Showing metabocard for L-Ribulose (MMDBc0000237)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2020-10-27 23:40:52 UTC
Update Date2022-08-31 00:15:53 UTC
Metabolite IDMMDBc0000237
Metabolite Identification
Common NameL-Ribulose
DescriptionL-Ribulose (CAS: 2042-27-5) is a ketopentose - a monosaccharide containing five carbon atoms, including a ketone functional group. It has the chemical formula C5H10O5.
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007fecab11a068>


  Mrv1652309241918532D          

 10 10  0  0  0  0            999 V2000
10000.779010000.8748    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.494110000.4635    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.6963 9999.9317    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.2705 9999.0121    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9998.4758 9999.0204    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9999.389710000.9566    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9998.722310000.4716    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.9772 9999.6870    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9999.8022 9999.6870    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
10000.057110000.4716    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  6  7  1  0  0  0  0
  6 10  1  0  0  0  0
  1 10  1  0  0  0  0
 10  3  1  6  0  0  0
  9  4  1  1  0  0  0
  8  5  1  1  0  0  0
M  END
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3D MOL for #<Metabolite:0x00007fecab11a068>

HMDB0003371
     RDKit          3D
L-Ribulose
 20 20  0  0  0  0  0  0  0  0999 V2000
   -2.2857    0.3240   -1.1996 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9815    0.5271    0.1216 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5211    0.4467    0.4338 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.2288    0.6526    1.7652 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2380    1.3468   -0.3085 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5422    0.9309   -0.2632 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5633   -0.5011    0.2069 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.4086   -1.3068   -0.5187 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0976   -0.8746    0.0285 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.1779   -1.0592   -1.3213 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1639   -0.1324   -1.2475 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4897   -0.2585    0.7347 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3245    1.5447    0.3971 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0007    0.8971    2.3211 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0997    1.5597    0.4644 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0698    1.0571   -1.2400 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7670   -0.5407    1.3089 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0452   -2.2423   -0.4744 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2080   -1.7106    0.6603 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5504   -0.6606   -1.8696 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  1
  3  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
  9  3  1  0
  1 11  1  0
  2 12  1  0
  2 13  1  0
  4 14  1  0
  6 15  1  0
  6 16  1  0
  7 17  1  1
  8 18  1  0
  9 19  1  1
 10 20  1  0
M  END
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3D SDF for #<Metabolite:0x00007fecab11a068>


  Mrv1652309241918532D          

 10 10  0  0  0  0            999 V2000
10000.779010000.8748    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.494110000.4635    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.6963 9999.9317    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.2705 9999.0121    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9998.4758 9999.0204    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9999.389710000.9566    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9998.722310000.4716    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.9772 9999.6870    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9999.8022 9999.6870    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
10000.057110000.4716    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  6  7  1  0  0  0  0
  6 10  1  0  0  0  0
  1 10  1  0  0  0  0
 10  3  1  6  0  0  0
  9  4  1  1  0  0  0
  8  5  1  1  0  0  0
M  END
> <DATABASE_ID>
MMDBc0000237

> <DATABASE_NAME>
MIME

> <SMILES>
OC[C@]1(O)OC[C@H](O)[C@@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C5H10O5/c6-2-5(9)4(8)3(7)1-10-5/h3-4,6-9H,1-2H2/t3-,4-,5-/m0/s1

> <INCHI_KEY>
LQXVFWRQNMEDEE-YUPRTTJUSA-N

> <FORMULA>
C5H10O5

> <MOLECULAR_WEIGHT>
150.13

> <EXACT_MASS>
150.052823422

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
20

> <JCHEM_AVERAGE_POLARIZABILITY>
13.523314220028105

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,3S,4S)-2-(hydroxymethyl)oxolane-2,3,4-triol

> <ALOGPS_LOGP>
-2.20

> <JCHEM_LOGP>
-2.1276643760000002

> <ALOGPS_LOGS>
0.94

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.844123223152558

> <JCHEM_PKA_STRONGEST_ACIDIC>
10.292639879315793

> <JCHEM_PKA_STRONGEST_BASIC>
-3.450695969467499

> <JCHEM_POLAR_SURFACE_AREA>
90.15

> <JCHEM_REFRACTIVITY>
30.3983

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.31e+03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S,3S,4S)-2-(hydroxymethyl)oxolane-2,3,4-triol

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x00007fecab11a068>

HMDB0003371
     RDKit          3D
L-Ribulose
 20 20  0  0  0  0  0  0  0  0999 V2000
   -2.2857    0.3240   -1.1996 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9815    0.5271    0.1216 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5211    0.4467    0.4338 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.2288    0.6526    1.7652 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2380    1.3468   -0.3085 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5422    0.9309   -0.2632 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5633   -0.5011    0.2069 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.4086   -1.3068   -0.5187 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0976   -0.8746    0.0285 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.1779   -1.0592   -1.3213 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1639   -0.1324   -1.2475 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4897   -0.2585    0.7347 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3245    1.5447    0.3971 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0007    0.8971    2.3211 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0997    1.5597    0.4644 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0698    1.0571   -1.2400 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7670   -0.5407    1.3089 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0452   -2.2423   -0.4744 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2080   -1.7106    0.6603 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5504   -0.6606   -1.8696 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  1
  3  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
  9  3  1  0
  1 11  1  0
  2 12  1  0
  2 13  1  0
  4 14  1  0
  6 15  1  0
  6 16  1  0
  7 17  1  1
  8 18  1  0
  9 19  1  1
 10 20  1  0
M  END
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PDB for #<Metabolite:0x00007fecab11a068>

