Pyrithiobac-sodium (T3D3917)

IdentificationTaxonomyBiological PropertiesPhysical PropertiesToxicity ProfileSpectraConcentrationsLinksReferencesGene RegulationTargets (7)XML
Targets (7)
Record Information
Version2.0
Creation Date2013-04-25 07:56:54 UTC
Update Date2014-12-24 20:26:34 UTC
Accession NumberT3D3917
Identification
Common NamePyrithiobac-sodium
ClassSmall Molecule
DescriptionPyrithiobac-sodium is a post-emergence herbicide for the control of broad-leaved weeds in cotton and other crops. It has a high aqueous solubility, is non-volatile and, based on its chemical properties, it is very mobile and has high potential to leach to groundwater. It is generally moderately persistent in soil systems but tends to be non-persistent in aquatic systems. It has a low mammalian toxicity but may bioaccumulate.
Compound Type
  • Ester
  • Ether
  • Herbicide
  • Organic Compound
  • Organochloride
  • Pesticide
  • Synthetic Compound
Chemical Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
Synonym
Pyrithiobac sodium
Chemical FormulaC13H10ClN2NaO4S
Average Molecular Mass348.737 g/mol
Monoisotopic Mass347.995 g/mol
CAS Registry Number123343-16-8
IUPAC Namesodium 2-chloro-6-[(4,6-dimethoxypyrimidin-2-yl)sulfanyl]benzoate
Traditional Namesodium 2-chloro-6-[(4,6-dimethoxypyrimidin-2-yl)sulfanyl]benzoate
SMILES[Na+].COC1=CC(OC)=NC(SC2=C(C([O-])=O)C(Cl)=CC=C2)=N1
InChI IdentifierInChI=1S/C13H11ClN2O4S.Na/c1-19-9-6-10(20-2)16-13(15-9)21-8-5-3-4-7(14)11(8)12(17)18;/h3-6H,1-2H3,(H,17,18);/q;+1/p-1
InChI KeyInChIKey=CNILNQMBAHKMFS-UHFFFAOYSA-M
Chemical Taxonomy
Description belongs to the class of organic compounds known as 2-pyrimidinylthiobenzoic acids. These are benzoic acids that carry a 2-thiopyrimidine at the 2-position of the benzene ring.
KingdomOrganic compounds
Super ClassBenzenoids
ClassBenzene and substituted derivatives
Sub ClassBenzoic acids and derivatives
Direct Parent2-pyrimidinylthiobenzoic acids
Alternative Parents
Substituents
  • 2-pyrimidinylthiobenzoic acid
  • Diarylthioether
  • O-sulfanylbenzoic acid
  • O-sulfanylbenzoic acid or derivatives
  • 2-halobenzoic acid or derivatives
  • Halobenzoic acid or derivatives
  • 2-halobenzoic acid
  • Halobenzoic acid
  • Aryl thioether
  • Thiophenol ether
  • 1-carboxy-2-haloaromatic compound
  • Benzoyl
  • Chlorobenzene
  • Halobenzene
  • Alkyl aryl ether
  • Vinylogous thioester
  • Pyrimidine
  • Aryl chloride
  • Aryl halide
  • Heteroaromatic compound
  • Vinylogous halide
  • Carboxylic acid salt
  • Azacycle
  • Organic metal halide
  • Organic alkali metal salt
  • Carboxylic acid
  • Ether
  • Organoheterocyclic compound
  • Monocarboxylic acid or derivatives
  • Thioether
  • Sulfenyl compound
  • Carboxylic acid derivative
  • Organopnictogen compound
  • Organic salt
  • Hydrocarbon derivative
  • Organohalogen compound
  • Organochloride
  • Organonitrogen compound
  • Organooxygen compound
  • Organosulfur compound
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organic zwitterion
  • Organic sodium salt
  • Organic oxide
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Biological Properties
StatusDetected and Not Quantified
OriginExogenous
Cellular Locations
  • Membrane
Biofluid LocationsNot Available
Tissue LocationsNot Available
PathwaysNot Available
ApplicationsNot Available
Biological RolesNot Available
Chemical RolesNot Available
Physical Properties
StateSolid
AppearanceWhite powder.
