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Showing NP-Card for Glycylglycine (NP0331788)

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Record Information
Version1.0
Created at2023-09-05 20:00:26 UTC
Updated at2024-04-19 09:51:36 UTC
NP-MRD IDNP0331788
Secondary Accession NumbersNone
Natural Product Identification
Common NameGlycylglycine
DescriptionGlycyl-glycine, also known as gly-gly or GLY2, belongs to the class of organic compounds known as dipeptides. These are organic compounds containing a sequence of exactly two alpha-amino acids joined by a peptide bond. Glycyl-glycine is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. It was first documented in 2019 (PMID: 31384710). Based on a literature review a significant number of articles have been published on Glycyl-glycine (PMID: 34351843) (PMID: 34281200) (PMID: 34097420) (PMID: 32784576) (PMID: 32366964) (PMID: 32316345).
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0331788 (Glycylglycine)


  Mrv1652305271900142D          

  9  8  0  0  0  0            999 V2000
   14.8200  -19.8164    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.2325  -17.6734    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.2325  -19.1019    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.8200  -16.9589    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.9951  -19.8164    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   14.8200  -18.3873    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   16.0574  -19.1019    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.2325  -16.2443    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.9951  -16.9589    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  5  1  0  0  0  0
  1  3  1  0  0  0  0
  2  6  1  0  0  0  0
  2  4  1  0  0  0  0
  3  7  2  0  0  0  0
  3  6  1  0  0  0  0
  4  8  1  0  0  0  0
  4  9  2  0  0  0  0
M  END
Download

3D MOL for NP0331788 (Glycylglycine)

HMDB0011733
     RDKit          3D
Glycyl-glycine
 17 16  0  0  0  0  0  0  0  0999 V2000
    3.3210   -0.7556    0.0101 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1426   -0.3399    0.7055 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9434   -0.3520   -0.1545 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0552   -0.7037   -1.3450 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3246    0.0252    0.3413 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5182    0.0236   -0.4770 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6858    0.4600    0.3001 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5472    0.7661    1.4968 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9284    0.5328   -0.2836 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1023   -0.1191    0.3042 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1762   -0.5934   -1.0141 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2744    0.6850    1.1586 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9124   -0.9973    1.5837 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4274    0.3232    1.3446 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7241   -1.0071   -0.8733 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3089    0.6654   -1.3557 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4628    1.3869   -0.2896 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  3  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  7  9  1  0
  1 10  1  0
  1 11  1  0
  2 12  1  0
  2 13  1  0
  5 14  1  0
  6 15  1  0
  6 16  1  0
  9 17  1  0
M  END
Download

3D SDF for NP0331788 (Glycylglycine)


  Mrv1652305271900142D          

  9  8  0  0  0  0            999 V2000
   14.8200  -19.8164    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.2325  -17.6734    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.2325  -19.1019    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.8200  -16.9589    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.9951  -19.8164    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   14.8200  -18.3873    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   16.0574  -19.1019    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.2325  -16.2443    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.9951  -16.9589    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  5  1  0  0  0  0
  1  3  1  0  0  0  0
  2  6  1  0  0  0  0
  2  4  1  0  0  0  0
  3  7  2  0  0  0  0
  3  6  1  0  0  0  0
  4  8  1  0  0  0  0
  4  9  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0331788

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C4H8N2O3/c5-1-3(7)6-2-4(8)9/h1-2,5H2,(H,6,7)(H,8,9)

> <INCHI_KEY>
YMAWOPBAYDPSLA-UHFFFAOYSA-N

> <FORMULA>
C4H8N2O3

> <MOLECULAR_WEIGHT>
132.1179

> <EXACT_MASS>
132.053492132

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
17

> <JCHEM_AVERAGE_POLARIZABILITY>
12.008808377400777

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-(2-aminoacetamido)acetic acid

