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Record Information

Version

5.0

Status

Detected and Quantified

Creation Date

2007-05-30 12:04:10 UTC

Update Date

2022-09-22 18:34:55 UTC

HMDB ID

HMDB0006695

Secondary Accession Numbers

HMDB0029018
HMDB06695
HMDB29018

Metabolite Identification

Common Name

Prolylhydroxyproline

Description

Prolylhydroxyproline is a dipeptide. Prolylhydroxyproline is a marker of bone collagen degradation, showing high sensitivity for the diagnosis of osteoporosis. Prolylhydroxyproline has been suggested as a possible alternative to hydroxyproline determination in bone resorption studies. Prolylhydroxyproline is one of the iminodipeptides present in the urine of patients with prolidase deficiency. Prolidase (X-Pro dipeptidase EC 3.4.13.9) splits iminodipeptides containing C-terminal proline or hydroxyproline (X-Pro or X-Hyp) to X+Pro or X+Hyp. Prolidase deficiency is a rare autosomal recessive disease characterized by chronic ulcerative dermatitis and mental retardation. These patients excrete large amounts of iminodipeptides containing C-terminal proline in the urine due to hereditary prolidase deficiency (PMID: 12636053 , 11863289 , 2387877 , 1874885 , 9586797 ).

Structure

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

HMDB0006695
     RDKit          3D
Prolylhydroxyproline
 32 33  0  0  0  0  0  0  0  0999 V2000
   -3.9392    1.3679   -1.8568 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6883    1.0613   -1.7472 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8930    1.6488   -2.6806 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3247    0.1695   -0.6871 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.7165    0.6352    0.7017 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8994   -0.3259    1.5807 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.7475   -1.1156    2.3489 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1457   -1.1976    0.6069 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9669   -0.2015   -0.4865 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.2755    0.1510   -1.0278 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4455    0.9618   -1.9692 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5316   -0.4601   -0.4748 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9072    0.1826    0.8395 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4044   -0.0848    0.9410 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7776   -0.4799   -0.4590 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6750   -0.0098   -1.2929 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6224    2.6194   -2.7159 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8881   -0.8123   -0.8023 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3898    1.6450    0.9397 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7920    0.4482    0.9149 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1950    0.2372    2.2308 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1259   -1.8010    1.7491 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2338   -1.6393    0.9473 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8833   -1.9098    0.1757 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4491   -1.5381   -0.4689 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7192    1.2663    0.7443 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4576   -0.2376    1.7280 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6142   -0.8966    1.6389 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8968    0.8731    1.2096 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7167    0.0038   -0.7704 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8616   -1.5811   -0.5696 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7196    1.0198   -1.2879 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  2  0
 10 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
  9  4  1  0
 16 12  1  0
  3 17  1  0
  4 18  1  6
  5 19  1  0
  5 20  1  0
  6 21  1  1
  7 22  1  0
  8 23  1  0
  8 24  1  0
 12 25  1  1
 13 26  1  0
 13 27  1  0
 14 28  1  0
 14 29  1  0
 15 30  1  0
 15 31  1  0
 16 32  1  0
M  END


  Mrv1652307041922002D          

 16 17  0  0  0  0            999 V2000
10002.1009 9999.6179    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10002.8128 9999.2054    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10002.100910000.4412    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9999.8095 9997.7700    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.7175 9999.7002    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
10000.0502 9999.2152    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.3051 9998.4306    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
10001.1301 9998.4306    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.3850 9999.2152    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
10000.717510000.5252    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.432010000.9377    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.003110000.9377    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9999.916810001.7581    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9999.109810001.9297    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.697310001.2152    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.249410000.6022    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  5  6  1  0  0  0  0
  5  9  1  0  0  0  0
  7  4  1  1  0  0  0
  9  1  1  6  0  0  0
  5 10  1  0  0  0  0
 10 11  2  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 12 16  1  0  0  0  0
 13 14  1  0  0  0  0
 12 13  1  0  0  0  0
 12 10  1  6  0  0  0
M  END
> <DATABASE_ID>
HMDB0006695

> <DATABASE_NAME>
hmdb

> <SMILES>
O[C@@H]1C[C@H](N(C1)C(=O)[C@@H]1CCCN1)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C10H16N2O4/c13-6-4-8(10(15)16)12(5-6)9(14)7-2-1-3-11-7/h6-8,11,13H,1-5H2,(H,15,16)/t6-,7+,8+/m1/s1

