Tmic
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Record Information
Version2.0
Creation Date2009-06-17 21:02:15 UTC
Update Date2014-12-24 20:22:55 UTC
Accession NumberT3D0890
Identification
Common NamePendimethalin
ClassSmall Molecule
DescriptionPendimethalin is a preemergent herbicide used to prevent crabgrass from germinating. Pendimethalin was included in a biocide ban proposed by the Swedish Chemicals Agency and approved by the European Parliament in January 13, 2009 (6).
Compound Type
  • Amine
  • Aromatic Hydrocarbon
  • Herbicide
  • Household Toxin
  • Lachrymator
  • Organic Compound
  • Organochloride
  • Pesticide
  • Synthetic Compound
Chemical Structure
Thumb
Synonyms
Synonym
3,4-Dimethyl-2,6-dinitro-N-(1-ethylpropyl)aniline
Accotab
Caswell No. 454BB
Go-go-san
Herbadox
Herbodox
N-(1-ethylpropyl)-2,6-dinitro-3,4-xylidine
N-(1-Ethylpropyl)-3,4-dimethyl-2,6-dinitroaniline
N-(1-Ethylpropyl)-3,4-dimethyl-2,6-dinitrobenzenamine
N-(3-Pentyl)-3,4-dimethyl-2,6-dinitroaniline
Pay-off
Pendimethaline
Penoxalin
Penoxyn
Pentagon
Phenoxalin
Pre-M 60DG
Prowl
Prowl 3.3E
Prowl 4E
Sipaxol
Southern weed grass control
Stomp
Stomp 330D
Stomp 330E
Stomp h
SWGC
Tendimethalin
Wax up
Way up
Wayup
Chemical FormulaC13H19N3O4
Average Molecular Mass281.308 g/mol
Monoisotopic Mass281.138 g/mol
CAS Registry Number40487-42-1
IUPAC Name3,4-dimethyl-2,6-dinitro-N-(pentan-3-yl)aniline
Traditional Nameway up
SMILESCCC(CC)NC1=C(C=C(C)C(C)=C1[N+]([O-])=O)[N+]([O-])=O
InChI IdentifierInChI=1S/C13H19N3O4/c1-5-10(6-2)14-12-11(15(17)18)7-8(3)9(4)13(12)16(19)20/h7,10,14H,5-6H2,1-4H3
InChI KeyInChIKey=CHIFOSRWCNZCFN-UHFFFAOYSA-N
Chemical Taxonomy
Description belongs to the class of organic compounds known as dinitroanilines. These are organic compounds containing an aniline moiety, which is substituted at 2 positions by a nitro group.
KingdomOrganic compounds
Super ClassBenzenoids
ClassBenzene and substituted derivatives
Sub ClassAniline and substituted anilines
Direct ParentDinitroanilines
Alternative Parents
Substituents
  • Dinitroaniline
  • Nitrobenzene
  • Nitrotoluene
  • Phenylalkylamine
  • Nitroaromatic compound
  • Xylene
  • O-xylene
  • Secondary aliphatic/aromatic amine
  • C-nitro compound
  • Organic nitro compound
  • Organic oxoazanium
  • Secondary amine
  • Organic 1,3-dipolar compound
  • Propargyl-type 1,3-dipolar organic compound
  • Allyl-type 1,3-dipolar organic compound
  • Organopnictogen compound
  • Organic zwitterion
  • Amine
  • Organonitrogen compound
  • Organic oxygen compound
  • Hydrocarbon derivative
  • Organic nitrogen compound
  • Organic oxide
  • Aromatic homomonocyclic compound
Molecular FrameworkAromatic homomonocyclic 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
AppearanceOrange-yellow crystals (4).
