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Showing metabocard for 3-Hydroxyproline (HMDB0245903)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-10 22:57:03 UTC
Update Date2022-09-22 17:44:19 UTC
HMDB IDHMDB0245903
Secondary Accession NumbersNone
Metabolite Identification
Common Name3-Hydroxyproline
Description3-Hydroxyproline belongs to the class of organic compounds known as proline and derivatives. Proline and derivatives are compounds containing proline or a derivative thereof resulting from reaction of proline at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. Based on a literature review very few articles have been published on 3-Hydroxyproline. This compound has been identified in human blood as reported by (PMID: 31557052 ). 3-hydroxyproline is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 3-Hydroxyproline is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0245903 (3-Hydroxyproline)

  Mrv1652305221920172D          

  9  9  0  0  0  0            999 V2000
    0.1553   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.9393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8843    0.8843    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1467    2.3518    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2822    2.3518    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  1  1  0  0  0  0
  4  3  1  0  0  0  0
  5  4  1  0  0  0  0
  6  2  1  0  0  0  0
  6  4  1  0  0  0  0
  7  3  1  0  0  0  0
  8  5  2  0  0  0  0
  9  5  1  0  0  0  0
M  END
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3D MOL for HMDB0245903 (3-Hydroxyproline)

HMDB0245903
     RDKit          3D
3-Hydroxyproline
 18 18  0  0  0  0  0  0  0  0999 V2000
    2.5193   -0.1147   -0.1289 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6217   -0.9408   -0.2438 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7480   -2.1324    0.3748 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4339   -0.5730   -1.0169 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8296   -1.0942   -0.5423 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5737   -0.2828    0.2461 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0984    1.1069   -0.0588 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2288    0.9771   -0.7488 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2006    1.5060    0.1156 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9529   -2.9882   -0.1363 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6533   -0.6820   -2.0435 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3910   -1.3006   -1.4762 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6664   -0.3212    0.0087 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4270   -0.5147    1.3161 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0068    1.6655    0.9060 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7780    1.6601   -0.7244 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2707    1.5425   -1.7113 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1418    2.4865    0.0786 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
  7  8  1  0
  8  9  1  0
  8  4  1  0
  3 10  1  0
  4 11  1  0
  5 12  1  0
  6 13  1  0
  6 14  1  0
  7 15  1  0
  7 16  1  0
  8 17  1  0
  9 18  1  0
M  END
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3D SDF for HMDB0245903 (3-Hydroxyproline)

  Mrv1652305221920172D          

  9  9  0  0  0  0            999 V2000
    0.1553   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.9393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8843    0.8843    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1467    2.3518    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2822    2.3518    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  1  1  0  0  0  0
  4  3  1  0  0  0  0
  5  4  1  0  0  0  0
  6  2  1  0  0  0  0
  6  4  1  0  0  0  0
  7  3  1  0  0  0  0
  8  5  2  0  0  0  0
  9  5  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0245903

> <DATABASE_NAME>
hmdb

> <SMILES>
OC1CCNC1C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C5H9NO3/c7-3-1-2-6-4(3)5(8)9/h3-4,6-7H,1-2H2,(H,8,9)

> <INCHI_KEY>
BJBUEDPLEOHJGE-UHFFFAOYSA-N

> <FORMULA>
C5H9NO3

> <MOLECULAR_WEIGHT>
131.1299

> <EXACT_MASS>
131.058243159

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
18

> <JCHEM_AVERAGE_POLARIZABILITY>
12.353827390249975

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-hydroxypyrrolidine-2-carboxylic acid

> <ALOGPS_LOGP>
-3.18

> <JCHEM_LOGP>
-3.716320522797164

> <ALOGPS_LOGS>
0.52

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.58501555709157

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.6109755599539857

> <JCHEM_PKA_STRONGEST_BASIC>
10.616535665776542

> <JCHEM_POLAR_SURFACE_AREA>
69.56

> <JCHEM_REFRACTIVITY>
29.3822

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.31e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-hydroxypyrrolidine-2-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0245903 (3-Hydroxyproline)

