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Record Information
Version4.0
StatusExpected but not Quantified
Creation Date2009-07-25 00:10:11 UTC
Update Date2020-02-26 21:37:59 UTC
HMDB IDHMDB0012937
Secondary Accession Numbers
  • HMDB12937
Metabolite Identification
Common NameDynorphin B (6-9)
DescriptionDynorphin B (6-9) is fraction of Dynorphin B with only Arg-Arg-Gln-Phe peptide chain. Dynorphin B is an agonist of nuclear opioid receptors coupling nuclear protein Kinase C activation to the transcription of cardiogenic genes in GTR1 embryonic stem cells. Dynorphin B is a form of dynorphin.Dynorphins are a class of opioid peptides that arise from the precursor protein prodynorphin. When prodynorphin is cleaved during processing by proprotein convertase 2 (PC2), multiple active peptides are released: dynorphin A, dynorphin B, and a/b-neo-endorphin. Depolarization of a neuron containing prodynorphin stimulates PC2 processing, which occurs within synaptic vesicles in the presynaptic terminal. Occasionally, prodynorphin is not fully processed, leading to the release of "big dynorphin."This 32-amino acid molecule consists of both dynorphin A and dynorphin B.Dynorphin A, dynorphin B, and big dynorphin all contain a high proportion of basic amino acid residues, in particular lysine and arginine (29.4%, 23.1%, and 31.2% basic residues, respectively), as well as many hydrophobic residues (41.2%, 30.8%, and 34.4% hydrophobic residues, respectively). Although dynorphins are found widely distributed in the CNS, they have the highest concentrations in the hypothalamus, medulla, pons, midbrain, and spinal cord. Dynorphins are stored in large (80-120 nm diameter) dense-core vesicles that are considerably larger than vesicles storing neurotransmitters. These large dense-core vesicles differ from small synaptic vesicles in that a more intense and prolonged stimulus is needed to cause the large vesicles to release their contents into the synaptic cleft. Dense-core vesicle storage is characteristic of opioid peptides storage. The first clues to the functionality of dynorphins came from Goldstein et al. in their work with opioid peptides. The group discovered an endogenous opioid peptide in the porcine pituitary that proved difficult to isolate. By sequencing the first 13 amino acids of the peptide, they created a synthetic version of the peptide with a similar potency to the natural peptide. Goldstein et al. applied the synthetic peptide to the guinea ileum longitudinal muscle and found it to be an extraordinarily potent opioid peptide. The peptide was called dynorphin (from the Greek dynamis=power) to describe its potency. Dynorphins exert their effects primarily through the κ-opioid receptor (KOR), a G-protein-coupled receptor. Two subtypes of KORs have been identified: K1 and K2. Although KOR is the primary receptor for all dynorphins, the peptides do have some affinity for the μ-opioid receptor (MOR), d-opioid receptor (DOR), N-methyl-D-aspartic acid (NMDA)-type glutamate receptor. Different dynorphins show different receptor selectivities and potencies at receptors. Big dynorphin and dynorphin A have the same selectivity for human KOR, but dynorphin A is more selective for KOR over MOR and DOR than is big dynorphin. Big dynorphin is more potent at KORs than is dynorphin A. Both big dynorphin and dynorphin A are more potent and more selective than dynorphin B (Wikipedia).