Experimental Properties
PropertyValue
Melting Point56°C
Boiling PointNot Available
Solubility0.0003 mg/mL at 20°C [TOMLIN,C (1997)]
LogPNot Available
Predicted Properties
PropertyValueSource
Water Solubility0.032 g/LALOGPS
logP4.36ALOGPS
logP4.82ChemAxon
logS-3.9ALOGPS
pKa (Strongest Acidic)10.94ChemAxon
pKa (Strongest Basic)-1ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area103.67 ŲChemAxon
Rotatable Bond Count6ChemAxon
Refractivity79.2 m³·mol⁻¹ChemAxon
Polarizability28.32 ųChemAxon
Number of Rings1ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash Key
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-001i-1090000000-b42ada96d131b12ec1cfView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-05fr-1090000000-64c713bc372170357a7eView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-00di-9020000000-a1d45e05bba4c7623a01View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-001i-0090000000-8662412b6faad754679aView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-001i-0090000000-1f45ad080ef2f91e7c2aView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-00di-4190000000-f588e443de7d72c5fea9View in MoNA
MSMass Spectrum (Electron Ionization)splash10-0udi-6970000000-c257c6cd513d6c161144View in MoNA
Toxicity Profile
Route of ExposureInhalation (8) ; oral (8) ; dermal (8).
Mechanism of ToxicityInhibits cell division and cell elongation (6).
MetabolismPendimethalin which does become absorbed into the bloodstream from the gastrointestinal tract is rapidly metabolized in the kidneys and liver and is then excreted in the urine. The major metabolic routes of pendimethalin involved hydroxylation of the 4-methyl and the N-1-ethyl group, oxidation of these alkyl groups to carboxylic acids, nitro reduction, cyclization, and conjugation based on the identification of the 12 metabolites in urine and tissues. Products of cyclization reactions giving rise to methylbenzimidazole carboxylic acids were unique to liver and kidney (2, 7).
Toxicity ValuesLD50: >5000 mg/kg (Oral, Rat) (7) LD50: >5000 mg/kg (Dermal, Rabbit) (7)
Lethal DoseNot Available
Carcinogenicity (IARC Classification)No indication of carcinogenicity to humans (not listed by IARC).
Uses/SourcesPendimethalin is a selective herbicide used to control most annual grasses and certain broadleaf weeds in field corn, potatoes, rice, cotton, soybeans, tobacco, peanuts and sunflowers. It is used both preemergence, that is before weed seeds have sprouted, and early postemergence (1).
Minimum Risk LevelNot Available
Health EffectsPoisoning can produce an allergic hypersensitivity dermatitis or asthma with bronchospasm and wheezing with chronic exposure. Moreover, abnormalities of the hematopoietic system, liver, and kidneys may follow (3).
SymptomsSymptoms include headache, dizziness, weakness, and nausea. Irritation of the eyes, skin, and respiratory tract, burns of the esophagus or gastrointestinal tract may follow, depending on the route of exposure (3).
TreatmentIn case of oral exposure, administer charcoal as a slurry. Consider gastric lavage after ingestion of a potentially life-threatening amount of poison if it can be performed soon after ingestion (generally within 1 hour). Protect airway by placement in Trendelenburg and left lateral decubitus position or by endotracheal intubation. Control any seizures first. In case of inhalation, move patient to fresh air, monitor for respiratory distress. If the exposure occurred via eye contact, irrigate exposed eyes with copious amounts of room temperature water for at least 15 minutes. Remove contaminated clothing and wash exposed area thoroughly with soap and water if the exposure occurred via dermal contact. (3)
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
DrugBank IDNot Available
HMDB IDNot Available
PubChem Compound ID38479
ChEMBL IDCHEMBL1256630
ChemSpider ID35265
KEGG IDC11019
UniProt IDNot Available
OMIM ID
ChEBI IDNot Available
BioCyc IDNot Available
CTD IDC030856
Stitch IDPendimethalin
PDB IDNot Available
ACToR ID6504
Wikipedia LinkNot Available
References
Synthesis ReferenceNot Available
MSDST3D0890.pdf
General References
  1. Bychkov PV, Shekhovtsova TN, Milaeva ER: Inhibition of horse liver alcohol dehydrogenase by methyltin compounds. Bioinorg Chem Appl. 2005:191-9. doi: 10.1155/BCA.2005.191. [18365099 ]
  2. Matsumoto M, Kojima T, Togashi H, Mori K, Ohashi S, Ueno K, Yoshioka M: Differential characteristics of endogenous serotonin-mediated synaptic transmission in the hippocampal CA1 and CA3 fields of anaesthetized rats. Naunyn Schmiedebergs Arch Pharmacol. 2002 Dec;366(6):570-7. Epub 2002 Oct 1. [12444499 ]
  3. Rumack BH (2009). POISINDEX(R) Information System. Englewood, CO: Micromedex, Inc. CCIS Volume 141, edition expires Aug, 2009.
