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Showing NP-Card for Glycyl-glycine (NP0000189)

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Record Information
Version2.0
Created at2009-03-03 10:25:52 UTC
Updated at2021-10-07 20:41:17 UTC
NP-MRD IDNP0000189
Secondary Accession NumbersNone
Natural Product Identification
Common NameGlycyl-glycine
DescriptionThe simplest peptide, made of two glycine molecules; used in the synthesis of more complicated peptides. Glycine is a simple, nonessential amino acid, although experimental animals show reduced growth on low-glycine diets. The average adult ingests 3 to 5 grams of glycine daily. Glycine is involved in the body's production of DNA, phospholipids and collagen, and in release of energy. Glycine levels are effectively measured in plasma in both normal patients and those with inborn errors of glycine metabolism. (Http://Www.Dcnutrition.Com/AminoAcids/) Nonketotic hyperglycinaemia (OMIM 606899 ) is an autosomal recessive condition caused by deficient enzyme activity of the glycine cleavage enzyme system (EC 2.1.1.10). The glycine cleavage enzyme system comprises four proteins: P-, T-, H- and L-proteins (EC 1.4.4.2, EC 2.1.2.10 And EC 1.8.1.4 For P-, T- and L-proteins). Mutations have been described in the GLDC (OMIM 238300 ), AMT (OMIM 238310 ), and GCSH (OMIM 238330 ) genes encoding the P-, T-, and H-proteins respectively. The glycine cleavage system catalyses the oxidative conversion of glycine into carbon dioxide and ammonia, with the remaining one-carbon unit transferred to folate as methylenetetrahydrofolate. It is the main catabolic pathway for glycine and it also contributes to one-carbon metabolism. Patients with a deficiency of this enzyme system have increased glycine in plasma, urine and cerebrospinal fluid (CSF) with an increased CSF: Plasma glycine ratio. (PMID 16151895 ).
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0000189 (Glycyl-glycine)


  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 NP0000189 (Glycyl-glycine)

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 NP0000189 (Glycyl-glycine)


  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>
NP0000189

> <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 NP0000189 (Glycyl-glycine)

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 NP0000189 (Glycyl-glycine)

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 NP0000189 (Glycyl-glycine)

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 NP0000189 (Glycyl-glycine)

NCC(=O)NCC(O)=O
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INCHI for NP0000189 (Glycyl-glycine)

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 Number556-50-3
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 NMR1H NMR Spectrum (1D, 500 MHz, H2O, simulated)V.dorna832021-09-05View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, simulated)V.dorna832021-09-05View Spectrum
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
Chemical Shift Submissions
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, simulated)v.dorna83@yahoo.comNot AvailableNot Available2021-08-15View Spectrum
Species
Species of Origin
Species NameSourceReference
Anas platyrhynchosFooDB
AnatidaeFooDB
Anser anserFooDB
Bison bisonFooDB
Blighia sapidaLOTUS Database
Bos taurusFooDB
Bos taurus X Bison bisonFooDB
Bubalus bubalisFooDB
Capra aegagrus hircusFooDB
Carica papayaKNApSAcK Database
Carica papaya L.Plant
CervidaeFooDB
Cervus canadensisFooDB
ColumbaFooDB
ColumbidaeFooDB
Daphnia pulexLOTUS Database
Dromaius novaehollandiaeFooDB
Equus caballusFooDB
Gallus gallusFooDB
Lagopus mutaFooDB
LeporidaeFooDB
Lepus timidusFooDB
Melanitta fuscaFooDB
Meleagris gallopavoFooDB
Numida meleagrisFooDB
OdocoileusFooDB
OryctolagusFooDB
Ovis ariesFooDB
PhasianidaeFooDB
Phasianus colchicusFooDB
Struthio camelusFooDB
Sus scrofaFooDB
Sus scrofa domesticaFooDB
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
StateSolid
Experimental Properties
PropertyValueReference
Melting Point215 °CNot Available
Boiling Point453.24 °C. @ 760.00 mm Hg (est)The Good Scents Company Information System
Water Solubility166 mg/mL at 21 °CNot Available
LogP-2.92Hansch CH, Leo A and Hoekman DH. "Exploring QSAR: Hydrophobic, Electronic, and Steric Constraints. Volume 1" ACS Publications (1995).
Predicted Properties
PropertyValueSource
Water Solubility82.1 g/LALOGPS
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. 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 ]
  2. 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 ]