> <ALOGPS_LOGP>
-3.23

> <JCHEM_LOGP>
-4.517595069268154

> <ALOGPS_LOGS>
-0.21

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.324273544852911

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.520069043804431

> <JCHEM_PKA_STRONGEST_BASIC>
8.139868083148611

> <JCHEM_POLAR_SURFACE_AREA>
92.41999999999999

> <JCHEM_REFRACTIVITY>
28.806900000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.21e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
Gly-Gly

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0331788 (Glycylglycine)

HMDB0011733
     RDKit          3D
Glycyl-glycine
 17 16  0  0  0  0  0  0  0  0999 V2000
    3.3210   -0.7556    0.0101 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1426   -0.3399    0.7055 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9434   -0.3520   -0.1545 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0552   -0.7037   -1.3450 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3246    0.0252    0.3413 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5182    0.0236   -0.4770 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6858    0.4600    0.3001 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5472    0.7661    1.4968 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9284    0.5328   -0.2836 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1023   -0.1191    0.3042 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1762   -0.5934   -1.0141 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2744    0.6850    1.1586 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9124   -0.9973    1.5837 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4274    0.3232    1.3446 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7241   -1.0071   -0.8733 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3089    0.6654   -1.3557 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4628    1.3869   -0.2896 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  3  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  7  9  1  0
  1 10  1  0
  1 11  1  0
  2 12  1  0
  2 13  1  0
  5 14  1  0
  6 15  1  0
  6 16  1  0
  9 17  1  0
M  END
Download

PDB for NP0331788 (Glycylglycine)

HEADER    PROTEIN                                 27-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-MAY-19         0                                  
HETATM    1  C   UNK     0      27.664 -36.991   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      28.434 -32.990   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      28.434 -35.657   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      27.664 -31.657   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0      26.124 -36.991   0.000  0.00  0.00           N+0
HETATM    6  N   UNK     0      27.664 -34.323   0.000  0.00  0.00           N+0
HETATM    7  O   UNK     0      29.974 -35.657   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      28.434 -30.323   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      26.124 -31.657   0.000  0.00  0.00           O+0
CONECT    1    5    3                                                       
CONECT    2    6    4                                                       
CONECT    3    1    7    6                                                  
CONECT    4    2    8    9                                                  
CONECT    5    1                                                            
CONECT    6    2    3                                                       
CONECT    7    3                                                            
CONECT    8    4                                                            
CONECT    9    4                                                            
MASTER        0    0    0    0    0    0    0    0    9    0   16    0
END
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3D PDB for NP0331788 (Glycylglycine)

COMPND    HMDB0011733
HETATM    1  N1  UNL     1       3.321  -0.756   0.010  1.00  0.00           N  
HETATM    2  C1  UNL     1       2.143  -0.340   0.705  1.00  0.00           C  
HETATM    3  C2  UNL     1       0.943  -0.352  -0.154  1.00  0.00           C  
HETATM    4  O1  UNL     1       1.055  -0.704  -1.345  1.00  0.00           O  
HETATM    5  N2  UNL     1      -0.325   0.025   0.341  1.00  0.00           N  
HETATM    6  C3  UNL     1      -1.518   0.024  -0.477  1.00  0.00           C  
HETATM    7  C4  UNL     1      -2.686   0.460   0.300  1.00  0.00           C  
HETATM    8  O2  UNL     1      -2.547   0.766   1.497  1.00  0.00           O  
HETATM    9  O3  UNL     1      -3.928   0.533  -0.284  1.00  0.00           O  
HETATM   10  H1  UNL     1       4.102  -0.119   0.304  1.00  0.00           H  
HETATM   11  H2  UNL     1       3.176  -0.593  -1.014  1.00  0.00           H  
HETATM   12  H3  UNL     1       2.274   0.685   1.159  1.00  0.00           H  
HETATM   13  H4  UNL     1       1.912  -0.997   1.584  1.00  0.00           H  
HETATM   14  H5  UNL     1      -0.427   0.323   1.345  1.00  0.00           H  
HETATM   15  H6  UNL     1      -1.724  -1.007  -0.873  1.00  0.00           H  
HETATM   16  H7  UNL     1      -1.309   0.665  -1.356  1.00  0.00           H  
HETATM   17  H8  UNL     1      -4.463   1.387  -0.290  1.00  0.00           H  
CONECT    1    2   10   11
CONECT    2    3   12   13
CONECT    3    4    4    5
CONECT    5    6   14
CONECT    6    7   15   16
CONECT    7    8    8    9
CONECT    9   17
END
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SMILES for NP0331788 (Glycylglycine)

