trans-Diamminedinitro-palladium(II) (T3D1588)

IdentificationTaxonomyBiological PropertiesPhysical PropertiesToxicity ProfileSpectraConcentrationsLinksReferencesGene RegulationTargets (6)XML
Targets (6)
Record Information
Version2.0
Creation Date2009-06-19 21:59:00 UTC
Update Date2014-12-24 20:24:15 UTC
Accession NumberT3D1588
Identification
Common Nametrans-Diamminedinitro-palladium(II)
ClassSmall Molecule
Descriptiontrans- Diamminedinitro-palladium(II) is a chemical compound of palladium. Palladium is a chemical element with the chemical symbol Pd and an atomic number of 46. It is found as a free metal alloyed with gold and other platinum group metals and in the rare minerals cooperite and polarite. (2)
Compound Type
  • Amine
  • Industrial/Workplace Toxin
  • Inorganic Compound
  • Nitrite
  • Organic Compound
  • Organometallic
  • Palladium Compound
  • Synthetic Compound
Chemical Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
Synonym
Diamminebis(nitrito-o)palladium
Dinitritodiamminepalladium (II)
Chemical FormulaH8N4O4Pd
Average Molecular Mass234.510 g/mol
Monoisotopic Mass233.958 g/mol
CAS Registry Number28068-05-5
IUPAC Namebis(nitrous acid) diamine palladium
Traditional Namebis(nitrous acid) diamine palladium
SMILESN.N.[Pd].ON=O.ON=O
InChI IdentifierInChI=1S/2HNO2.2H3N.Pd/c2*2-1-3;;;/h2*(H,2,3);2*1H3;
InChI KeyInChIKey=PTOOLXWNOYYJDB-UHFFFAOYSA-N
Chemical Taxonomy
Description belongs to the class of inorganic compounds known as transition metal nitrites. These are inorganic compounds in which the largest oxoanion is nitrite, and in which the heaviest atom not in an oxoanion is a transition metal.
KingdomInorganic compounds
Super ClassMixed metal/non-metal compounds
ClassTransition metal oxoanionic compounds
Sub ClassTransition metal nitrites
Direct ParentTransition metal nitrites
Alternative Parents
Substituents
  • Transition metal nitrite
  • Inorganic nitrite
  • Inorganic oxide
  • Inorganic salt
Molecular FrameworkNot Available
External DescriptorsNot Available
Biological Properties
StatusDetected and Not Quantified
OriginExogenous
Cellular Locations
  • Cytoplasm
  • Extracellular
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
logP0.17ChemAxon
pKa (Strongest Acidic)3.32ChemAxon
pKa (Strongest Basic)-3.5ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area49.66 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity8.72 m³·mol⁻¹ChemAxon
Polarizability2.81 ųChemAxon
Number of Rings0ChemAxon
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, Positivesplash10-001i-0090000000-4ee38c66498439f601ce2016-08-01View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-001i-0090000000-4ee38c66498439f601ce2016-08-01View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-001i-0090000000-4ee38c66498439f601ce2016-08-01View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-001i-0090000000-7f3e9d928bcfae3007b82016-08-03View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-001i-0090000000-7f3e9d928bcfae3007b82016-08-03View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-001i-0090000000-7f3e9d928bcfae3007b82016-08-03View Spectrum
Toxicity Profile
Route of ExposureNot Available
Mechanism of ToxicityDue to their ability to form strong complexes with both inorganic and organic ligands, palladium ions can disturb cellular equilibria, replace other essential ions, and interact with functional groups of macromolecules, such as proteins or DNA. Palladium complexes binding to DNA and RNA leads to strand breakage. Palladium ions are able to inhibit most major cellular functions, including DNA and RNA synthesis. Palladium compounds have been shown to bind to and inhibit various enzymes, including creatine kinase and prolyl hydroxylase. (3)
MetabolismPalladium may be absorbed through oral, dermal, and inhalation exposure. Once in the body it distributes to the kidney, liver, spleen, lymph nodes, adrenal gland, lung and bone. Palladium's ability to form complexes allows it the bind to amino acids, proteins, DNA, and other macromolecules. Palladium and its metabolites are excreted in the urine and faeces. (1)
Toxicity ValuesNot Available
Lethal DoseNot Available
Carcinogenicity (IARC Classification)No indication of carcinogenicity to humans (not listed by IARC).
Uses/SourcesNot Available
Minimum Risk LevelNot Available
Health EffectsContact with palladium may cause palladium sensitivity and allergy. Animal studies have shown that palladium may damage the liver and kidney. (3)
SymptomsSkin contact with palladium may cause contact dermatitis, erythema, and oedema. (3)
TreatmentEYES: irrigate opened eyes for several minutes under running water. INGESTION: do not induce vomiting. Rinse mouth with water (never give anything by mouth to an unconscious person). Seek immediate medical advice. SKIN: should be treated immediately by rinsing the affected parts in cold running water for at least 15 minutes, followed by thorough washing with soap and water. If necessary, the person should shower and change contaminated clothing and shoes, and then must seek medical attention. INHALATION: supply fresh air. If required provide artificial respiration.
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
DrugBank IDNot Available
HMDB IDNot Available
PubChem Compound ID168754
ChEMBL IDNot Available
ChemSpider IDNot Available
KEGG IDNot Available
UniProt IDNot Available
OMIM ID
ChEBI IDNot Available
BioCyc IDNot Available
CTD IDNot Available
Stitch IDDiamminedinitro-palladium(II), trans-
PDB IDNot Available
ACToR IDNot Available
Wikipedia LinkNot Available
References
Synthesis ReferenceNot Available
MSDSNot Available
General References
  1. Smith DR, Kahng MW, Quintanilla-Vega B, Fowler BA: High-affinity renal lead-binding proteins in environmentally-exposed humans. Chem Biol Interact. 1998 Aug 14;115(1):39-52. [9817074 ]
  2. Wikipedia. Palladium. Last Updated 14 June 2009. [Link]
  3. International Programme on Chemical Safety (IPCS) INCHEM (2002). Environmental Health Criteria for Palladium. [Link]
Gene Regulation
Up-Regulated GenesNot Available
Down-Regulated GenesNot Available

