MiMeDB: Showing metabocard for L-ribulose 5-phosphate (MMDBc0032117)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-18 02:03:07 UTC

Update Date

2022-08-31 18:30:41 UTC

Metabolite ID

MMDBc0032117

Metabolite Identification

Common Name

L-ribulose 5-phosphate

Description

L-Ribulose 5-phosphate is a member of the chemical class known as Pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms. In Escherichia coli, RpiA catalyzes the interconversion of ribose-5-phosphate and ribulose-5-phosphate and is a key enzyme in the pentose phosphate pathway. (PMID 12182339 ) Interconversion of D-ribose-5-phosphate (R5P) and D-ribulose-5-phosphate is an important step in the pentose phosphate pathway. (PMID 18640127 ) A key player in LPS synthesis is the enzyme D-arabinose-5-phosphate isomerase (API), which catalyzes the reversible isomerization of D-ribulose-5-phosphate to D-arabinose-5-phosphate, a precursor of 3-deoxy-D-manno-octulosonate that is an essential residue of the LPS inner core. (PMID 20954237 ) Dihydroxybutanone phosphate synthase (DS) catalyzes a commitment step in riboflavin biosynthesis where ribulose 5-phosphate is converted to dihydroxybutanone phosphate and formate. (PMID 11053863 ) Ribose-5-phosphate isomerase A (RpiA) plays an important role in interconverting between ribose-5-phosphate (R5P) and ribulose-5-phosphate in the pentose phosphate pathway and the Calvin cycle. (PMID 19214439 )

Structure

MOL SDF PDB SMILES InChI

  Mrv0541 04061520222D          

 14 13  0  0  0  0            999 V2000
   -2.8578   -0.2062    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -1.0312    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7144    0.2062    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7144    1.0312    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.2062    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0000   -1.0312    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7144    0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.2062    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    0.2062    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    2.8578    0.6187    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    2.5559   -0.5082    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    1.7309    0.9207    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  3  5  1  0  0  0  0
  5  6  1  1  0  0  0
  5  7  1  0  0  0  0
  7  8  1  6  0  0  0
  7  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 11 13  1  0  0  0  0
 11 14  2  0  0  0  0
M  CHG  2  12  -1  13  -1
M  END
> <DATABASE_ID>
MMDBc0032117

> <DATABASE_NAME>
MIME

> <SMILES>
OCC(=O)[C@@H](O)[C@@H](O)COP([O-])([O-])=O

> <INCHI_IDENTIFIER>
InChI=1S/C5H11O8P/c6-1-3(7)5(9)4(8)2-13-14(10,11)12/h4-6,8-9H,1-2H2,(H2,10,11,12)/p-2/t4-,5+/m0/s1

> <INCHI_KEY>
FNZLKVNUWIIPSJ-CRCLSJGQSA-L

> <FORMULA>
C5H9O8P

> <MOLECULAR_WEIGHT>
228.094

> <EXACT_MASS>
228.004601408

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
23

> <JCHEM_AVERAGE_POLARIZABILITY>
17.58827706808278

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
-2

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3S,4S)-1,3,4-trihydroxy-5-(phosphonatooxy)pentan-2-one

> <ALOGPS_LOGP>
-1.86

> <JCHEM_LOGP>
-2.7602629813333333

> <ALOGPS_LOGS>
-0.63

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.504370847667953

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.4785529591465414

> <JCHEM_PKA_STRONGEST_BASIC>
-3.3276267100529333

> <JCHEM_POLAR_SURFACE_AREA>
150.18

> <JCHEM_REFRACTIVITY>
40.2288

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.23e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
L-ribulose 5-phosphate(2-)

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 06-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-APR-15         0                                  
HETATM    1  O   UNK     0      -5.335  -0.385   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      -4.001   0.385   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -2.667  -0.385   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      -2.667  -1.925   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0      -1.334   0.385   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -1.334   1.925   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       0.000  -0.385   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       0.000  -1.925   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       1.334   0.385   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       2.667  -0.385   0.000  0.00  0.00           O+0
HETATM   11  P   UNK     0       4.001   0.385   0.000  0.00  0.00           P+0
HETATM   12  O   UNK     0       5.335   1.155   0.000  0.00  0.00           O-1
HETATM   13  O   UNK     0       4.771  -0.949   0.000  0.00  0.00           O-1
HETATM   14  O   UNK     0       3.231   1.719   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   13   14                                             
CONECT   12   11                                                            
CONECT   13   11                                                            
CONECT   14   11                                                            
MASTER        0    0    0    0    0    0    0    0   14    0   26    0
END

Synonyms

Value	Source
5-O-Phosphonato-L-erythro-pent-2-ulose	ChEBI
5-O-Phosphonato-L-ribulose	ChEBI
L-Ribulose 5-phosphate	ChEBI
L-Ribulose 5-phosphate dianion	ChEBI
L-Ribulose 5-phosphoric acid	Generator
L-Ribulose 5-phosphoric acid dianion	Generator
L-Ribulose 5-phosphoric acid	Generator

Molecular Formula

C₅H₉O₈P

Average Mass

228.094

Monoisotopic Mass

228.004601408

IUPAC Name

(3S,4S)-1,3,4-trihydroxy-5-(phosphonatooxy)pentan-2-one

Traditional Name

L-ribulose 5-phosphate(2-)

CAS Registry Number

Not Available

SMILES

OCC(=O)[C@@H](O)[C@@H](O)COP([O-])([O-])=O

InChI Identifier

InChI=1S/C5H11O8P/c6-1-3(7)5(9)4(8)2-13-14(10,11)12/h4-6,8-9H,1-2H2,(H2,10,11,12)/p-2/t4-,5+/m0/s1

InChI Key

FNZLKVNUWIIPSJ-CRCLSJGQSA-L

Chemical Taxonomy

Functional Ontology

Physical Properties

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-004i-0190000000-ef3f7bd4cdeda4061c48	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-014i-9880000000-eaef27e08562aab3ca0c	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-07vl-9500000000-8951ba09bc0e89c6cc60	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-004r-9080000000-6604b3c77ebb8474d36a	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0a4r-9130000000-eff140f298e64291a4b2	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0a4l-9000000000-1245d9ba8d7374f9a253	2015-09-15	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-20	View Spectrum

Biological Properties

Human Proteins and Enzymes

Human Pathways

Metabolic Reactions

Health Effects and Bioactivity

Microbial Sources

Exposure Sources

Host Biospecimen and Location

External Links

References

Showing metabocard for L-ribulose 5-phosphate (MMDBc0032117)

MOL for #<Metabolite:0x00007fb7edfa30a0>

3D MOL for #<Metabolite:0x00007fb7edfa30a0>

3D SDF for #<Metabolite:0x00007fb7edfa30a0>

3D-SDF for #<Metabolite:0x00007fb7edfa30a0>

PDB for #<Metabolite:0x00007fb7edfa30a0>

3D PDB for #<Metabolite:0x00007fb7edfa30a0>

SMILES for #<Metabolite:0x00007fb7edfa30a0>

INCHI for #<Metabolite:0x00007fb7edfa30a0>

Structure for #<Metabolite:0x00007fb7edfa30a0>

3D Structure for #<Metabolite:0x00007fb7edfa30a0>