> <INCHI_KEY>
ONPXCLZMBSJLSP-CSMHCCOUSA-N

> <FORMULA>
C10H16N2O4

> <MOLECULAR_WEIGHT>
228.245

> <EXACT_MASS>
228.11100701

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
32

> <JCHEM_AVERAGE_POLARIZABILITY>
22.319425498540514

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,4R)-4-hydroxy-1-[(2S)-pyrrolidine-2-carbonyl]pyrrolidine-2-carboxylic acid

> <JCHEM_LOGP>
-3.980841221369723

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.826419781209651

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.5386018000615693

> <JCHEM_PKA_STRONGEST_BASIC>
9.817399252166704

> <JCHEM_POLAR_SURFACE_AREA>
89.86999999999999

> <JCHEM_REFRACTIVITY>
54.36870000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
proline-hydroxyproline

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0006695
     RDKit          3D
Prolylhydroxyproline
 32 33  0  0  0  0  0  0  0  0999 V2000
   -3.9392    1.3679   -1.8568 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6883    1.0613   -1.7472 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8930    1.6488   -2.6806 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3247    0.1695   -0.6871 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.7165    0.6352    0.7017 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8994   -0.3259    1.5807 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.7475   -1.1156    2.3489 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1457   -1.1976    0.6069 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9669   -0.2015   -0.4865 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.2755    0.1510   -1.0278 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4455    0.9618   -1.9692 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5316   -0.4601   -0.4748 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9072    0.1826    0.8395 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4044   -0.0848    0.9410 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7776   -0.4799   -0.4590 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6750   -0.0098   -1.2929 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6224    2.6194   -2.7159 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8881   -0.8123   -0.8023 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3898    1.6450    0.9397 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7920    0.4482    0.9149 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1950    0.2372    2.2308 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1259   -1.8010    1.7491 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2338   -1.6393    0.9473 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8833   -1.9098    0.1757 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4491   -1.5381   -0.4689 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7192    1.2663    0.7443 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4576   -0.2376    1.7280 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6142   -0.8966    1.6389 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8968    0.8731    1.2096 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7167    0.0038   -0.7704 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8616   -1.5811   -0.5696 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7196    1.0198   -1.2879 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  2  0
 10 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
  9  4  1  0
 16 12  1  0
  3 17  1  0
  4 18  1  6
  5 19  1  0
  5 20  1  0
  6 21  1  1
  7 22  1  0
  8 23  1  0
  8 24  1  0
 12 25  1  1
 13 26  1  0
 13 27  1  0
 14 28  1  0
 14 29  1  0
 15 30  1  0
 15 31  1  0
 16 32  1  0
M  END

HEADER    PROTEIN                                 04-JUL-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-JUL-19         0                                  
HETATM    1  C   UNK     0    8670.5888665.953   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0    8671.9178665.183   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0    8670.5888667.490   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0    8666.3118662.504   0.000  0.00  0.00           O+0
HETATM    5  N   UNK     0    8668.0068666.107   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0    8666.7608665.202   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0    8667.2368663.737   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0    8668.7768663.737   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0    8669.2528665.202   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0    8668.0068667.647   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0    8669.3408668.417   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0    8666.6728668.417   0.000  0.00  0.00           C+0
HETATM   13  N   UNK     0    8666.5118669.948   0.000  0.00  0.00           N+0
HETATM   14  C   UNK     0    8665.0058670.269   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0    8664.2358668.935   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0    8665.2668667.791   0.000  0.00  0.00           C+0
CONECT    1    2    3    9                                                  
CONECT    2    1                                                            
CONECT    3    1                                                            
CONECT    4    7                                                            
CONECT    5    6    9   10                                                  
CONECT    6    7    5                                                       
CONECT    7    6    8    4                                                  
CONECT    8    7    9                                                       
CONECT    9    8    5    1                                                  
CONECT   10    5   11   12                                                  
CONECT   11   10                                                            
CONECT   12   16   13   10                                                  
CONECT   13   14   12                                                       
CONECT   14   15   13                                                       
CONECT   15   14   16                                                       
CONECT   16   15   12                                                       
MASTER        0    0    0    0    0    0    0    0   16    0   34    0
END