Targets

Target Details
1. Creatine kinase M-type
General Function:
Creatine kinase activity
Specific Function:
Reversibly catalyzes the transfer of phosphate between ATP and various phosphogens (e.g. creatine phosphate). Creatine kinase isoenzymes play a central role in energy transduction in tissues with large, fluctuating energy demands, such as skeletal muscle, heart, brain and spermatozoa.
Gene Name:
CKM
Uniprot ID:
P06732
Molecular Weight:
43100.91 Da
References
  1. Liu TZ, Khayam-Bashi H, Bhatnagar RS: Inhibition of creatine kinase activity and alterations in electrophoretic mobility by palladium ions. J Environ Pathol Toxicol. 1979 Jan-Feb;2(3):907-16. [422942 ]
Target Details
2. Prolyl 4-hydroxylase subunit alpha-1
General Function:
Procollagen-proline 4-dioxygenase activity
Specific Function:
Catalyzes the post-translational formation of 4-hydroxyproline in -Xaa-Pro-Gly- sequences in collagens and other proteins.
Gene Name:
P4HA1
Uniprot ID:
P13674
Molecular Weight:
61048.775 Da
References
  1. Rapaka RS, Sorensen KR, Lee SD, Bhatnagar RS: Inhibition of hydroxyproline synthesis by palladium ions. Biochim Biophys Acta. 1976 Mar 11;429(1):63-71. [177068 ]
Target Details
3. Prolyl 4-hydroxylase subunit alpha-2
General Function:
Procollagen-proline 4-dioxygenase activity
Specific Function:
Catalyzes the post-translational formation of 4-hydroxyproline in -Xaa-Pro-Gly- sequences in collagens and other proteins.
Gene Name:
P4HA2
Uniprot ID:
O15460
Molecular Weight:
60901.42 Da
References
  1. Rapaka RS, Sorensen KR, Lee SD, Bhatnagar RS: Inhibition of hydroxyproline synthesis by palladium ions. Biochim Biophys Acta. 1976 Mar 11;429(1):63-71. [177068 ]
Target Details
4. Prolyl 4-hydroxylase subunit alpha-3
General Function:
Procollagen-proline 4-dioxygenase activity
Specific Function:
Catalyzes the post-translational formation of 4-hydroxyproline in -Xaa-Pro-Gly- sequences in collagens and other proteins.
Gene Name:
P4HA3
Uniprot ID:
Q7Z4N8
Molecular Weight:
61125.675 Da
References
  1. Rapaka RS, Sorensen KR, Lee SD, Bhatnagar RS: Inhibition of hydroxyproline synthesis by palladium ions. Biochim Biophys Acta. 1976 Mar 11;429(1):63-71. [177068 ]
Target Details
5. Transmembrane prolyl 4-hydroxylase
General Function:
Oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors
Specific Function:
Catalyzes the post-translational formation of 4-hydroxyproline in hypoxia-inducible factor (HIF) alpha proteins. Hydroxylates HIF1A at 'Pro-402' and 'Pro-564'. May function as a cellular oxygen sensor and, under normoxic conditions, may target HIF through the hydroxylation for proteasomal degradation via the von Hippel-Lindau ubiquitination complex.
Gene Name:
P4HTM
Uniprot ID:
Q9NXG6
Molecular Weight:
56660.535 Da
References
  1. Rapaka RS, Sorensen KR, Lee SD, Bhatnagar RS: Inhibition of hydroxyproline synthesis by palladium ions. Biochim Biophys Acta. 1976 Mar 11;429(1):63-71. [177068 ]
6. DNA
General Function:
Used for biological information storage.
Specific Function:
DNA contains the instructions needed for an organism to develop, survive and reproduce.
Molecular Weight:
2.15 x 1012 Da