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

Record Information

Version

5.0

Status

Detected and Quantified

Creation Date

2008-10-29 15:23:07 UTC

Update Date

2023-02-21 17:17:28 UTC

HMDB ID

HMDB0011178

Secondary Accession Numbers

HMDB11178

Metabolite Identification

Common Name

Prolylglycine

Description

Prolylglycine is a dipeptide composed of proline and glycine. It is an incomplete breakdown product of protein digestion or protein catabolism. Some dipeptides are known to have physiological or cell-signaling effects although most are simply short-lived intermediates on their way to specific amino acid degradation pathways following further proteolysis. It is found in urine (PMID: 3782411 ).

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

HEADER    PROTEIN                                 16-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   16-MAY-19         0                                  
HETATM    1  C   UNK     0    4665.9114667.051   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0    4667.2464666.282   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0    4668.5804667.051   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0    4669.9194666.282   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0    4671.2534667.051   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0    4669.9194664.741   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0    4665.9114668.592   0.000  0.00  0.00           O+0
HETATM    8  N   UNK     0    4663.3244667.205   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0    4662.0784666.299   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0    4662.5544664.835   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0    4664.0944664.835   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0    4664.5704666.299   0.000  0.00  0.00           C+0
CONECT    1    2    7   12                                                  
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4                                                            
CONECT    7    1                                                            
CONECT    8    9   12                                                       
CONECT    9   10    8                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11    8    1                                                  
MASTER        0    0    0    0    0    0    0    0   12    0   24    0
END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
L-Pro-gly	ChEBI
L-Prolinylglycine	ChEBI
P-G	ChEBI
PG	ChEBI
Pro-gly	ChEBI
L-Prolylglycine	HMDB
N-L-Prolylglycine	HMDB
N-Prolylglycine	HMDB
NSC 89175	HMDB
p-g Dipeptide	HMDB
PG Dipeptide	HMDB
Proline glycine dipeptide	HMDB
Proline-glycine dipeptide	HMDB
Prolyl-glycine	HMDB
Prolylglycine	ChEBI

Chemical Formula

C₇H₁₂N₂O₃

Average Molecular Weight

172.1818

Monoisotopic Molecular Weight

172.08479226

IUPAC Name

2-{[(2S)-pyrrolidin-2-yl]formamido}acetic acid

Traditional Name

Pro-Gly

CAS Registry Number

2578-57-6

SMILES

OC(=O)CNC(=O)[C@@H]1CCCN1

InChI Identifier

InChI=1S/C7H12N2O3/c10-6(11)4-9-7(12)5-2-1-3-8-5/h5,8H,1-4H2,(H,9,12)(H,10,11)/t5-/m0/s1

InChI Key

RNKSNIBMTUYWSH-YFKPBYRVSA-N

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.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Dipeptides

Alternative Parents

Substituents

Alpha-dipeptide
Proline or derivatives
N-acyl-alpha-amino acid
N-acyl-alpha amino acid or derivatives
Alpha-amino acid amide
Alpha-amino acid or derivatives
Pyrrolidine carboxylic acid or derivatives
Pyrrolidine-2-carboxamide
Pyrrolidine
Amino acid or derivatives
Carboxamide group
Amino acid
Secondary carboxylic acid amide
Carboxylic acid
Secondary aliphatic amine
Monocarboxylic acid or derivatives
Azacycle
Organoheterocyclic compound
Secondary amine
Organic oxygen compound
Organic nitrogen compound
Organic oxide
Hydrocarbon derivative
Amine
Organonitrogen compound
Organooxygen compound
Organopnictogen compound
Carbonyl group
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

dipeptide (CHEBI:61695 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (HMDB: HMDB0011178)
Saliva (PMID: 31026179)

Excreta

Biofluid or Excreta

Urine (PMID: 10219662)
Feces (PMID: 27543620)

Source

Endogenous

Endogenous (HMDB: HMDB0011178)

Process

Not Available

Role

Not Available

Physical Properties

State

Solid

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
Water Solubility	6.91 g/L	ALOGPS
logP	-2.9	ALOGPS
logP	-3.7	ChemAxon
logS	-1.4	ALOGPS
pKa (Strongest Acidic)	3.66	ChemAxon
pKa (Strongest Basic)	9.81	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	78.43 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	40.87 m³·mol⁻¹	ChemAxon
Polarizability	16.79 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 Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DeepCCS	[M+H]+	130.883	30932474
DeepCCS	[M-H]-	128.445	30932474
DeepCCS	[M-2H]-	164.086	30932474
DeepCCS	[M+Na]+	139.338	30932474