Experimental Properties
PropertyValue
Melting PointNot Available
Boiling PointNot Available
SolubilityNot Available
LogPNot Available
Predicted Properties
PropertyValueSource
Water Solubility0.044 g/LALOGPS
logP3.36ALOGPS
logP3.89ChemAxon
logS-3.9ALOGPS
pKa (Strongest Acidic)2.21ChemAxon
pKa (Strongest Basic)0.53ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area84.37 ŲChemAxon
Rotatable Bond Count5ChemAxon
Refractivity91.8 m³·mol⁻¹ChemAxon
Polarizability29.86 ųChemAxon
Number of Rings2ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyDeposition DateView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-01ot-0319000000-182d70c8865e27dff8a22019-02-22View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-054w-2329000000-896139ddf5b8748957d62019-02-22View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-053r-9400000000-bde5d067221e3893b6bc2019-02-22View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0005-0069000000-557fbbcc9780f55343352019-02-23View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-052g-3094000000-59897cfb95e4c80acde02019-02-23View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0a4i-9310000000-20153c3f3010116ea1ae2019-02-23View Spectrum
Toxicity Profile
Route of ExposureNot Available
Mechanism of ToxicityNot Available
MetabolismNot Available
Toxicity ValuesNot Available
Lethal DoseNot Available
Carcinogenicity (IARC Classification)No indication of carcinogenicity to humans (not listed by IARC).
Uses/SourcesThis is a man-made compound that is used as a pesticide.
Minimum Risk LevelNot Available
Health EffectsNot Available
SymptomsNot Available
TreatmentNot Available
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
DrugBank IDNot Available
HMDB IDNot Available
PubChem Compound ID23682187
ChEMBL IDNot Available
ChemSpider ID82877
KEGG IDC18805
UniProt IDNot Available
OMIM ID
ChEBI IDNot Available
BioCyc IDNot Available
CTD IDNot Available
Stitch IDNot Available
PDB IDNot Available
ACToR IDNot Available
Wikipedia LinkNot Available
References
Synthesis ReferenceNot Available
MSDST3D3917.pdf
General ReferencesNot Available
Gene Regulation
Up-Regulated GenesNot Available
Down-Regulated GenesNot Available

Targets

Target Details
1. Nuclear receptor subfamily 1 group I member 2
General Function:
Zinc ion binding
Specific Function:
Nuclear receptor that binds and is activated by variety of endogenous and xenobiotic compounds. Transcription factor that activates the transcription of multiple genes involved in the metabolism and secretion of potentially harmful xenobiotics, drugs and endogenous compounds. Activated by the antibiotic rifampicin and various plant metabolites, such as hyperforin, guggulipid, colupulone, and isoflavones. Response to specific ligands is species-specific. Activated by naturally occurring steroids, such as pregnenolone and progesterone. Binds to a response element in the promoters of the CYP3A4 and ABCB1/MDR1 genes.
Gene Name:
NR1I2
Uniprot ID:
O75469
Molecular Weight:
49761.245 Da
Binding/Activity Constants
TypeValueAssay TypeAssay Source
AC500.02 uMNVS_NR_hPXRNovascreen
References
  1. Sipes NS, Martin MT, Kothiya P, Reif DM, Judson RS, Richard AM, Houck KA, Dix DJ, Kavlock RJ, Knudsen TB: Profiling 976 ToxCast chemicals across 331 enzymatic and receptor signaling assays. Chem Res Toxicol. 2013 Jun 17;26(6):878-95. doi: 10.1021/tx400021f. Epub 2013 May 16. [23611293 ]
Target Details
2. Solute carrier organic anion transporter family member 1B1
General Function:
Sodium-independent organic anion transmembrane transporter activity
Specific Function:
Mediates the Na(+)-independent uptake of organic anions such as pravastatin, taurocholate, methotrexate, dehydroepiandrosterone sulfate, 17-beta-glucuronosyl estradiol, estrone sulfate, prostaglandin E2, thromboxane B2, leukotriene C3, leukotriene E4, thyroxine and triiodothyronine. Involved in the clearance of bile acids and organic anions from the liver.
Gene Name:
SLCO1B1
Uniprot ID:
Q9Y6L6
Molecular Weight:
76447.99 Da
Binding/Activity Constants
TypeValueAssay TypeAssay Source
AC500.07 uMCLZD_SLCO1B1_48CellzDirect
AC500.07 uMCLZD_SLCO1B1_48CellzDirect
References
  1. Sipes NS, Martin MT, Kothiya P, Reif DM, Judson RS, Richard AM, Houck KA, Dix DJ, Kavlock RJ, Knudsen TB: Profiling 976 ToxCast chemicals across 331 enzymatic and receptor signaling assays. Chem Res Toxicol. 2013 Jun 17;26(6):878-95. doi: 10.1021/tx400021f. Epub 2013 May 16. [23611293 ]
Target Details
3. Hydroxymethylglutaryl-CoA synthase, mitochondrial
General Function:
Hydroxymethylglutaryl-coa synthase activity
Specific Function:
This enzyme condenses acetyl-CoA with acetoacetyl-CoA to form HMG-CoA, which is the substrate for HMG-CoA reductase.