COMPND    HMDB0006695
HETATM    1  O1  UNL     1      -3.939   1.368  -1.857  1.00  0.00           O  
HETATM    2  C1  UNL     1      -2.688   1.061  -1.747  1.00  0.00           C  
HETATM    3  O2  UNL     1      -1.893   1.649  -2.681  1.00  0.00           O  
HETATM    4  C2  UNL     1      -2.325   0.169  -0.687  1.00  0.00           C  
HETATM    5  C3  UNL     1      -2.717   0.635   0.702  1.00  0.00           C  
HETATM    6  C4  UNL     1      -1.899  -0.326   1.581  1.00  0.00           C  
HETATM    7  O3  UNL     1      -2.748  -1.116   2.349  1.00  0.00           O  
HETATM    8  C5  UNL     1      -1.146  -1.198   0.607  1.00  0.00           C  
HETATM    9  N1  UNL     1      -0.967  -0.202  -0.486  1.00  0.00           N  
HETATM   10  C6  UNL     1       0.276   0.151  -1.028  1.00  0.00           C  
HETATM   11  O4  UNL     1       0.445   0.962  -1.969  1.00  0.00           O  
HETATM   12  C7  UNL     1       1.532  -0.460  -0.475  1.00  0.00           C  
HETATM   13  C8  UNL     1       1.907   0.183   0.839  1.00  0.00           C  
HETATM   14  C9  UNL     1       3.404  -0.085   0.941  1.00  0.00           C  
HETATM   15  C10 UNL     1       3.778  -0.480  -0.459  1.00  0.00           C  
HETATM   16  N2  UNL     1       2.675  -0.010  -1.293  1.00  0.00           N  
HETATM   17  H1  UNL     1      -1.622   2.619  -2.716  1.00  0.00           H  
HETATM   18  H2  UNL     1      -2.888  -0.812  -0.802  1.00  0.00           H  
HETATM   19  H3  UNL     1      -2.390   1.645   0.940  1.00  0.00           H  
HETATM   20  H4  UNL     1      -3.792   0.448   0.915  1.00  0.00           H  
HETATM   21  H5  UNL     1      -1.195   0.237   2.231  1.00  0.00           H  
HETATM   22  H6  UNL     1      -3.126  -1.801   1.749  1.00  0.00           H  
HETATM   23  H7  UNL     1      -0.234  -1.639   0.947  1.00  0.00           H  
HETATM   24  H8  UNL     1      -1.883  -1.910   0.176  1.00  0.00           H  
HETATM   25  H9  UNL     1       1.449  -1.538  -0.469  1.00  0.00           H  
HETATM   26  H10 UNL     1       1.719   1.266   0.744  1.00  0.00           H  
HETATM   27  H11 UNL     1       1.458  -0.238   1.728  1.00  0.00           H  
HETATM   28  H12 UNL     1       3.614  -0.897   1.639  1.00  0.00           H  
HETATM   29  H13 UNL     1       3.897   0.873   1.210  1.00  0.00           H  
HETATM   30  H14 UNL     1       4.717   0.004  -0.770  1.00  0.00           H  
HETATM   31  H15 UNL     1       3.862  -1.581  -0.570  1.00  0.00           H  
HETATM   32  H16 UNL     1       2.720   1.020  -1.288  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3   17
CONECT    4    5    9   18
CONECT    5    6   19   20
CONECT    6    7    8   21
CONECT    7   22
CONECT    8    9   23   24
CONECT    9   10
CONECT   10   11   11   12
CONECT   12   13   16   25
CONECT   13   14   26   27
CONECT   14   15   28   29
CONECT   15   16   30   31
CONECT   16   32
END