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.	1.15 minutes	32390414
Predicted by Siyang on May 30, 2022	8.4931 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	7.98 minutes	32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid	303.5 seconds	40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	514.3 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	258.2 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	66.4 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	164.5 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	50.0 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	257.9 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	238.0 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	734.1 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	550.3 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	59.1 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	726.4 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	177.8 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	189.7 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	691.1 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	439.0 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	265.9 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Prolylglycine	OC(=O)CNC(=O)[C@@H]1CCCN1	2822.8	Standard polar	33892256
Prolylglycine	OC(=O)CNC(=O)[C@@H]1CCCN1	1674.5	Standard non polar	33892256
Prolylglycine	OC(=O)CNC(=O)[C@@H]1CCCN1	1837.8	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Prolylglycine,1TMS,isomer #1	C[Si](C)(C)OC(=O)CNC(=O)[C@@H]1CCCN1	1797.3	Semi standard non polar	33892256
Prolylglycine,1TMS,isomer #2	C[Si](C)(C)N(CC(=O)O)C(=O)[C@@H]1CCCN1	1774.7	Semi standard non polar	33892256
Prolylglycine,1TMS,isomer #3	C[Si](C)(C)N1CCC[C@H]1C(=O)NCC(=O)O	1826.0	Semi standard non polar	33892256
Prolylglycine,2TMS,isomer #1	C[Si](C)(C)OC(=O)CN(C(=O)[C@@H]1CCCN1)[Si](C)(C)C	1752.7	Semi standard non polar	33892256
Prolylglycine,2TMS,isomer #1	C[Si](C)(C)OC(=O)CN(C(=O)[C@@H]1CCCN1)[Si](C)(C)C	1785.9	Standard non polar	33892256
Prolylglycine,2TMS,isomer #1	C[Si](C)(C)OC(=O)CN(C(=O)[C@@H]1CCCN1)[Si](C)(C)C	2574.8	Standard polar	33892256
Prolylglycine,2TMS,isomer #2	C[Si](C)(C)OC(=O)CNC(=O)[C@@H]1CCCN1[Si](C)(C)C	1795.5	Semi standard non polar	33892256
Prolylglycine,2TMS,isomer #2	C[Si](C)(C)OC(=O)CNC(=O)[C@@H]1CCCN1[Si](C)(C)C	1817.0	Standard non polar	33892256
Prolylglycine,2TMS,isomer #2	C[Si](C)(C)OC(=O)CNC(=O)[C@@H]1CCCN1[Si](C)(C)C	2468.9	Standard polar	33892256
Prolylglycine,2TMS,isomer #3	C[Si](C)(C)N(CC(=O)O)C(=O)[C@@H]1CCCN1[Si](C)(C)C	1737.5	Semi standard non polar	33892256
Prolylglycine,2TMS,isomer #3	C[Si](C)(C)N(CC(=O)O)C(=O)[C@@H]1CCCN1[Si](C)(C)C	1825.8	Standard non polar	33892256
Prolylglycine,2TMS,isomer #3	C[Si](C)(C)N(CC(=O)O)C(=O)[C@@H]1CCCN1[Si](C)(C)C	2315.9	Standard polar	33892256
Prolylglycine,3TMS,isomer #1	C[Si](C)(C)OC(=O)CN(C(=O)[C@@H]1CCCN1[Si](C)(C)C)[Si](C)(C)C	1792.6	Semi standard non polar	33892256
Prolylglycine,3TMS,isomer #1	C[Si](C)(C)OC(=O)CN(C(=O)[C@@H]1CCCN1[Si](C)(C)C)[Si](C)(C)C	1889.2	Standard non polar	33892256
Prolylglycine,3TMS,isomer #1	C[Si](C)(C)OC(=O)CN(C(=O)[C@@H]1CCCN1[Si](C)(C)C)[Si](C)(C)C	2145.6	Standard polar	33892256
Prolylglycine,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)CNC(=O)[C@@H]1CCCN1	2045.6	Semi standard non polar	33892256
Prolylglycine,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)N(CC(=O)O)C(=O)[C@@H]1CCCN1	2018.2	Semi standard non polar	33892256
Prolylglycine,1TBDMS,isomer #3	CC(C)(C)[Si](C)(C)N1CCC[C@H]1C(=O)NCC(=O)O	2078.1	Semi standard non polar	33892256
Prolylglycine,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)CN(C(=O)[C@@H]1CCCN1)[Si](C)(C)C(C)(C)C	2227.7	Semi standard non polar	33892256
Prolylglycine,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)CN(C(=O)[C@@H]1CCCN1)[Si](C)(C)C(C)(C)C	2205.9	Standard non polar	33892256
Prolylglycine,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)CN(C(=O)[C@@H]1CCCN1)[Si](C)(C)C(C)(C)C	2609.8	Standard polar	33892256
Prolylglycine,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC(=O)CNC(=O)[C@@H]1CCCN1[Si](C)(C)C(C)(C)C	2292.2	Semi standard non polar	33892256
Prolylglycine,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC(=O)CNC(=O)[C@@H]1CCCN1[Si](C)(C)C(C)(C)C	2225.0	Standard non polar	33892256
Prolylglycine,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC(=O)CNC(=O)[C@@H]1CCCN1[Si](C)(C)C(C)(C)C	2575.8	Standard polar	33892256
Prolylglycine,2TBDMS,isomer #3	CC(C)(C)[Si](C)(C)N(CC(=O)O)C(=O)[C@@H]1CCCN1[Si](C)(C)C(C)(C)C	2247.9	Semi standard non polar	33892256
Prolylglycine,2TBDMS,isomer #3	CC(C)(C)[Si](C)(C)N(CC(=O)O)C(=O)[C@@H]1CCCN1[Si](C)(C)C(C)(C)C	2233.0	Standard non polar	33892256
Prolylglycine,2TBDMS,isomer #3	CC(C)(C)[Si](C)(C)N(CC(=O)O)C(=O)[C@@H]1CCCN1[Si](C)(C)C(C)(C)C	2509.8	Standard polar	33892256
Prolylglycine,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)CN(C(=O)[C@@H]1CCCN1[Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	2481.7	Semi standard non polar	33892256
Prolylglycine,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)CN(C(=O)[C@@H]1CCCN1[Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	2476.8	Standard non polar	33892256
Prolylglycine,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)CN(C(=O)[C@@H]1CCCN1[Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	2492.9	Standard polar	33892256

