Showing metabocard for trans-3-hydroxy-L-proline (MMDBc0054679)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2022-06-05 23:23:57 UTC
Update Date2024-04-30 20:55:28 UTC
Metabolite IDMMDBc0054679
Metabolite Identification
Common Nametrans-3-hydroxy-L-proline
DescriptionTrans-3-hydroxy-l-proline is a substrate for: Trans-L-3-hydroxyproline dehydratase.
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00005645ca02f718>


  Mrv0541 09041212392D          

 11 11  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  1  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  1  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
   -0.6830    0.0460    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1673    1.4888    0.0000 H   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
  4  5  1  1  0  0  0
  6  2  1  0  0  0  0
  6  4  1  0  0  0  0
  3  7  1  6  0  0  0
  8  5  2  0  0  0  0
  9  5  1  0  0  0  0
  3 10  1  1  0  0  0
  4 11  1  6  0  0  0
M  END
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3D MOL for #<Metabolite:0x00005645ca02f718>

HMDB0059659
     RDKit          3D
Trans-3-hydroxy-L-proline
 18 18  0  0  0  0  0  0  0  0999 V2000
    2.4773   -1.8003    0.6238 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8360   -0.7364    0.3248 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6478    0.3723    0.0198 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3606   -0.6739    0.3014 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.2210    0.2111    1.2619 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9708    1.1708    0.5522 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7868    0.9457   -0.9425 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3490   -0.4908   -0.9937 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.5284   -1.2389   -1.0587 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7899    1.0487    0.6827 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0433   -1.7339    0.6753 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5969   -0.2221    2.0879 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5955    2.1740    0.7733 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0240    1.1429    0.8429 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7470    1.0419   -1.4939 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0046    1.5579   -1.3955 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2523   -0.7666   -1.8468 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5832   -2.0023   -0.4148 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  1
  5 12  1  0
  6 13  1  0
  6 14  1  0
  7 15  1  0
  7 16  1  0
  8 17  1  6
  9 18  1  0
M  END
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3D SDF for #<Metabolite:0x00005645ca02f718>


  Mrv0541 09041212392D          

 11 11  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  1  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  1  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
   -0.6830    0.0460    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1673    1.4888    0.0000 H   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
  4  5  1  1  0  0  0
  6  2  1  0  0  0  0
  6  4  1  0  0  0  0
  3  7  1  6  0  0  0
  8  5  2  0  0  0  0
  9  5  1  0  0  0  0
  3 10  1  1  0  0  0
  4 11  1  6  0  0  0
M  END
> <DATABASE_ID>
MMDBc0054679

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@]1(O)CCN[C@]1([H])C(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)/t3-,4-/m0/s1

> <INCHI_KEY>
BJBUEDPLEOHJGE-IMJSIDKUSA-N

> <FORMULA>
C5H9NO3

> <MOLECULAR_WEIGHT>
131.1299

> <EXACT_MASS>
131.058243159

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
12.32618056129625

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,3S)-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>
1.6109755599539874

> <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>
trans-3-hydroxy-L-proline

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x00005645ca02f718>

HMDB0059659
     RDKit          3D
Trans-3-hydroxy-L-proline
 18 18  0  0  0  0  0  0  0  0999 V2000
    2.4773   -1.8003    0.6238 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8360   -0.7364    0.3248 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6478    0.3723    0.0198 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3606   -0.6739    0.3014 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.2210    0.2111    1.2619 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9708    1.1708    0.5522 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7868    0.9457   -0.9425 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3490   -0.4908   -0.9937 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.5284   -1.2389   -1.0587 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7899    1.0487    0.6827 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0433   -1.7339    0.6753 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5969   -0.2221    2.0879 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5955    2.1740    0.7733 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0240    1.1429    0.8429 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7470    1.0419   -1.4939 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0046    1.5579   -1.3955 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2523   -0.7666   -1.8468 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5832   -2.0023   -0.4148 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  1
  5 12  1  0
  6 13  1  0
  6 14  1  0
  7 15  1  0
  7 16  1  0
  8 17  1  6
  9 18  1  0
M  END
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PDB for #<Metabolite:0x00005645ca02f718>