HMDB0006695
     RDKit          3D
Prolylhydroxyproline
 32 33  0  0  0  0  0  0  0  0999 V2000
   -3.9392    1.3679   -1.8568 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6883    1.0613   -1.7472 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8930    1.6488   -2.6806 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3247    0.1695   -0.6871 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.7165    0.6352    0.7017 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8994   -0.3259    1.5807 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.7475   -1.1156    2.3489 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1457   -1.1976    0.6069 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9669   -0.2015   -0.4865 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.2755    0.1510   -1.0278 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4455    0.9618   -1.9692 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5316   -0.4601   -0.4748 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9072    0.1826    0.8395 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4044   -0.0848    0.9410 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7776   -0.4799   -0.4590 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6750   -0.0098   -1.2929 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6224    2.6194   -2.7159 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8881   -0.8123   -0.8023 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3898    1.6450    0.9397 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7920    0.4482    0.9149 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1950    0.2372    2.2308 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1259   -1.8010    1.7491 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2338   -1.6393    0.9473 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8833   -1.9098    0.1757 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4491   -1.5381   -0.4689 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7192    1.2663    0.7443 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4576   -0.2376    1.7280 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6142   -0.8966    1.6389 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8968    0.8731    1.2096 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7167    0.0038   -0.7704 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8616   -1.5811   -0.5696 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7196    1.0198   -1.2879 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  2  0
 10 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
  9  4  1  0
 16 12  1  0
  3 17  1  0
  4 18  1  6
  5 19  1  0
  5 20  1  0
  6 21  1  1
  7 22  1  0
  8 23  1  0
  8 24  1  0
 12 25  1  1
 13 26  1  0
 13 27  1  0
 14 28  1  0
 14 29  1  0
 15 30  1  0
 15 31  1  0
 16 32  1  0
M  END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
L-Pro-L-hyp	ChEBI
L-Prolyl-L-hydroxyproline	ChEBI
(4R)-L-Prolyl-4-hydroxy-L-proline	HMDB
4-Hydroxy-1-L-prolyl-proline	HMDB
L-4-Hydroxy-1-L-prolyl-proline	HMDB
Proline-hydroxyproline	HMDB
trans-4-Hydroxy-1-L-prolyl-proline	HMDB
Prolylhydroxyproline	ChEBI
Pro-hydroxy-Pro	HMDB
Pro-Hyp	HMDB
Proline hydroxyproline dipeptide	HMDB
Proline-hydroxyproline dipeptide	HMDB

Chemical Formula

C₁₀H₁₆N₂O₄

Average Molecular Weight

228.245

Monoisotopic Molecular Weight

228.11100701

IUPAC Name

(2S,4R)-4-hydroxy-1-[(2S)-pyrrolidine-2-carbonyl]pyrrolidine-2-carboxylic acid

Traditional Name

proline-hydroxyproline

CAS Registry Number

18684-24-7

SMILES

O[C@@H]1C[C@H](N(C1)C(=O)[C@@H]1CCCN1)C(O)=O

InChI Identifier

InChI=1S/C10H16N2O4/c13-6-4-8(10(15)16)12(5-6)9(14)7-2-1-3-11-7/h6-8,11,13H,1-5H2,(H,15,16)/t6-,7+,8+/m1/s1

InChI Key

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

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

dipeptide (CHEBI:74767 )

Ontology

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	109 g/L	ALOGPS
logP	-4	ChemAxon
pKa (Strongest Acidic)	3.54	ChemAxon
pKa (Strongest Basic)	9.82	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	89.87 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	54.37 m³·mol⁻¹	ChemAxon
Polarizability	22.32 Å³	ChemAxon
Number of Rings	2	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
DarkChem	[M+H]+	151.272	31661259
DarkChem	[M-H]-	150.291	31661259
DeepCCS	[M+H]+	150.373	30932474
DeepCCS	[M-H]-	147.978	30932474
DeepCCS	[M-2H]-	181.042	30932474
DeepCCS	[M+Na]+	156.286	30932474
AllCCS	[M+H]+	151.1	32859911
AllCCS	[M+H-H2O]+	147.3	32859911
AllCCS	[M+NH4]+	154.7	32859911
AllCCS	[M+Na]+	155.7	32859911
AllCCS	[M-H]-	150.4	32859911
AllCCS	[M+Na-2H]-	150.3	32859911
AllCCS	[M+HCOO]-	150.4	32859911