HEADER    PROTEIN                                 24-SEP-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-SEP-19         0                                  
HETATM    1  C   UNK     0    8668.1218668.300   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0    8669.4568667.532   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0    8667.9668666.539   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0    8667.1728664.823   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0    8663.8218664.838   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0    8665.5278668.452   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0    8664.2828667.547   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0    8664.7578666.082   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0    8666.2978666.082   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0    8666.7738667.547   0.000  0.00  0.00           C+0
CONECT    1    2   10                                                       
CONECT    2    1                                                            
CONECT    3   10                                                            
CONECT    4    9                                                            
CONECT    5    8                                                            
CONECT    6    7   10                                                       
CONECT    7    8    6                                                       
CONECT    8    7    9    5                                                  
CONECT    9    8   10    4                                                  
CONECT   10    9    6    1    3                                             
MASTER        0    0    0    0    0    0    0    0   10    0   20    0
END
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3D PDB for #<Metabolite:0x00007fecab11a068>

COMPND    HMDB0003371
HETATM    1  O1  UNL     1      -2.286   0.324  -1.200  1.00  0.00           O  
HETATM    2  C1  UNL     1      -1.982   0.527   0.122  1.00  0.00           C  
HETATM    3  C2  UNL     1      -0.521   0.447   0.434  1.00  0.00           C  
HETATM    4  O2  UNL     1      -0.229   0.653   1.765  1.00  0.00           O  
HETATM    5  O3  UNL     1       0.238   1.347  -0.308  1.00  0.00           O  
HETATM    6  C3  UNL     1       1.542   0.931  -0.263  1.00  0.00           C  
HETATM    7  C4  UNL     1       1.563  -0.501   0.207  1.00  0.00           C  
HETATM    8  O4  UNL     1       2.409  -1.307  -0.519  1.00  0.00           O  
HETATM    9  C5  UNL     1       0.098  -0.875   0.028  1.00  0.00           C  
HETATM   10  O5  UNL     1      -0.178  -1.059  -1.321  1.00  0.00           O  
HETATM   11  H1  UNL     1      -3.164  -0.132  -1.247  1.00  0.00           H  
HETATM   12  H2  UNL     1      -2.490  -0.258   0.735  1.00  0.00           H  
HETATM   13  H3  UNL     1      -2.324   1.545   0.397  1.00  0.00           H  
HETATM   14  H4  UNL     1      -1.001   0.897   2.321  1.00  0.00           H  
HETATM   15  H5  UNL     1       2.100   1.560   0.464  1.00  0.00           H  
HETATM   16  H6  UNL     1       2.070   1.057  -1.240  1.00  0.00           H  
HETATM   17  H7  UNL     1       1.767  -0.541   1.309  1.00  0.00           H  
HETATM   18  H8  UNL     1       2.045  -2.242  -0.474  1.00  0.00           H  
HETATM   19  H9  UNL     1      -0.208  -1.711   0.660  1.00  0.00           H  
HETATM   20  H10 UNL     1       0.550  -0.661  -1.870  1.00  0.00           H  
CONECT    1    2   11
CONECT    2    3   12   13
CONECT    3    4    5    9
CONECT    4   14
CONECT    5    6
CONECT    6    7   15   16
CONECT    7    8    9   17
CONECT    8   18
CONECT    9   10   19
CONECT   10   20
END
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SMILES for #<Metabolite:0x00007fecab11a068>

OC[C@]1(O)OC[C@H](O)[C@@H]1O
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INCHI for #<Metabolite:0x00007fecab11a068>

InChI=1S/C5H10O5/c6-2-5(9)4(8)3(7)1-10-5/h3-4,6-9H,1-2H2/t3-,4-,5-/m0/s1
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Synonyms
ValueSource
b-L-RibulofuranoseHMDB
Β-L-ribulofuranoseHMDB
L-Erythro-pentuloseHMDB
Β-L-erythro-2-pentulofuranoseHMDB
Β-L-ribuloseHMDB
beta-L-RibuloseHMDB
beta-L-Erythro-2-pentulofuranoseHMDB
L-RibuloseHMDB
Molecular FormulaC5H10O5
Average Mass150.13
Monoisotopic Mass150.052823422
IUPAC Name(2S,3S,4S)-2-(hydroxymethyl)oxolane-2,3,4-triol
Traditional Name(2S,3S,4S)-2-(hydroxymethyl)oxolane-2,3,4-triol
CAS Registry Number130271-85-1
SMILES
OC[C@]1(O)OC[C@H](O)[C@@H]1O
InChI Identifier
InChI=1S/C5H10O5/c6-2-5(9)4(8)3(7)1-10-5/h3-4,6-9H,1-2H2/t3-,4-,5-/m0/s1
InChI KeyLQXVFWRQNMEDEE-YUPRTTJUSA-N