Spectra

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood
Feces
Saliva
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 Available	Not Available	Normal	Not Available	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	27543620	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	25037050	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	29808030	details
Urine	Detected and Quantified	0.31 +/- 0.16 umol/mmol creatinine	Adult (>18 years old)	Both	Normal	10219662	details

Abnormal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Colorectal cancer	25037050	details
Saliva	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Male	Attachment loss	31026179	details
Saliva	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Male	Missing teeth	31026179	details
Saliva	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Male	Periodontal Probing Depth	31026179	details

Associated Disorders and Diseases

Disease References

Colorectal cancer
Goedert JJ, Sampson JN, Moore SC, Xiao Q, Xiong X, Hayes RB, Ahn J, Shi J, Sinha R: Fecal metabolomics: assay performance and association with colorectal cancer. Carcinogenesis. 2014 Sep;35(9):2089-96. doi: 10.1093/carcin/bgu131. Epub 2014 Jul 18. [PubMed:25037050 ]
Attachment loss
Liebsch C, Pitchika V, Pink C, Samietz S, Kastenmuller G, Artati A, Suhre K, Adamski J, Nauck M, Volzke H, Friedrich N, Kocher T, Holtfreter B, Pietzner M: The Saliva Metabolome in Association to Oral Health Status. J Dent Res. 2019 Jun;98(6):642-651. doi: 10.1177/0022034519842853. Epub 2019 Apr 26. [PubMed:31026179 ]
Missing teeth
Liebsch C, Pitchika V, Pink C, Samietz S, Kastenmuller G, Artati A, Suhre K, Adamski J, Nauck M, Volzke H, Friedrich N, Kocher T, Holtfreter B, Pietzner M: The Saliva Metabolome in Association to Oral Health Status. J Dent Res. 2019 Jun;98(6):642-651. doi: 10.1177/0022034519842853. Epub 2019 Apr 26. [PubMed:31026179 ]
Periodontal Probing Depth
Liebsch C, Pitchika V, Pink C, Samietz S, Kastenmuller G, Artati A, Suhre K, Adamski J, Nauck M, Volzke H, Friedrich N, Kocher T, Holtfreter B, Pietzner M: The Saliva Metabolome in Association to Oral Health Status. J Dent Res. 2019 Jun;98(6):642-651. doi: 10.1177/0022034519842853. Epub 2019 Apr 26. [PubMed:31026179 ]

Associated OMIM IDs

114500 (Colorectal cancer)

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

C00011257

Chemspider ID

4932143

KEGG Compound ID

Not Available

BioCyc ID

CPD0-2182

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

6426709

PDB ID

Not Available

ChEBI ID

61695

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

Jandke J, Spiteller G: Dipeptide analysis in human urine. J Chromatogr. 1986 Oct 31;382:39-45. [PubMed:3782411 ]

Showing metabocard for Prolylglycine (HMDB0011178)

MOL for HMDB0011178 (Prolylglycine)

3D MOL for HMDB0011178 (Prolylglycine)

3D SDF for HMDB0011178 (Prolylglycine)

3D-SDF for HMDB0011178 (Prolylglycine)

PDB for HMDB0011178 (Prolylglycine)

3D PDB for HMDB0011178 (Prolylglycine)

SMILES for HMDB0011178 (Prolylglycine)

INCHI for HMDB0011178 (Prolylglycine)

Structure for HMDB0011178 (Prolylglycine)

3D Structure for HMDB0011178 (Prolylglycine)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized