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Showing NP-Card for 2,5-Diketopiperazine (NP0061002)

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Record Information
Version2.0
Created at2022-04-28 05:56:33 UTC
Updated at2022-04-28 05:56:33 UTC
NP-MRD IDNP0061002
Secondary Accession NumbersNone
Natural Product Identification
Common Name2,5-Diketopiperazine
DescriptionPiperazine-2,5-dione, also known as diketopiperazine or glycine anhydride, belongs to the class of organic compounds known as alpha amino acids and derivatives. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon), or a derivative thereof. A cyclic peptide that is piperazine in which the hydrogens at positions 2 and 5 are replaced by oxo groups. 2,5-Diketopiperazine is found in Marine fungus M-3. 2,5-Diketopiperazine was first documented in 2003 (PMID: 12587880). Piperazine-2,5-dione is a very strong basic compound (based on its pKa) (PMID: 24618890) (PMID: 24917118).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0061002 (2,5-Diketopiperazine)


  Mrv0541 09041212392D          

  8  8  0  0  0  0            999 V2000
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  1  1  0  0  0  0
  5  4  2  0  0  0  0
  6  2  1  0  0  0  0
  6  3  2  0  0  0  0
  7  3  1  0  0  0  0
  8  4  1  0  0  0  0
M  END
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3D MOL for NP0061002 (2,5-Diketopiperazine)

     RDKit          3D

 14 14  0  0  0  0  0  0  0  0999 V2000
   -2.6888    0.0865   -0.8115 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3674    0.0145   -0.4116 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7202   -1.0666   -0.6041 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6564   -1.1617   -0.1949 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3939    0.0966   -0.2679 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7418    0.1712   -0.5415 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7322    1.1857   -0.0628 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6925    1.1536    0.2294 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3781   -0.6009   -0.5302 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1323   -1.9258   -0.8701 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7153   -1.5583    0.8616 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4443    0.3753    0.1857 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1027    2.1366   -0.0920 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8666    1.0935    1.3352 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  5  7  2  0
  7  8  1  0
  8  2  1  0
  1  9  1  0
  4 10  1  0
  4 11  1  0
  6 12  1  0
  8 13  1  0
  8 14  1  0
M  END
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3D SDF for NP0061002 (2,5-Diketopiperazine)


  Mrv0541 09041212392D          

  8  8  0  0  0  0            999 V2000
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  1  1  0  0  0  0
  5  4  2  0  0  0  0
  6  2  1  0  0  0  0
  6  3  2  0  0  0  0
  7  3  1  0  0  0  0
  8  4  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0061002

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC1=NCC(O)=NC1

> <INCHI_IDENTIFIER>
InChI=1S/C4H6N2O2/c7-3-1-5-4(8)2-6-3/h1-2H2,(H,5,8)(H,6,7)

> <INCHI_KEY>
BXRNXXXXHLBUKK-UHFFFAOYSA-N

> <FORMULA>
C4H6N2O2

> <MOLECULAR_WEIGHT>
114.1026

> <EXACT_MASS>
114.042927446

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
10.17358401412922

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3,6-dihydropyrazine-2,5-diol

> <ALOGPS_LOGP>
-1.26

> <JCHEM_LOGP>
-1.1489690839980826

> <ALOGPS_LOGS>
-1.32

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.405764960415763

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.069394103866179

> <JCHEM_PKA_STRONGEST_BASIC>
5.640931412336054

> <JCHEM_POLAR_SURFACE_AREA>
65.18

> <JCHEM_REFRACTIVITY>
26.650399999999994

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.51e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3,6-dihydropyrazine-2,5-diol

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0061002 (2,5-Diketopiperazine)

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PDB for NP0061002 (2,5-Diketopiperazine)
HEADER    PROTEIN                                 04-SEP-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-12         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM    6  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM    7  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
CONECT    1    3    5                                                       
CONECT    2    4    6                                                       
CONECT    3    1    6    7                                                  
CONECT    4    2    5    8                                                  
CONECT    5    1    4                                                       
CONECT    6    2    3                                                       
CONECT    7    3                                                            
CONECT    8    4                                                            
MASTER        0    0    0    0    0    0    0    0    8    0   16    0
END

