You are using an unsupported browser. Please upgrade your browser to a newer version to get the best experience on Human Metabolome Database.

Jump To Section:

Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References XML

Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2022-09-09 19:26:09 UTC

Update Date

2022-09-22 18:35:03 UTC

HMDB ID

HMDB0341162

Secondary Accession Numbers

None

Metabolite Identification

Common Name

Gly-Pro-Asp

Description

Gly-Pro-Asp 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. Based on a literature review a significant number of articles have been published on Gly-Pro-Asp.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652309092222042D          

 22 22  0  0  1  0            999 V2000
    0.1904   -2.2254    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9049   -2.6379    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.1904   -3.0504    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1904   -3.8754    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5240   -4.2879    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9049   -4.2879    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9049   -1.8129    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6194   -1.4004    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3338   -1.8129    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6194   -0.5754    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.3545   -0.9499    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9519   -0.0904    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2069    0.6942    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0319    0.6942    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2868   -0.0904    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.0714   -0.3454    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2430   -1.1524    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6845    0.2066    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5130    1.0136    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6194   -3.0504    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3338   -2.6379    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6194   -3.8754    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  4  6  2  0  0  0  0
  2  7  1  6  0  0  0
  7  8  2  0  0  0  0
  8  9  1  4  0  0  0
 10  8  1  6  0  0  0
 10 11  1  1  0  0  0
 10 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 10 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  2  0  0  0  0
 16 18  1  0  0  0  0
 18 19  1  0  0  0  0
  2 20  1  0  0  0  0
 20 21  1  0  0  0  0
 20 22  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0341162

> <DATABASE_NAME>
hmdb

> <SMILES>
[H][C@@](CC(O)=O)(N=C(O)[C@]1([H])CCCN1C(=O)CN)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C11H17N3O6/c12-5-8(15)14-3-1-2-7(14)10(18)13-6(11(19)20)4-9(16)17/h6-7H,1-5,12H2,(H,13,18)(H,16,17)(H,19,20)/t6-,7-/m0/s1

> <INCHI_KEY>
WDXLKVQATNEAJQ-BQBZGAKWSA-N

> <FORMULA>
C11H17N3O6

> <MOLECULAR_WEIGHT>
287.272

> <EXACT_MASS>
287.111735279

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
37

> <JCHEM_AVERAGE_POLARIZABILITY>
26.891088589191142

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-2-({[(2S)-1-(2-aminoacetyl)pyrrolidin-2-yl](hydroxy)methylidene}amino)butanedioic acid

> <JCHEM_LOGP>
-4.244375884404438

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
4.347403056316175

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.305013735521896

> <JCHEM_PKA_STRONGEST_BASIC>
8.132866772493998

> <JCHEM_POLAR_SURFACE_AREA>
153.51999999999998

> <JCHEM_REFRACTIVITY>
64.84440000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(2S)-2-({[(2S)-1-(2-aminoacetyl)pyrrolidin-2-yl](hydroxy)methylidene}amino)butanedioic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 09-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   09-SEP-22         0                                  
HETATM    1  H   UNK     0       0.355  -4.154   0.000  0.00  0.00           H+0
HETATM    2  C   UNK     0       1.689  -4.924   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.355  -5.694   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.355  -7.234   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      -0.978  -8.004   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0       1.689  -8.004   0.000  0.00  0.00           O+0
HETATM    7  N   UNK     0       1.689  -3.384   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0       3.023  -2.614   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       4.357  -3.384   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       3.023  -1.074   0.000  0.00  0.00           C+0
HETATM   11  H   UNK     0       4.395  -1.773   0.000  0.00  0.00           H+0
HETATM   12  C   UNK     0       1.777  -0.169   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       2.253   1.296   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       3.793   1.296   0.000  0.00  0.00           C+0
HETATM   15  N   UNK     0       4.269  -0.169   0.000  0.00  0.00           N+0
HETATM   16  C   UNK     0       5.733  -0.645   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       6.054  -2.151   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       6.878   0.386   0.000  0.00  0.00           C+0
HETATM   19  N   UNK     0       6.558   1.892   0.000  0.00  0.00           N+0
HETATM   20  C   UNK     0       3.023  -5.694   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       4.357  -4.924   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       3.023  -7.234   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    7   20                                             
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4                                                            
CONECT    7    2    8                                                       
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11   12   15                                             
CONECT   11   10                                                            
CONECT   12   10   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   10   16                                                  
CONECT   16   15   17   18                                                  
CONECT   17   16                                                            
CONECT   18   16   19                                                       
CONECT   19   18                                                            
CONECT   20    2   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20                                                            
MASTER        0    0    0    0    0    0    0    0   22    0   44    0
END