HMDB0245903
     RDKit          3D
3-Hydroxyproline
 18 18  0  0  0  0  0  0  0  0999 V2000
    2.5193   -0.1147   -0.1289 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6217   -0.9408   -0.2438 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7480   -2.1324    0.3748 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4339   -0.5730   -1.0169 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8296   -1.0942   -0.5423 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5737   -0.2828    0.2461 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0984    1.1069   -0.0588 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2288    0.9771   -0.7488 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2006    1.5060    0.1156 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9529   -2.9882   -0.1363 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6533   -0.6820   -2.0435 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3910   -1.3006   -1.4762 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6664   -0.3212    0.0087 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4270   -0.5147    1.3161 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0068    1.6655    0.9060 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7780    1.6601   -0.7244 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2707    1.5425   -1.7113 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1418    2.4865    0.0786 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
  7  8  1  0
  8  9  1  0
  8  4  1  0
  3 10  1  0
  4 11  1  0
  5 12  1  0
  6 13  1  0
  6 14  1  0
  7 15  1  0
  7 16  1  0
  8 17  1  0
  9 18  1  0
M  END
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PDB for HMDB0245903 (3-Hydroxyproline)

HEADER    PROTEIN                                 22-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   22-MAY-19         0                                  
HETATM    1  C   UNK     0       0.290  -0.290   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.830  -0.290   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.186   1.175   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.060   2.080   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.060   3.620   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0       2.306   1.175   0.000  0.00  0.00           N+0
HETATM    7  O   UNK     0      -1.651   1.651   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      -0.274   4.390   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       2.393   4.390   0.000  0.00  0.00           O+0
CONECT    1    2    3                                                       
CONECT    2    1    6                                                       
CONECT    3    1    4    7                                                  
CONECT    4    3    5    6                                                  
CONECT    5    4    8    9                                                  
CONECT    6    2    4                                                       
CONECT    7    3                                                            
CONECT    8    5                                                            
CONECT    9    5                                                            
MASTER        0    0    0    0    0    0    0    0    9    0   18    0
END
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3D PDB for HMDB0245903 (3-Hydroxyproline)

COMPND    HMDB0245903
HETATM    1  O1  UNL     1       2.519  -0.115  -0.129  1.00  0.00           O  
HETATM    2  C1  UNL     1       1.622  -0.941  -0.244  1.00  0.00           C  
HETATM    3  O2  UNL     1       1.748  -2.132   0.375  1.00  0.00           O  
HETATM    4  C2  UNL     1       0.434  -0.573  -1.017  1.00  0.00           C  
HETATM    5  N1  UNL     1      -0.830  -1.094  -0.542  1.00  0.00           N  
HETATM    6  C3  UNL     1      -1.574  -0.283   0.246  1.00  0.00           C  
HETATM    7  C4  UNL     1      -1.098   1.107  -0.059  1.00  0.00           C  
HETATM    8  C5  UNL     1       0.229   0.977  -0.749  1.00  0.00           C  
HETATM    9  O3  UNL     1       1.201   1.506   0.116  1.00  0.00           O  
HETATM   10  H1  UNL     1       1.953  -2.988  -0.136  1.00  0.00           H  
HETATM   11  H2  UNL     1       0.653  -0.682  -2.044  1.00  0.00           H  
HETATM   12  H3  UNL     1      -1.391  -1.301  -1.476  1.00  0.00           H  
HETATM   13  H4  UNL     1      -2.666  -0.321   0.009  1.00  0.00           H  
HETATM   14  H5  UNL     1      -1.427  -0.515   1.316  1.00  0.00           H  
HETATM   15  H6  UNL     1      -1.007   1.665   0.906  1.00  0.00           H  
HETATM   16  H7  UNL     1      -1.778   1.660  -0.724  1.00  0.00           H  
HETATM   17  H8  UNL     1       0.271   1.543  -1.711  1.00  0.00           H  
HETATM   18  H9  UNL     1       1.142   2.486   0.079  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3   10
CONECT    4    5    8   11
CONECT    5    6   12
CONECT    6    7   13   14
CONECT    7    8   15   16
CONECT    8    9   17
CONECT    9   18
END
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SMILES for HMDB0245903 (3-Hydroxyproline)

OC1CCNC1C(O)=O
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INCHI for HMDB0245903 (3-Hydroxyproline)