Structure
Data?1582753079
Synonyms
ValueSource
Arg-arg-GLN-pheHMDB
(2S)-2-{[(2R)-2-{[(2S)-2-{[(2R)-2-amino-5-carbamimidamido-1-hydroxypentylidene]amino}-5-carbamimidamido-1-hydroxypentylidene]amino}-1-hydroxy-4-(C-hydroxycarbonimidoyl)butylidene]amino}-3-phenylpropanoateGenerator
Chemical FormulaC26H43N11O6
Average Molecular Weight605.6897
Monoisotopic Molecular Weight605.339778163
IUPAC Name(2S)-2-[(2R)-2-[(2S)-2-[(2R)-2-amino-5-carbamimidamidopentanamido]-5-carbamimidamidopentanamido]-4-(C-hydroxycarbonimidoyl)butanamido]-3-phenylpropanoic acid
Traditional Name(2S)-2-[(2R)-2-[(2S)-2-[(2R)-2-amino-5-carbamimidamidopentanamido]-5-carbamimidamidopentanamido]-4-(C-hydroxycarbonimidoyl)butanamido]-3-phenylpropanoic acid
CAS Registry NumberNot Available
SMILES
N[C@H](CCCNC(N)=N)C(=O)N[C@@H](CCCNC(N)=N)C(=O)N[C@H](CCC(O)=N)C(=O)N[C@@H](CC1=CC=CC=C1)C(O)=O
InChI Identifier
InChI=1S/C26H43N11O6/c27-16(8-4-12-33-25(29)30)21(39)35-17(9-5-13-34-26(31)32)22(40)36-18(10-11-20(28)38)23(41)37-19(24(42)43)14-15-6-2-1-3-7-15/h1-3,6-7,16-19H,4-5,8-14,27H2,(H2,28,38)(H,35,39)(H,36,40)(H,37,41)(H,42,43)(H4,29,30,33)(H4,31,32,34)/t16-,17+,18-,19+/m1/s1
InChI KeyYTMBNLHIDIKJIU-HCXYKTFWSA-N
Chemical Taxonomy
Description belongs to the class of organic compounds known as oligopeptides. These are organic compounds containing a sequence of between three and ten alpha-amino acids joined by peptide bonds.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct ParentOligopeptides
Alternative Parents
Substituents
  • Alpha-oligopeptide
  • Phenylalanine or derivatives
  • Glutamine or derivatives
  • N-acyl-l-alpha-amino acid
  • N-acyl-alpha-amino acid
  • N-acyl-alpha amino acid or derivatives
  • Alpha-amino acid amide
  • 3-phenylpropanoic-acid
  • N-substituted-alpha-amino acid
  • Alpha-amino acid or derivatives
  • Amphetamine or derivatives
  • Monocyclic benzene moiety
  • Fatty amide
  • Fatty acyl
  • N-acyl-amine
  • Benzenoid
  • Amino acid or derivatives
  • Amino acid
  • Carboxamide group
  • Guanidine
  • Secondary carboxylic acid amide
  • Primary carboxylic acid amide
  • Propargyl-type 1,3-dipolar organic compound
  • Organic 1,3-dipolar compound
  • Monocarboxylic acid or derivatives
  • Carboximidamide
  • Carboxylic acid
  • Organic oxide
  • Hydrocarbon derivative
  • Amine
  • Organopnictogen compound
  • Carbonyl group
  • Organic oxygen compound
  • Primary aliphatic amine
  • Organonitrogen compound
  • Organooxygen compound
  • Organic nitrogen compound
  • Primary amine
  • Aromatic homomonocyclic compound
Molecular FrameworkAromatic homomonocyclic compounds
External DescriptorsNot Available
Ontology
Disposition

Source:

Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility0.15 g/LALOGPS
logP-3.3ALOGPS
logP-6ChemAxon
logS-3.6ALOGPS
pKa (Strongest Acidic)-1.2ChemAxon
pKa (Strongest Basic)12.29ChemAxon
Physiological Charge2ChemAxon
Hydrogen Acceptor Count14ChemAxon
Hydrogen Donor Count13ChemAxon
Polar Surface Area318.5 ŲChemAxon
Rotatable Bond Count20ChemAxon
Refractivity187.41 m³·mol⁻¹ChemAxon
Polarizability62.93 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-06r6-7522690000-dbb40ccb16d3dd298b3dSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positivesplash10-004i-4901022000-8a222065df6505d626eaSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-06tr-2621392000-e91d36309394d78448d8Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-01t9-3931130000-ee5de69cbe8a54525f00Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-01t9-9720000000-8ea09f8f28cf817114bbSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0ik9-1000091000-74bf31786b93b83f2e7fSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0btc-4110290000-64d5702022ce84812877Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-052f-9300100000-ee1dcdcc14270bb8711aSpectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB029217
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound53481557
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available