View in JSmol View Stereo Labels

Synonyms

Not Available

Chemical Formula

C₁₁H₁₇N₃O₆

Average Molecular Weight

287.272

Monoisotopic Molecular Weight

287.111735279

IUPAC Name

(2S)-2-({[(2S)-1-(2-aminoacetyl)pyrrolidin-2-yl](hydroxy)methylidene}amino)butanedioic acid

Traditional Name

(2S)-2-({[(2S)-1-(2-aminoacetyl)pyrrolidin-2-yl](hydroxy)methylidene}amino)butanedioic acid

CAS Registry Number

Not Available

SMILES

[H][C@@](CC(O)=O)(N=C(O)[C@]1([H])CCCN1C(=O)CN)C(O)=O

InChI Identifier

InChI=1S/C11H17N3O6/c12-5-8(15)14-3-1-2-7(14)10(18)13-6(11(19)20)4-9(16)17/h6-7H,1-5,12H2,(H,13,18)(H,16,17)(H,19,20)/t6-,7-/m0/s1

InChI Key

WDXLKVQATNEAJQ-BQBZGAKWSA-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.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Oligopeptides

Alternative Parents

Substituents

Alpha-oligopeptide
Aspartic acid or derivatives
Proline or derivatives
N-acyl-alpha-amino acid
N-acyl-alpha amino acid or derivatives
N-acyl-l-alpha-amino acid
Alpha-amino acid amide
Alpha-amino acid or derivatives
N-acylpyrrolidine
Pyrrolidine carboxylic acid or derivatives
Pyrrolidine-2-carboxamide
Heterocyclic fatty acid
Dicarboxylic acid or derivatives
Fatty acyl
Fatty acid
Pyrrolidine
Tertiary carboxylic acid amide
Secondary carboxylic acid amide
Amino acid or derivatives
Carboxamide group
Amino acid
Organoheterocyclic compound
Azacycle
Carboxylic acid
Organic oxygen compound
Primary aliphatic amine
Organic oxide
Hydrocarbon derivative
Organonitrogen compound
Carbonyl group
Organooxygen compound
Amine
Primary amine
Organic nitrogen compound
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

Not Available

Ontology

Not Available

Physical Properties

State

Not Available

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
logP	-4.2	ChemAxon
pKa (Strongest Acidic)	3.31	ChemAxon
pKa (Strongest Basic)	8.13	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	153.52 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	64.84 m³·mol⁻¹	ChemAxon
Polarizability	26.89 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Kovats Retention Indices

Not Available

Spectra

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood
Urine

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	34436864	details
Urine	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	34436864	details

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

23260816

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

44402569

PDB ID

Not Available

ChEBI ID

163954

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Neto FC, Raftery D: Expanding Urinary Metabolite Annotation through Integrated Mass Spectral Similarity Networking. Anal Chem. 2021 Sep 7;93(35):12001-12010. doi: 10.1021/acs.analchem.1c02041. Epub 2021 Aug 26. [PubMed:34436864 ]

Showing metabocard for Gly-Pro-Asp (HMDB0341162)

MOL for HMDB0341162 (Gly-Pro-Asp)

3D MOL for HMDB0341162 (Gly-Pro-Asp)

3D SDF for HMDB0341162 (Gly-Pro-Asp)

3D-SDF for HMDB0341162 (Gly-Pro-Asp)

PDB for HMDB0341162 (Gly-Pro-Asp)

3D PDB for HMDB0341162 (Gly-Pro-Asp)

SMILES for HMDB0341162 (Gly-Pro-Asp)

INCHI for HMDB0341162 (Gly-Pro-Asp)

Structure for HMDB0341162 (Gly-Pro-Asp)

3D Structure for HMDB0341162 (Gly-Pro-Asp)

Predicted Kovats Retention Indices