  4. Hartley D and Kidd H (1987). The Agrochemicals Handbook. 2nd ed. Lechworth, Herts, England: The Royal Society of Chemistry.
  5. Zulalian, J. 1990. Study of the absorption, excretion, metabolism, and residues in tissues of rats treated with carbon-14-labeled pendimethalin, Prowl herbicide. J. Agric. Food Chem. 38: 1743-54.
  6. Wikipedia. Pendimethalin. Last Updated 14 June 2009. [Link]
  7. Extension Toxicology Network (1993). [Link]
  8. ATSDR - Agency for Toxic Substances and Disease Registry (1992). Toxicological profile for antimony. U.S. Public Health Service in collaboration with U.S. Environmental Protection Agency (EPA). [Link]
Gene Regulation
Up-Regulated GenesNot Available
Down-Regulated GenesNot Available

Targets

General Function:
Zinc ion binding
Specific Function:
Nuclear hormone receptor. Binds estrogens with an affinity similar to that of ESR1, and activates expression of reporter genes containing estrogen response elements (ERE) in an estrogen-dependent manner (PubMed:20074560). Isoform beta-cx lacks ligand binding ability and has no or only very low ere binding activity resulting in the loss of ligand-dependent transactivation ability. DNA-binding by ESR1 and ESR2 is rapidly lost at 37 degrees Celsius in the absence of ligand while in the presence of 17 beta-estradiol and 4-hydroxy-tamoxifen loss in DNA-binding at elevated temperature is more gradual.
Gene Name:
ESR2
Uniprot ID:
Q92731
Molecular Weight:
59215.765 Da
Binding/Activity Constants
TypeValueAssay TypeAssay Source
AC509.56 uMOT_ER_ERbERb_0480Odyssey Thera
References
  1. Taccone-Gallucci M, Manca-di-Villahermosa S, Battistini L, Stuffler RG, Tedesco M, Maccarrone M: N-3 PUFAs reduce oxidative stress in ESRD patients on maintenance HD by inhibiting 5-lipoxygenase activity. Kidney Int. 2006 Apr;69(8):1450-4. [16531984 ]
  2. 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 ]
  3. Luft S, Milki E, Glustrom E, Ampiah-Bonney R, O'Hara P. Binding of Organochloride and Pyrethroid Pesticides To Estrogen Receptors α and β: A Fluorescence Polarization Assay. Biophysical Journal 2009;96(3):444a.
General Function:
Zinc ion binding
Specific Function:
Nuclear hormone receptor. The steroid hormones and their receptors are involved in the regulation of eukaryotic gene expression and affect cellular proliferation and differentiation in target tissues. Ligand-dependent nuclear transactivation involves either direct homodimer binding to a palindromic estrogen response element (ERE) sequence or association with other DNA-binding transcription factors, such as AP-1/c-Jun, c-Fos, ATF-2, Sp1 and Sp3, to mediate ERE-independent signaling. Ligand binding induces a conformational change allowing subsequent or combinatorial association with multiprotein coactivator complexes through LXXLL motifs of their respective components. Mutual transrepression occurs between the estrogen receptor (ER) and NF-kappa-B in a cell-type specific manner. Decreases NF-kappa-B DNA-binding activity and inhibits NF-kappa-B-mediated transcription from the IL6 promoter and displace RELA/p65 and associated coregulators from the promoter. Recruited to the NF-kappa-B response element of the CCL2 and IL8 promoters and can displace CREBBP. Present with NF-kappa-B components RELA/p65 and NFKB1/p50 on ERE sequences. Can also act synergistically with NF-kappa-B to activate transcription involving respective recruitment adjacent response elements; the function involves CREBBP. Can activate the transcriptional activity of TFF1. Also mediates membrane-initiated estrogen signaling involving various kinase cascades. Isoform 3 is involved in activation of NOS3 and endothelial nitric oxide production. Isoforms lacking one or several functional domains are thought to modulate transcriptional activity by competitive ligand or DNA binding and/or heterodimerization with the full length receptor. Essential for MTA1-mediated transcriptional regulation of BRCA1 and BCAS3. Isoform 3 can bind to ERE and inhibit isoform 1.