Gene Name:
HMGCS2
Uniprot ID:
P54868
Molecular Weight:
56634.915 Da
Binding/Activity Constants
TypeValueAssay TypeAssay Source
AC500.09 uMCLZD_HMGCS2_48CellzDirect
AC505.13 uMCLZD_HMGCS2_24CellzDirect
AC500.09 uMCLZD_HMGCS2_48CellzDirect
References
  1. Sipes NS, Martin MT, Kothiya P, Reif DM, Judson RS, Richard AM, Houck KA, Dix DJ, Kavlock RJ, Knudsen TB: Profiling 976 ToxCast chemicals across 331 enzymatic and receptor signaling assays. Chem Res Toxicol. 2013 Jun 17;26(6):878-95. doi: 10.1021/tx400021f. Epub 2013 May 16. [23611293 ]
Target Details
4. Cytochrome P450 2B6
General Function:
Steroid hydroxylase activity
Specific Function:
Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It oxidizes a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics. Acts as a 1,4-cineole 2-exo-monooxygenase.
Gene Name:
CYP2B6
Uniprot ID:
P20813
Molecular Weight:
56277.81 Da
Binding/Activity Constants
TypeValueAssay TypeAssay Source
AC500.20 uMCLZD_CYP2B6_48CellzDirect
AC500.20 uMCLZD_CYP2B6_48CellzDirect
References
  1. Sipes NS, Martin MT, Kothiya P, Reif DM, Judson RS, Richard AM, Houck KA, Dix DJ, Kavlock RJ, Knudsen TB: Profiling 976 ToxCast chemicals across 331 enzymatic and receptor signaling assays. Chem Res Toxicol. 2013 Jun 17;26(6):878-95. doi: 10.1021/tx400021f. Epub 2013 May 16. [23611293 ]
Target Details
5. ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1
General Function:
Transferase activity
Specific Function:
Synthesizes the second messagers cyclic ADP-ribose and nicotinate-adenine dinucleotide phosphate, the former a second messenger for glucose-induced insulin secretion. Also has cADPr hydrolase activity. Also moonlights as a receptor in cells of the immune system.
Gene Name:
CD38
Uniprot ID:
P28907
Molecular Weight:
34328.145 Da
Binding/Activity Constants
TypeValueAssay TypeAssay Source
AC501.48 uMBSK_SAg_CD38_upBioSeek
References
  1. Sipes NS, Martin MT, Kothiya P, Reif DM, Judson RS, Richard AM, Houck KA, Dix DJ, Kavlock RJ, Knudsen TB: Profiling 976 ToxCast chemicals across 331 enzymatic and receptor signaling assays. Chem Res Toxicol. 2013 Jun 17;26(6):878-95. doi: 10.1021/tx400021f. Epub 2013 May 16. [23611293 ]
Target Details
6. Vascular cell adhesion protein 1
General Function:
Primary amine oxidase activity
Specific Function:
Important in cell-cell recognition. Appears to function in leukocyte-endothelial cell adhesion. Interacts with integrin alpha-4/beta-1 (ITGA4/ITGB1) on leukocytes, and mediates both adhesion and signal transduction. The VCAM1/ITGA4/ITGB1 interaction may play a pathophysiologic role both in immune responses and in leukocyte emigration to sites of inflammation.
Gene Name:
VCAM1
Uniprot ID:
P19320
Molecular Weight:
81275.43 Da
Binding/Activity Constants
TypeValueAssay TypeAssay Source
AC501.48 uMBSK_hDFCGF_VCAM1_upBioSeek
References
  1. Sipes NS, Martin MT, Kothiya P, Reif DM, Judson RS, Richard AM, Houck KA, Dix DJ, Kavlock RJ, Knudsen TB: Profiling 976 ToxCast chemicals across 331 enzymatic and receptor signaling assays. Chem Res Toxicol. 2013 Jun 17;26(6):878-95. doi: 10.1021/tx400021f. Epub 2013 May 16. [23611293 ]
Target Details
7. Bile salt sulfotransferase
General Function:
Sulfotransferase activity
Specific Function:
Sulfotransferase that utilizes 3'-phospho-5'-adenylyl sulfate (PAPS) as sulfonate donor to catalyze the sulfonation of steroids and bile acids in the liver and adrenal glands.
Gene Name:
SULT2A1
Uniprot ID:
Q06520
Molecular Weight:
33779.57 Da
Binding/Activity Constants
TypeValueAssay TypeAssay Source
AC504.71 uMCLZD_SULT2A1_48CellzDirect
References
  1. Sipes NS, Martin MT, Kothiya P, Reif DM, Judson RS, Richard AM, Houck KA, Dix DJ, Kavlock RJ, Knudsen TB: Profiling 976 ToxCast chemicals across 331 enzymatic and receptor signaling assays. Chem Res Toxicol. 2013 Jun 17;26(6):878-95. doi: 10.1021/tx400021f. Epub 2013 May 16. [23611293 ]