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.	1.44 minutes	32390414
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.	1.96 minutes	32390414
Predicted by Siyang on May 30, 2022	8.8068 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	6.99 minutes	32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid	387.7 seconds	40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	418.0 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	243.6 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	62.7 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	164.7 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	45.2 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	272.5 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	247.0 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	840.6 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	547.7 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	45.9 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	716.8 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	183.0 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	217.9 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	764.2 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	535.5 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	334.2 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Prolylhydroxyproline	O[C@@H]1C[C@H](N(C1)C(=O)[C@@H]1CCCN1)C(O)=O	3401.2	Standard polar	33892256
Prolylhydroxyproline	O[C@@H]1C[C@H](N(C1)C(=O)[C@@H]1CCCN1)C(O)=O	2172.6	Standard non polar	33892256
Prolylhydroxyproline	O[C@@H]1C[C@H](N(C1)C(=O)[C@@H]1CCCN1)C(O)=O	2268.2	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Prolylhydroxyproline,1TMS,isomer #1	C[Si](C)(C)O[C@@H]1C[C@@H](C(=O)O)N(C(=O)[C@@H]2CCCN2)C1	2141.1	Semi standard non polar	33892256
Prolylhydroxyproline,1TMS,isomer #2	C[Si](C)(C)OC(=O)[C@@H]1C[C@@H](O)CN1C(=O)[C@@H]1CCCN1	2078.7	Semi standard non polar	33892256
Prolylhydroxyproline,1TMS,isomer #3	C[Si](C)(C)N1CCC[C@H]1C(=O)N1C[C@H](O)C[C@H]1C(=O)O	2036.4	Semi standard non polar	33892256
Prolylhydroxyproline,2TMS,isomer #1	C[Si](C)(C)OC(=O)[C@@H]1C[C@@H](O[Si](C)(C)C)CN1C(=O)[C@@H]1CCCN1	2144.4	Semi standard non polar	33892256
Prolylhydroxyproline,2TMS,isomer #2	C[Si](C)(C)O[C@@H]1C[C@@H](C(=O)O)N(C(=O)[C@@H]2CCCN2[Si](C)(C)C)C1	2084.6	Semi standard non polar	33892256
Prolylhydroxyproline,2TMS,isomer #3	C[Si](C)(C)OC(=O)[C@@H]1C[C@@H](O)CN1C(=O)[C@@H]1CCCN1[Si](C)(C)C	2062.6	Semi standard non polar	33892256
Prolylhydroxyproline,3TMS,isomer #1	C[Si](C)(C)OC(=O)[C@@H]1C[C@@H](O[Si](C)(C)C)CN1C(=O)[C@@H]1CCCN1[Si](C)(C)C	2152.3	Semi standard non polar	33892256
Prolylhydroxyproline,3TMS,isomer #1	C[Si](C)(C)OC(=O)[C@@H]1C[C@@H](O[Si](C)(C)C)CN1C(=O)[C@@H]1CCCN1[Si](C)(C)C	2224.4	Standard non polar	33892256
Prolylhydroxyproline,3TMS,isomer #1	C[Si](C)(C)OC(=O)[C@@H]1C[C@@H](O[Si](C)(C)C)CN1C(=O)[C@@H]1CCCN1[Si](C)(C)C	2678.3	Standard polar	33892256
Prolylhydroxyproline,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)O[C@@H]1C[C@@H](C(=O)O)N(C(=O)[C@@H]2CCCN2)C1	2372.8	Semi standard non polar	33892256
Prolylhydroxyproline,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC(=O)[C@@H]1C[C@@H](O)CN1C(=O)[C@@H]1CCCN1	2332.0	Semi standard non polar	33892256
Prolylhydroxyproline,1TBDMS,isomer #3	CC(C)(C)[Si](C)(C)N1CCC[C@H]1C(=O)N1C[C@H](O)C[C@H]1C(=O)O	2303.9	Semi standard non polar	33892256
Prolylhydroxyproline,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)[C@@H]1C[C@@H](O[Si](C)(C)C(C)(C)C)CN1C(=O)[C@@H]1CCCN1	2599.9	Semi standard non polar	33892256
Prolylhydroxyproline,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)O[C@@H]1C[C@@H](C(=O)O)N(C(=O)[C@@H]2CCCN2[Si](C)(C)C(C)(C)C)C1	2582.5	Semi standard non polar	33892256
Prolylhydroxyproline,2TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OC(=O)[C@@H]1C[C@@H](O)CN1C(=O)[C@@H]1CCCN1[Si](C)(C)C(C)(C)C	2546.4	Semi standard non polar	33892256
Prolylhydroxyproline,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)[C@@H]1C[C@@H](O[Si](C)(C)C(C)(C)C)CN1C(=O)[C@@H]1CCCN1[Si](C)(C)C(C)(C)C	2830.1	Semi standard non polar	33892256
Prolylhydroxyproline,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)[C@@H]1C[C@@H](O[Si](C)(C)C(C)(C)C)CN1C(=O)[C@@H]1CCCN1[Si](C)(C)C(C)(C)C	2799.3	Standard non polar	33892256
Prolylhydroxyproline,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)[C@@H]1C[C@@H](O[Si](C)(C)C(C)(C)C)CN1C(=O)[C@@H]1CCCN1[Si](C)(C)C(C)(C)C	2970.4	Standard polar	33892256