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3D PDB for NP0061002 (2,5-Diketopiperazine)
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SMILES for NP0061002 (2,5-Diketopiperazine)
OC1=NCC(O)=NC1
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INCHI for NP0061002 (2,5-Diketopiperazine)
InChI=1S/C4H6N2O2/c7-3-1-5-4(8)2-6-3/h1-2H2,(H,5,8)(H,6,7)
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Synonyms
ValueSource
2,5-Diazacyclohexane-1,4-dioneChEBI
2,5-DioxopiperazineChEBI
2,5-PiperazinedioneChEBI
Cyclo-(gly-gly)ChEBI
DiketopiperazineChEBI
Glycine anhydrideChEBI
cyclo(Glycylglycyl)MeSH
cyclo(Gly-gly)MeSH
2,5-DiketopiperazineMeSH
Chemical FormulaC4H6N2O2
Average Mass114.1026 Da
Monoisotopic Mass114.04293 Da
IUPAC Name3,6-dihydropyrazine-2,5-diol
Traditional Name3,6-dihydropyrazine-2,5-diol
CAS Registry NumberNot Available
SMILES
OC1=NCC(O)=NC1
InChI Identifier
InChI=1S/C4H6N2O2/c7-3-1-5-4(8)2-6-3/h1-2H2,(H,5,8)(H,6,7)
InChI KeyBXRNXXXXHLBUKK-UHFFFAOYSA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Marine fungus M-3-
Chemical Taxonomy
Description Belongs to the class of organic compounds known as alpha amino acids and derivatives. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon), or a derivative thereof.
KingdomOrganic compounds  
Super ClassOrganic acids and derivatives  
ClassCarboxylic acids and derivatives  
Sub ClassAmino acids, peptides, and analogues  
Direct ParentAlpha amino acids and derivatives  
Alternative Parents
Substituents
  • Alpha-amino acid or derivatives
    • 

  • Dioxopiperazine
    • 

  • 2,5-dioxopiperazine
    • 

  • 1,4-diazinane
    • 

  • Piperazine
    • 

  • Secondary carboxylic acid amide
    • 

  • Lactam
    • 

  • Carboxamide group
    • 

  • Azacycle
    • 

  • Organoheterocyclic compound
    • 

  • Organopnictogen compound
    • 

  • Organic nitrogen compound
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Organic oxygen compound
    • 

  • Carbonyl group
    • 

  • Hydrocarbon derivative
    • 

  • Organic oxide
    • 

  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP-1.3ALOGPS
logP-1.1ChemAxon
logS-1.3ALOGPS
pKa (Strongest Acidic)4.07ChemAxon
pKa (Strongest Basic)5.64ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area65.18 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity26.65 m³·mol⁻¹ChemAxon
Polarizability10.17 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDC00014894  
Chemspider IDNot Available
KEGG Compound IDC02777  
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkDiketopiperazine  
METLIN IDNot Available
PubChem Compound7817  
PDB IDNot Available
ChEBI ID16535  
Good Scents IDNot Available
References
General References
  1. Fischer PM: Diketopiperazines in peptide and combinatorial chemistry. J Pept Sci. 2003 Jan;9(1):9-35. doi: 10.1002/psc.446. [PubMed:12587880  ] 
  2. Morrison LJ, Chamot-Rooke J, Wysocki VH: IR action spectroscopy shows competitive oxazolone and diketopiperazine formation in peptides depends on peptide length and identity of terminal residue in the departing fragment. Analyst. 2014 May 7;139(9):2137-43. doi: 10.1039/c4an00064a. [PubMed:24618890  ] 
  3. Fuchida S, Masuda H, Shinoda K: Peptide formation mechanism on montmorillonite under thermal conditions. Orig Life Evol Biosph. 2014 Feb;44(1):13-28. doi: 10.1007/s11084-014-9359-4. Epub 2014 Jun 11. [PubMed:24917118  ]