Gene Name:
ESR1
Uniprot ID:
P03372
Molecular Weight:
66215.45 Da
References
  1. Taccone-Gallucci M, Manca-di-Villahermosa S, Battistini L, Stuffler RG, Tedesco M, Maccarrone M: N-3 PUFAs reduce oxidative stress in ESRD patients on maintenance HD by inhibiting 5-lipoxygenase activity. Kidney Int. 2006 Apr;69(8):1450-4. [16531984 ]
  2. Luft S, Milki E, Glustrom E, Ampiah-Bonney R, O'Hara P. Binding of Organochloride and Pyrethroid Pesticides To Estrogen Receptors α and β: A Fluorescence Polarization Assay. Biophysical Journal 2009;96(3):444a.
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
References
  1. Kojima H, Sata F, Takeuchi S, Sueyoshi T, Nagai T: Comparative study of human and mouse pregnane X receptor agonistic activity in 200 pesticides using in vitro reporter gene assays. Toxicology. 2011 Feb 27;280(3):77-87. doi: 10.1016/j.tox.2010.11.008. Epub 2010 Nov 27. [21115097 ]
General Function:
Temperature-gated cation channel activity
Specific Function:
Receptor-activated non-selective cation channel involved in detection of pain and possibly also in cold perception and inner ear function (PubMed:25389312, PubMed:25855297). Has a central role in the pain response to endogenous inflammatory mediators and to a diverse array of volatile irritants, such as mustard oil, cinnamaldehyde, garlic and acrolein, an irritant from tears gas and vehicule exhaust fumes (PubMed:25389312, PubMed:20547126). Is also activated by menthol (in vitro)(PubMed:25389312). Acts also as a ionotropic cannabinoid receptor by being activated by delta(9)-tetrahydrocannabinol (THC), the psychoactive component of marijuana (PubMed:25389312). May be a component for the mechanosensitive transduction channel of hair cells in inner ear, thereby participating in the perception of sounds. Probably operated by a phosphatidylinositol second messenger system (By similarity).
Gene Name:
TRPA1
Uniprot ID:
O75762
Molecular Weight:
127499.88 Da
References
  1. Nilius B, Prenen J, Owsianik G: Irritating channels: the case of TRPA1. J Physiol. 2011 Apr 1;589(Pt 7):1543-9. doi: 10.1113/jphysiol.2010.200717. Epub 2010 Nov 15. [21078588 ]
General Function:
Serine-type endopeptidase activity
Specific Function:
Specifically cleaves the zymogen plasminogen to form the active enzyme plasmin.
Gene Name:
PLAU
Uniprot ID:
P00749
Molecular Weight:
48507.09 Da
Binding/Activity Constants
TypeValueAssay TypeAssay Source
AC501.48 uMBSK_BE3C_uPA_downBioSeek
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 ]
General Function:
Oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen
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. Most active in catalyzing 2-hydroxylation. Caffeine is metabolized primarily by cytochrome CYP1A2 in the liver through an initial N3-demethylation. Also acts in the metabolism of aflatoxin B1 and acetaminophen. Participates in the bioactivation of carcinogenic aromatic and heterocyclic amines. Catalizes the N-hydroxylation of heterocyclic amines and the O-deethylation of phenacetin.
Gene Name:
CYP1A2
Uniprot ID:
P05177
Molecular Weight:
58293.76 Da
Binding/Activity Constants
TypeValueAssay TypeAssay Source
AC505.46 uMCLZD_CYP1A2_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 ]
General Function:
Vitamin d 24-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.
Gene Name:
CYP1A1
Uniprot ID:
P04798
Molecular Weight:
58164.815 Da
Binding/Activity Constants
TypeValueAssay TypeAssay Source
AC505.75 uMCLZD_CYP1A1_24CellzDirect
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 ]
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
AC507.49 uMCLZD_CYP2B6_6CellzDirect
AC509.25 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 ]