NCC(=O)NCC(O)=O
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INCHI for NP0331788 (Glycylglycine)

InChI=1S/C4H8N2O3/c5-1-3(7)6-2-4(8)9/h1-2,5H2,(H,6,7)(H,8,9)
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View in JSmol
Synonyms
ValueSource
2-(Aminoacetamido)acetic acidChEBI
[(Aminoacetyl)amino]acetic acidChEBI
Gly-glyChEBI
Gly2ChEBI
Glycine dipeptideChEBI
N-GlycylglycineChEBI
2-(Aminoacetamido)acetateGenerator
[(Aminoacetyl)amino]acetateGenerator
((Aminoacetyl)amino)acetic acidHMDB
alpha-GlycylglycineHMDB
DiglycineHMDB
N-GLYCYL- glycineHMDB
Glycylglycine hydrochlorideHMDB
Glycyl glycineHMDB
Glycylglycine monohydrochlorideHMDB
Hydrochloride, glycylglycineHMDB
Monohydrochloride, glycylglycineHMDB
N GlycylglycineHMDB
Glycyl-glycineMeSH
Chemical FormulaC4H8N2O3
Average Mass132.1179 Da
Monoisotopic Mass132.05349 Da
IUPAC Name2-(2-aminoacetamido)acetic acid
Traditional NameGly-Gly
CAS Registry NumberNot Available
SMILES
NCC(=O)NCC(O)=O
InChI Identifier
InChI=1S/C4H8N2O3/c5-1-3(7)6-2-4(8)9/h1-2,5H2,(H,6,7)(H,8,9)
InChI KeyYMAWOPBAYDPSLA-UHFFFAOYSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR[1H, ] NMR Spectrum (2D, 600 MHz, CD3OD, experimental)bgnzk@missouri.eduMU Metabolomics Center, University of Missouri, Columbia. MO, USADr. Bharat Goel2023-09-05View Spectrum
1D NMR[1H, ] NMR Spectrum (2D, 600 MHz, CD3OD, experimental)bgnzk@missouri.eduMU Metabolomics Center, University of Missouri, Columbia. MO, USADr. Bharat Goel2023-09-05View Spectrum
1D NMR1H NMR Spectrum (1D, 600.133705802 MHz, CD3OD, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600.133705802 MHz, CD3OD, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of OriginNot Available
Chemical Taxonomy
Description Belongs to the class of organic compounds known as dipeptides. These are organic compounds containing a sequence of exactly two alpha-amino acids joined by a peptide bond.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct ParentDipeptides
Alternative Parents
Substituents
  • Alpha-dipeptide
  • N-acyl-alpha-amino acid
  • N-acyl-alpha amino acid or derivatives
  • Alpha-amino acid amide
  • Alpha-amino acid or derivatives
  • Amino acid or derivatives
  • Carboxamide group
  • Amino acid
  • Secondary carboxylic acid amide
  • Carboxylic acid
  • Monocarboxylic acid or derivatives
  • Organic nitrogen compound
  • Organonitrogen compound
  • Organooxygen compound
  • Primary amine
  • Primary aliphatic amine
  • Hydrocarbon derivative
  • Organic oxide
  • Carbonyl group
  • Organopnictogen compound
  • Amine
  • Organic oxygen compound
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic 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-3.2ALOGPS
logP-4.5ChemAxon
logS-0.21ALOGPS
pKa (Strongest Acidic)3.52ChemAxon
pKa (Strongest Basic)8.14ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area92.42 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity28.81 m³·mol⁻¹ChemAxon
Polarizability12.01 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0011733
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB028413
