity NPC3343
0.5769 Remote Similarity NPC278758
0.5769 Remote Similarity NPC149209
0.5769 Remote Similarity NPC286233
0.5769 Remote Similarity NPC259649
0.5769 Remote Similarity NPC230726
0.5769 Remote Similarity NPC314668
0.5652 Remote Similarity NPC260610

  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 NPC7922 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
0.7895 Intermediate Similarity NPD7364 Approved
0.7222 Intermediate Similarity NPD7362 Approved
0.7222 Intermediate Similarity NPD7363 Approved
0.7222 Intermediate Similarity NPD49 Approved
0.7222 Intermediate Similarity NPD7365 Approved
0.7222 Intermediate Similarity NPD47 Approved
0.7222 Intermediate Similarity NPD50 Approved
0.7222 Intermediate Similarity NPD105 Approved
0.7222 Intermediate Similarity NPD48 Approved
0.6818 Remote Similarity NPD8201 Phase 2
0.619 Remote Similarity NPD8200 Phase 2
0.5909 Remote Similarity NPD7356 Approved
0.5909 Remote Similarity NPD7352 Approved
0.5909 Remote Similarity NPD7357 Approved
0.5769 Remote Similarity NPD8189 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