HEADER    PROTEIN                                 04-SEP-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-12         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM    7  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   10  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   11  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
CONECT    1    2    3                                                       
CONECT    2    1    6                                                       
CONECT    3    1    4    7   10                                             
CONECT    4    3    5    6   11                                             
CONECT    5    4    8    9                                                  
CONECT    6    2    4                                                       
CONECT    7    3                                                            
CONECT    8    5                                                            
CONECT    9    5                                                            
CONECT   10    3                                                            
CONECT   11    4                                                            
MASTER        0    0    0    0    0    0    0    0   11    0   22    0
END
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3D PDB for #<Metabolite:0x00005645ca02f718>

COMPND    HMDB0059659
HETATM    1  O1  UNL     1       2.477  -1.800   0.624  1.00  0.00           O  
HETATM    2  C1  UNL     1       1.836  -0.736   0.325  1.00  0.00           C  
HETATM    3  O2  UNL     1       2.648   0.372   0.020  1.00  0.00           O  
HETATM    4  C2  UNL     1       0.361  -0.674   0.301  1.00  0.00           C  
HETATM    5  N1  UNL     1      -0.221   0.211   1.262  1.00  0.00           N  
HETATM    6  C3  UNL     1      -0.971   1.171   0.552  1.00  0.00           C  
HETATM    7  C4  UNL     1      -0.787   0.946  -0.943  1.00  0.00           C  
HETATM    8  C5  UNL     1      -0.349  -0.491  -0.994  1.00  0.00           C  
HETATM    9  O3  UNL     1      -1.528  -1.239  -1.059  1.00  0.00           O  
HETATM   10  H1  UNL     1       2.790   1.049   0.683  1.00  0.00           H  
HETATM   11  H2  UNL     1       0.043  -1.734   0.675  1.00  0.00           H  
HETATM   12  H3  UNL     1      -0.597  -0.222   2.088  1.00  0.00           H  
HETATM   13  H4  UNL     1      -0.596   2.174   0.773  1.00  0.00           H  
HETATM   14  H5  UNL     1      -2.024   1.143   0.843  1.00  0.00           H  
HETATM   15  H6  UNL     1      -1.747   1.042  -1.494  1.00  0.00           H  
HETATM   16  H7  UNL     1      -0.005   1.558  -1.395  1.00  0.00           H  
HETATM   17  H8  UNL     1       0.252  -0.767  -1.847  1.00  0.00           H  
HETATM   18  H9  UNL     1      -1.583  -2.002  -0.415  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 #<Metabolite:0x00005645ca02f718>

[H][C@]1(O)CCN[C@]1([H])C(O)=O
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INCHI for #<Metabolite:0x00005645ca02f718>

InChI=1S/C5H9NO3/c7-3-1-2-6-4(3)5(8)9/h3-4,6-7H,1-2H2,(H,8,9)/t3-,4-/m0/s1
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Synonyms
ValueSource
(2S,3S)-3-Hydroxypyrrolidine-2-carboxylic acidChEBI
3-trans-Hydroxy-L-prolineChEBI
L-Threo-3-hydroxyprolineChEBI
trans-L-3-HydroxyprolineChEBI
(2S,3S)-3-Hydroxypyrrolidine-2-carboxylateGenerator
Molecular FormulaC5H9NO3
Average Mass131.1299
Monoisotopic Mass131.058243159
IUPAC Name(2S,3S)-3-hydroxypyrrolidine-2-carboxylic acid
Traditional Nametrans-3-hydroxy-L-proline
CAS Registry NumberNot Available
SMILES
[H][C@]1(O)CCN[C@]1([H])C(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)/t3-,4-/m0/s1
InChI KeyBJBUEDPLEOHJGE-IMJSIDKUSA-N