Spectra

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood
Cerebrospinal Fluid (CSF)
Sweat
Urine

Tissue Locations

Placenta

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
Cerebrospinal Fluid (CSF)	Detected and Quantified	0.87 +/- 1.0 uM	Adult (>18 years old)	Both	Normal	15145598	details
Urine	Detected and Quantified	4.8-9.4 umol/mmol creatinine	Adult (>18 years old)	Female	Normal	27012787	details
Urine	Detected and Quantified	4.5-7.7 umol/mmol creatinine	Adult (>18 years old)	Male	Normal	27012787	details
Urine	Detected and Quantified	2.4-25.6 umol/mmol creatinine	Adult (>18 years old)	Both	Normal	22431455	details

Abnormal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Cerebrospinal Fluid (CSF)	Detected and Quantified	0.086 +/- 0.016 uM	Adult (>18 years old)	Both	Alzheimer's disease	17031479	details
Sweat	Detected but not Quantified	Not Quantified	Infant (0-1 year old)	Not Specified	screen-positive CF	Adriana Nori...	details
Urine	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Female	Epithelial ovarian cancer	23163809	details

Associated Disorders and Diseases

Disease References

Alzheimer's disease
Fonteh AN, Harrington RJ, Tsai A, Liao P, Harrington MG: Free amino acid and dipeptide changes in the body fluids from Alzheimer's disease subjects. Amino Acids. 2007 Feb;32(2):213-24. Epub 2006 Oct 10. [PubMed:17031479 ]
Cystic fibrosis
Adriana Nori de Macedo. Robust capillary electrophoresis methods for biomarker discovery and routine measurements in clinical and epidemiological applications. March 2017 [Link]

Associated OMIM IDs

104300 (Alzheimer's disease)
219700 (Cystic fibrosis)

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB024028

KNApSAcK ID

Not Available

Chemspider ID

10077215

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

11902892

PDB ID

Not Available

ChEBI ID

74767

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

MDB00000488

Good Scents ID

Not Available

References

Synthesis Reference

ustova, V.; Blaha, Karel. Amino acids and peptides. CXXVI. Dipeptides containing proline and 4-hydroxyproline. Collection of Czechoslovak Chemical Communications (1975), 40(3), 662-9.

Material Safety Data Sheet (MSDS)