KNApSAcK IDC00053264
Chemspider ID10690
KEGG Compound IDC02037
BioCyc IDGLYCYLGLYCINE
BiGG IDNot Available
Wikipedia LinkGlycylglycine
METLIN IDNot Available
PubChem Compound11163
PDB IDNot Available
ChEBI ID17201
Good Scents IDrw1248591
References
General References
  1. Alasbahy WM, Shamsi M: In vitro DNA binding, pBR322 cleavage and molecular docking studies of 1,2-diaminobenzene, dichloro glycyl glycinate tin(IV) and zirconium(IV) complexes. J Biomol Struct Dyn. 2021 Aug 5:1-11. doi: 10.1080/07391102.2021.1959402. [PubMed:34351843 ]
  2. Malecki PH, Mitkowski P, Jagielska E, Trochimiak K, Mesnage S, Sabala I: Structural Characterization of EnpA D,L-Endopeptidase from Enterococcus faecalis Prophage Provides Insights into Substrate Specificity of M23 Peptidases. Int J Mol Sci. 2021 Jul 1;22(13). pii: ijms22137136. doi: 10.3390/ijms22137136. [PubMed:34281200 ]
  3. Lau JK, Esuon F, Berden G, Oomens J, Hopkinson AC, Ryzhov V, Siu KWM: Generation, Characterization, and Dissociation of Radical Cations Derived from Prolyl-glycyl-glycine. J Phys Chem B. 2021 Jun 17;125(23):6121-6129. doi: 10.1021/acs.jpcb.1c01732. Epub 2021 Jun 7. [PubMed:34097420 ]
  4. Khalaf HS, Naglah AM, Al-Omar MA, Moustafa GO, Awad HM, Bakheit AH: Synthesis, Docking, Computational Studies, and Antimicrobial Evaluations of New Dipeptide Derivatives Based on Nicotinoylglycylglycine Hydrazide. Molecules. 2020 Aug 7;25(16). pii: molecules25163589. doi: 10.3390/molecules25163589. [PubMed:32784576 ]
  5. Kasumyan AO, Mouromtsev GE: The teleost fish, blue gourami Trichopodus trichopterus, distinguishes the taste of chemically similar substances. Sci Rep. 2020 May 4;10(1):7487. doi: 10.1038/s41598-020-64556-6. [PubMed:32366964 ]
  6. Araya-Hermosilla EA, Carlotti M, Picchioni F, Mattoli V, Pucci A: Electrically-Conductive Polyketone Nanocomposites Based on Reduced Graphene Oxide. Polymers (Basel). 2020 Apr 16;12(4). pii: polym12040923. doi: 10.3390/polym12040923. [PubMed:32316345 ]
  7. Duan J, Chen L, Tu J, Cao L, Xiao X: Folate-grafted glycyl-glycine-melphalan conjugate self-assembled amphilphilc nanomicelles augmented drug delivery, cytotoxicity and cellular uptake in human ovarian cancer cells. J Microencapsul. 2020 Jan 15:1-30. doi: 10.1080/02652048.2020.1714764. [PubMed:31937168 ]
  8. Kovalskaya NY, Herndon EE, Foster-Frey JA, Donovan DM, Hammond RW: Antimicrobial activity of bacteriophage derived triple fusion protein against Staphylococcus aureus. AIMS Microbiol. 2019 Jun 25;5(2):158-175. doi: 10.3934/microbiol.2019.2.158. eCollection 2019. [PubMed:31384710 ]
  9. Patil KR, Barge SS, Bhosale BD, Dagade DH: Influence of protic ionic liquids on hydration of glycine based peptides. Spectrochim Acta A Mol Biomol Spectrosc. 2022 Jan 15;265:120378. doi: 10.1016/j.saa.2021.120378. Epub 2021 Sep 10. [PubMed:34543989 ]
  10. Zhai R, Chen H, Shan Z: Exploration of collagen cavitation based on peptide electrolysis. Sci Rep. 2021 Aug 24;11(1):17080. doi: 10.1038/s41598-021-96533-y. [PubMed:34429475 ]