InChI=1S/C5H9NO3/c7-3-1-2-6-4(3)5(8)9/h3-4,6-7H,1-2H2,(H,8,9)
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
3-HydroxyprolinesChEBI
3-Hydroxypyrrolidine-2-carboxylic acidChEBI
3-Hydroxypyrrolidine-2-carboxylateGenerator
L-trans-3-Hydroxy-2-pyrrolidinecarboxylateHMDB
3-Hydroxyproline, DL-(cis)-isomerHMDB
3-Hydroxyproline, L-(cis)-isomerHMDB
3-Hydroxyproline, (L)-isomerHMDB
3-Hydroxyproline, DL-(trans)-isomerHMDB
3-Hydroxyproline, L-(trans)-isomerHMDB
3-HydroxyprolineMeSH
Chemical FormulaC5H9NO3
Average Molecular Weight131.1299
Monoisotopic Molecular Weight131.058243159
IUPAC Name3-hydroxypyrrolidine-2-carboxylic acid
Traditional Name3-hydroxypyrrolidine-2-carboxylic acid
CAS Registry NumberNot Available
SMILES
OC1CCNC1C(O)=O
InChI Identifier
InChI=1S/C5H9NO3/c7-3-1-2-6-4(3)5(8)9/h3-4,6-7H,1-2H2,(H,8,9)
InChI KeyBJBUEDPLEOHJGE-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as proline and derivatives. Proline and derivatives are compounds containing proline or a derivative thereof resulting from reaction of proline at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct ParentProline and derivatives
Alternative Parents
Substituents
  • Proline or derivatives
  • Alpha-amino acid
  • Pyrrolidine carboxylic acid
  • Pyrrolidine carboxylic acid or derivatives
  • Beta-hydroxy acid
  • Hydroxy acid
  • Pyrrolidine
  • Amino acid
  • Secondary alcohol
  • Carboxylic acid
  • Secondary aliphatic amine
  • Monocarboxylic acid or derivatives
  • Azacycle
  • Organoheterocyclic compound
  • Secondary amine
  • Organonitrogen compound
  • Organic nitrogen compound
  • Organopnictogen compound
  • Alcohol
  • Organooxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Amine
  • Organic oxygen compound
  • Carbonyl group
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
UrineDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedCancer patients undergoing total body irradiation details
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB011875
KNApSAcK IDC00050693
Chemspider ID486216
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkHydroxyproline
METLIN IDNot Available
PubChem Compound559314
PDB IDNot Available
ChEBI ID64368
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]

Enzymes

Enzyme Details
1. Prolyl 3-hydroxylase 1
General function:
Involved in oxidoreductase activity
Specific function:
Basement membrane-associated chondroitin sulfate proteoglycan (CSPG). Has prolyl 3-hydroxylase activity catalyzing the post-translational formation of 3-hydroxyproline in -Xaa-Pro-Gly- sequences in collagens, especially types IV and V. May be involved in the secretory pathway of cells. Has growth suppressive activity in fibroblasts.
Gene Name:
LEPRE1
Uniprot ID:
Q32P28
Molecular weight:
78921.41
Enzyme Details
2. Prolyl 3-hydroxylase 2
General function:
Involved in oxidoreductase activity
Specific function:
Shows prolyl 3-hydroxylase activity catalyzing the post-translational formation of 3-hydroxyproline in -Xaa-Pro-Gly-sequences in collagens, especially types II, IV and V (By similarity).
Gene Name:
LEPREL1
Uniprot ID:
Q8IVL5
Molecular weight:
60386.32
Enzyme Details
3. Prolyl 3-hydroxylase 2
General function:
Not Available
Specific function:
Prolyl 3-hydroxylase that catalyzes the post-translational formation of 3-hydroxyproline on collagens (PubMed:24368846, PubMed:25645914). Contributes to proline 3-hydroxylation of collagen COL4A1 and COL1A1 in tendons, the eye sclera and in the eye lens capsule (PubMed:25645914). Has high activity with the type IV collagen COL4A1, and lower activity with COL1A1. Catalyzes hydroxylation of the first Pro in Gly-Pro-Hyp sequences where Hyp is 4-hydroxyproline. Has no activity on substrates that have proline instead of 4-hydroxyproline in the third position (By similarity).
Gene Name:
P3H2
Uniprot ID:
Q8CG71
Molecular weight:
80153.56