Structure

Physi-Chem Properties

Molecular Weight:  93.98
Volume:  73.303
LogP:  0.221
LogD:  0.959
LogS:  0.599
# 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:  0.475
Synthetic Accessibility Score:  2.26
Fsp3:  0.5
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  2
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.653
MDCK Permeability:  0.0012674254830926657
Pgp-inhibitor:  0.0
Pgp-substrate:  0.002
Human Intestinal Absorption (HIA):  0.005
20% Bioavailability (F20%):  0.002
30% Bioavailability (F30%):  0.006

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.842
Plasma Protein Binding (PPB):  33.906768798828125%
Volume Distribution (VD):  0.254
Pgp-substrate:  67.81040954589844%

ADMET: Metabolism

CYP1A2-inhibitor:  0.021
CYP1A2-substrate:  0.114
CYP2C19-inhibitor:  0.028
CYP2C19-substrate:  0.064
CYP2C9-inhibitor:  0.007
CYP2C9-substrate:  0.906
CYP2D6-inhibitor:  0.012
CYP2D6-substrate:  0.237
CYP3A4-inhibitor:  0.008
CYP3A4-substrate:  0.045

ADMET: Excretion

Clearance (CL):  7.903
Half-life (T1/2):  0.901

ADMET: Toxicity

hERG Blockers:  0.113
Human Hepatotoxicity (H-HT):  0.052
Drug-inuced Liver Injury (DILI):  0.192
AMES Toxicity:  0.441
Rat Oral Acute Toxicity:  0.965
Maximum Recommended Daily Dose:  0.012
Skin Sensitization:  0.853
Carcinogencity:  0.304
Eye Corrosion:  0.997
Eye Irritation:  0.989
Respiratory Toxicity:  0.983

Download Data

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

  Natural Product: NPC158994

Natural Product ID:  NPC158994
Common Name*:   Chloroacetic Acid
IUPAC Name:   2-chloroacetic acid
Synonyms:   Chloroacetic acid
Standard InCHIKey:  FOCAUTSVDIKZOP-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C2H3ClO2/c3-1-2(4)5/h1H2,(H,4,5)
SMILES:  C(C(=O)O)Cl
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL14090
PubChem CID:   300
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
NPO18714 Rauvolfia verticillata Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18714 Rauvolfia verticillata Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCMID]

☑ 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
NPT152 Individual Protein Nuclear factor erythroid 2-related factor 2 Homo sapiens Potency n.a. 23472.9 nM PubChem BioAssay data set
NPT210 Individual Protein Thyroid stimulating hormone receptor Homo sapiens Potency = 31622.8 nM PMID[537395]
NPT152 Individual Protein Nuclear factor erythroid 2-related factor 2 Homo sapiens Potency n.a. 42163.2 nM PMID[537395]
NPT2 Others Unspecified Potency n.a. 18799.5 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 20920.2 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 59449.1 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 29550.6 nM PubChem BioAssay data set
NPT35 Others n.a. LogP = 0.22 n.a. PMID[537392]
NPT35 Others n.a. LogP = 0.37 n.a. PMID[537392]
NPT35 Others n.a. LogP = -1.92 n.a. PMID[537392]
NPT35 Others n.a. LogP = -1.6 n.a. PMID[537392]
NPT35 Others n.a. LogP = -2.56 n.a. PMID[537392]
NPT35 Others n.a. LogP = -3.14 n.a. PMID[537392]
NPT35 Others n.a. Log PNalk = -3.14 n.a. PMID[537393]
NPT566 Organism Salmonella typhimurium Salmonella enterica subsp. enterica serovar Typhimurium Activity = -1.943 n.a. PMID[537394]
NPT610 Others Molecular identity unknown Potency n.a. 74978.0 nM PMID[537395]

☑ 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 NPC158994 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
0.9167 High Similarity NPC278758
0.75 Intermediate Similarity NPC326511
0.6552 Remote Similarity NPC231957
0.6471 Remote Similarity NPC321569
0.625 Remote Similarity NPC7922
0.625 Remote Similarity NPC68873
0.5769 Remote Similarity NPC328456
0.56 Remote Similarity NPC283245

  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 NPC158994 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
0.8333 Intermediate Similarity NPD7350 Phase 1
0.8333 Intermediate Similarity NPD7349 Approved
0.75 Intermediate Similarity NPD7388 Approved
0.625 Remote Similarity NPD7364 Approved
0.5652 Remote Similarity NPD7362 Approved
0.5652 Remote Similarity NPD47 Approved
0.5652 Remote Similarity NPD50 Approved
0.5652 Remote Similarity NPD49 Approved
0.5652 Remote Similarity NPD48 Approved
0.5652 Remote Similarity NPD7363 Approved
0.5652 Remote Similarity NPD105 Approved
0.5652 Remote Similarity NPD7365 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