Not Available

General References

Husek P, Pohlidal A, Slabik D: Rapid screening of urinary proline-hydroxyproline dipeptide in bone turnover studies. J Chromatogr B Analyt Technol Biomed Life Sci. 2002 Feb 5;767(1):169-74. [PubMed:11863289 ]
Pohlidal A, Husek P, Palicka V, Slabik D, Hill M, Matucha P: Novel and traditional biomarkers of bone turnover in postmenopausal women. Clin Chem Lab Med. 2003 Jan;41(1):74-8. [PubMed:12636053 ]
Sugahara K, Kodama H: Liquid chromatography-mass spectrometry for simultaneous analyses of iminodipeptides containing an N-terminal or a C-terminal proline. J Chromatogr. 1991 Apr 19;565(1-2):408-15. [PubMed:1874885 ]
Kodama H, Nakamura H, Sugahara K, Numajiri Y: Liquid chromatography-mass spectrometry for the qualitative analyses of iminodipeptides in the urine of patients with prolidase deficiency. J Chromatogr. 1990 May 18;527(2):279-88. [PubMed:2387877 ]
Zhang J, Sugahara K, Yasuda K, Kodama H, Sagara Y, Kodama H: The effects of serum iminodipeptides and prednisolone on superoxide generation and tyrosyl phosphorylation of proteins in neutrophils from a patient with prolidase deficiency. Free Radic Biol Med. 1998 Mar 15;24(5):689-98. [PubMed:9586797 ]
Lowry M, Hall DE, Brosnan JT: Metabolism of glycine- and hydroxyproline-containing peptides by the isolated perfused rat kidney. Biochem J. 1985 Jul 15;229(2):545-9. [PubMed:4038280 ]
Kawaguchi T, Nanbu PN, Kurokawa M: Distribution of prolylhydroxyproline and its metabolites after oral administration in rats. Biol Pharm Bull. 2012;35(3):422-7. [PubMed:22382331 ]
Lampiaho K, Nikkari T, Pikkarainen J, Karkkainen J, Kulonen E: Unexpected occurrence of prolylhydroxyproline during the analysis of collagen-bound carbohydrates by gas-liquid chromatography. J Chromatogr. 1972 Feb 2;64(2):211-8. [PubMed:5013106 ]
Bienenstock HKIBRICK AC: Urinary excretion of prolylhydroxyproline in rheumatic diseases. Ann Rheum Dis. 1969 Jan;28(1):28-30. [PubMed:5305862 ]
Codini M, Palmerini CA, Fini C, Lucarelli C, Floridi A: High-performance liquid chromatographic method for the determination of prolyl peptides in urine. J Chromatogr. 1991 Jan 4;536(1-2):337-41. [PubMed:2050773 ]
KIBRICK AC, HASHIRO CQ, SCHULTZ RS, WALTERS MI, MILHORAT AT: PROLYLHYDROXYPROLINE IN URINE: ITS DETERMINATION AND OBSERVATIONS IN MUSCULAR DYSTROPHY. Clin Chim Acta. 1964 Oct;10:344-51. [PubMed:14219579 ]
Hueckel HJ, Rogers QR: Prolylhydroxyproline absorption in hamsters. Can J Biochem. 1972 Jul;50(7):782-90. [PubMed:5050935 ]
Kibrick AC, Power HL, Sevendal E, Milhorat AT: Prolylhydroxyproline in urine: improved method for detecting radioactivity with a scanner on full sheets of chromatography paper. Anal Biochem. 1968 Oct 24;25(1):40-5. [PubMed:5704756 ]
KIBRICK AC, HASHIRO CQ, WALTERS MI, MILHORAT AT: DIKETOPIPERAZINE OF PROLYLHYDROXYPROLINE IN NORMAL HUMAN URINE. Proc Soc Exp Biol Med. 1965 Jan;118:62-4. [PubMed:14254586 ]
Zhang A, Sun H, Han Y, Yuan Y, Wang P, Song G, Yuan X, Zhang M, Xie N, Wang X: Exploratory urinary metabolic biomarkers and pathways using UPLC-Q-TOF-HDMS coupled with pattern recognition approach. Analyst. 2012 Sep 21;137(18):4200-8. doi: 10.1039/c2an35780a. Epub 2012 Jul 31. [PubMed:22852134 ]
Elshenawy S, Pinney SE, Stuart T, Doulias PT, Zura G, Parry S, Elovitz MA, Bennett MJ, Bansal A, Strauss JF 3rd, Ischiropoulos H, Simmons RA: The Metabolomic Signature of the Placenta in Spontaneous Preterm Birth. Int J Mol Sci. 2020 Feb 4;21(3). pii: ijms21031043. doi: 10.3390/ijms21031043. [PubMed:32033212 ]

Showing metabocard for Prolylhydroxyproline (HMDB0006695)

MOL for HMDB0006695 (Prolylhydroxyproline)

3D MOL for HMDB0006695 (Prolylhydroxyproline)

3D SDF for HMDB0006695 (Prolylhydroxyproline)

3D-SDF for HMDB0006695 (Prolylhydroxyproline)

PDB for HMDB0006695 (Prolylhydroxyproline)

3D PDB for HMDB0006695 (Prolylhydroxyproline)

SMILES for HMDB0006695 (Prolylhydroxyproline)

INCHI for HMDB0006695 (Prolylhydroxyproline)

Structure for HMDB0006695 (Prolylhydroxyproline)

3D Structure for HMDB0006695 (Prolylhydroxyproline)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized