Showing metabocard for 5-Phosphoribosylamine (MMDBc0029566)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2021-11-17 23:32:33 UTC
Update Date2022-08-31 13:44:00 UTC
Metabolite IDMMDBc0029566
Metabolite Identification
Common Name5-Phosphoribosylamine
Description5-Phosphoribosylamine is a substrate for Amidophosphoribosyltransferase and Trifunctional purine biosynthetic protein adenosine-3.
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x0000560be02fa340>


  Mrv0541 02231218562D          

 14 14  0  0  1  0            999 V2000
   -1.5779    0.9195    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7493    0.9158    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3991    0.9195    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5742    1.7406    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5817    0.0946    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5827    0.1097    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2006   -0.1476    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.4502   -0.9346    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.8590    0.3329    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2752   -0.9346    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.0379   -1.5969    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5326   -0.1476    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.7596   -1.5969    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4255    0.3179    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  0  0  0
  1  5  2  0  0  0  0
  2  6  1  0  0  0  0
  7  6  1  1  0  0  0
  7  8  1  0  0  0  0
  7  9  1  0  0  0  0
  8 10  1  0  0  0  0
  8 11  1  6  0  0  0
  9 12  1  0  0  0  0
 10 13  1  6  0  0  0
 12 14  1  1  0  0  0
 10 12  1  0  0  0  0
M  END
Download

3D MOL for #<Metabolite:0x0000560be02fa340>

HMDB0001128
     RDKit          3D
5-Phosphoribosylamine
 26 26  0  0  0  0  0  0  0  0999 V2000
   -2.8627   -1.9733   -0.3955 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9785   -0.8670   -0.6289 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.6549   -1.2008   -0.3821 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0577   -0.0231   -0.2624 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.1066   -0.1190    0.8372 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1175   -0.9885    0.4707 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3601   -0.2290   -0.3695 P   0  0  0  0  0  5  0  0  0  0  0  0
    2.8239    0.3575   -1.6641 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1400    0.9269    0.5723 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5134   -1.3881   -0.7940 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9176    1.0746    0.0723 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.1717    1.7958   -1.0871 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1772    0.2669    0.3705 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.3315    0.9876    0.1216 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6748   -2.6734   -1.1411 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8488   -1.6540   -0.3628 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0240   -0.4619   -1.6568 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5327    0.1675   -1.2489 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4745    0.9033    1.0735 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5746   -0.4675    1.7470 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1525    1.7634    0.0622 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4569   -2.1998   -0.2207 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6111    1.7048    0.9149 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6767    2.6201   -0.9319 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1146   -0.1354    1.3922 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2664    1.8123    0.6828 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  7  9  1  0
  7 10  1  0
  4 11  1  0
 11 12  1  0
 11 13  1  0
 13 14  1  0
 13  2  1  0
  1 15  1  0
  1 16  1  0
  2 17  1  6
  4 18  1  6
  5 19  1  0
  5 20  1  0
  9 21  1  0
 10 22  1  0
 11 23  1  1
 12 24  1  0
 13 25  1  1
 14 26  1  0
M  END
Download

3D SDF for #<Metabolite:0x0000560be02fa340>


  Mrv0541 02231218562D          

 14 14  0  0  1  0            999 V2000
   -1.5779    0.9195    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7493    0.9158    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3991    0.9195    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5742    1.7406    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5817    0.0946    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5827    0.1097    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2006   -0.1476    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.4502   -0.9346    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.8590    0.3329    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2752   -0.9346    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.0379   -1.5969    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5326   -0.1476    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.7596   -1.5969    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4255    0.3179    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  0  0  0
  1  5  2  0  0  0  0
  2  6  1  0  0  0  0
  7  6  1  1  0  0  0
  7  8  1  0  0  0  0
  7  9  1  0  0  0  0
  8 10  1  0  0  0  0
  8 11  1  6  0  0  0
  9 12  1  0  0  0  0
 10 13  1  6  0  0  0
 12 14  1  1  0  0  0
 10 12  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0029566

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H12NO7P/c6-5-4(8)3(7)2(13-5)1-12-14(9,10)11/h2-5,7-8H,1,6H2,(H2,9,10,11)/t2-,3-,4-,5-/m1/s1

> <INCHI_KEY>
SKCBPEVYGOQGJN-TXICZTDVSA-N

> <FORMULA>
C5H12NO7P

> <MOLECULAR_WEIGHT>
229.125

> <EXACT_MASS>
229.035138255

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_AVERAGE_POLARIZABILITY>
18.663161093312503

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{[(2R,3S,4R,5R)-5-amino-3,4-dihydroxyoxolan-2-yl]methoxy}phosphonic acid

> <ALOGPS_LOGP>
-2.39

> <JCHEM_LOGP>
-3.545345242649598

> <ALOGPS_LOGS>
-0.78

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
6.243630161593156

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.2256230940421675

> <JCHEM_PKA_STRONGEST_BASIC>
8.000221098750375

> <JCHEM_POLAR_SURFACE_AREA>
142.47

> <JCHEM_REFRACTIVITY>
42.491299999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.82e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-phospho-β-D-ribosylamine

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x0000560be02fa340>

HMDB0001128
     RDKit          3D
5-Phosphoribosylamine
 26 26  0  0  0  0  0  0  0  0999 V2000
   -2.8627   -1.9733   -0.3955 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9785   -0.8670   -0.6289 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.6549   -1.2008   -0.3821 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0577   -0.0231   -0.2624 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.1066   -0.1190    0.8372 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1175   -0.9885    0.4707 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3601   -0.2290   -0.3695 P   0  0  0  0  0  5  0  0  0  0  0  0
    2.8239    0.3575   -1.6641 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1400    0.9269    0.5723 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5134   -1.3881   -0.7940 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9176    1.0746    0.0723 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.1717    1.7958   -1.0871 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1772    0.2669    0.3705 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.3315    0.9876    0.1216 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6748   -2.6734   -1.1411 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8488   -1.6540   -0.3628 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0240   -0.4619   -1.6568 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5327    0.1675   -1.2489 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4745    0.9033    1.0735 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5746   -0.4675    1.7470 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1525    1.7634    0.0622 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4569   -2.1998   -0.2207 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6111    1.7048    0.9149 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6767    2.6201   -0.9319 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1146   -0.1354    1.3922 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2664    1.8123    0.6828 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  7  9  1  0
  7 10  1  0
  4 11  1  0
 11 12  1  0
 11 13  1  0
 13 14  1  0
 13  2  1  0
  1 15  1  0
  1 16  1  0
  2 17  1  6
  4 18  1  6
  5 19  1  0
  5 20  1  0
  9 21  1  0
 10 22  1  0
 11 23  1  1
 12 24  1  0
 13 25  1  1
 14 26  1  0
M  END
Download

PDB for #<Metabolite:0x0000560be02fa340>

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  P   UNK     0      -2.945   1.716   0.000  0.00  0.00           P+0
HETATM    2  O   UNK     0      -1.399   1.709   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      -4.478   1.716   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      -2.939   3.249   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0      -2.953   0.177   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      -1.088   0.205   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.374  -0.276   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.840  -1.745   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       1.603   0.621   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       2.380  -1.745   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -0.071  -2.981   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       2.861  -0.276   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       3.285  -2.981   0.000  0.00  0.00           O+0
HETATM   14  N   UNK     0       4.528   0.593   0.000  0.00  0.00           N+0
CONECT    1    2    3    4    5                                             
CONECT    2    1    6                                                       
CONECT    3    1                                                            
CONECT    4    1                                                            
CONECT    5    1                                                            
CONECT    6    2    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7   10   11                                                  
CONECT    9    7   12                                                       
CONECT   10    8   13   12                                                  
CONECT   11    8                                                            
CONECT   12    9   14   10                                                  
CONECT   13   10                                                            
CONECT   14   12                                                            
MASTER        0    0    0    0    0    0    0    0   14    0   28    0
END
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3D PDB for #<Metabolite:0x0000560be02fa340>

COMPND    HMDB0001128
HETATM    1  N1  UNL     1      -2.863  -1.973  -0.396  1.00  0.00           N  
HETATM    2  C1  UNL     1      -1.979  -0.867  -0.629  1.00  0.00           C  
HETATM    3  O1  UNL     1      -0.655  -1.201  -0.382  1.00  0.00           O  
HETATM    4  C2  UNL     1       0.058  -0.023  -0.262  1.00  0.00           C  
HETATM    5  C3  UNL     1       1.107  -0.119   0.837  1.00  0.00           C  
HETATM    6  O2  UNL     1       2.117  -0.989   0.471  1.00  0.00           O  
HETATM    7  P1  UNL     1       3.360  -0.229  -0.369  1.00  0.00           P  
HETATM    8  O3  UNL     1       2.824   0.358  -1.664  1.00  0.00           O  
HETATM    9  O4  UNL     1       4.140   0.927   0.572  1.00  0.00           O  
HETATM   10  O5  UNL     1       4.513  -1.388  -0.794  1.00  0.00           O  
HETATM   11  C4  UNL     1      -0.918   1.075   0.072  1.00  0.00           C  
HETATM   12  O6  UNL     1      -1.172   1.796  -1.087  1.00  0.00           O  
HETATM   13  C5  UNL     1      -2.177   0.267   0.371  1.00  0.00           C  
HETATM   14  O7  UNL     1      -3.331   0.988   0.122  1.00  0.00           O  
HETATM   15  H1  UNL     1      -2.675  -2.673  -1.141  1.00  0.00           H  
HETATM   16  H2  UNL     1      -3.849  -1.654  -0.363  1.00  0.00           H  
HETATM   17  H3  UNL     1      -2.024  -0.462  -1.657  1.00  0.00           H  
HETATM   18  H4  UNL     1       0.533   0.167  -1.249  1.00  0.00           H  
HETATM   19  H5  UNL     1       1.475   0.903   1.074  1.00  0.00           H  
HETATM   20  H6  UNL     1       0.575  -0.467   1.747  1.00  0.00           H  
HETATM   21  H7  UNL     1       4.153   1.763   0.062  1.00  0.00           H  
HETATM   22  H8  UNL     1       4.457  -2.200  -0.221  1.00  0.00           H  
HETATM   23  H9  UNL     1      -0.611   1.705   0.915  1.00  0.00           H  
HETATM   24  H10 UNL     1      -1.677   2.620  -0.932  1.00  0.00           H  
HETATM   25  H11 UNL     1      -2.115  -0.135   1.392  1.00  0.00           H  
HETATM   26  H12 UNL     1      -3.266   1.812   0.683  1.00  0.00           H  
CONECT    1    2   15   16
CONECT    2    3   13   17
CONECT    3    4
CONECT    4    5   11   18
CONECT    5    6   19   20
CONECT    6    7
CONECT    7    8    8    9   10
CONECT    9   21
CONECT   10   22
CONECT   11   12   13   23
CONECT   12   24
CONECT   13   14   25
CONECT   14   26
END
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SMILES for #<Metabolite:0x0000560be02fa340>

N[C@@H]1O[C@H](COP(O)(O)=O)[C@@H](O)[C@H]1O
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INCHI for #<Metabolite:0x0000560be02fa340>

InChI=1S/C5H12NO7P/c6-5-4(8)3(7)2(13-5)1-12-14(9,10)11/h2-5,7-8H,1,6H2,(H2,9,10,11)/t2-,3-,4-,5-/m1/s1
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Synonyms
ValueSource
5-Phospho-D-ribosylamineChEBI
5-Phosphoribosyl-1-amineChEBI
5-Phospho-beta-D-ribosylamineKegg
5-Phospho-b-D-ribosylamineGenerator
5-Phospho-β-D-ribosylamineGenerator
5-P-beta-D-Ribosyl-amineHMDB
5-Phospho-beta-D-ribosyl-amineHMDB
PRAHMDB
Phosphoribosyl-1-amineHMDB
PhosphoribosylamineHMDB
beta-Phosphoribosyl-1-amineHMDB
β-Phosphoribosyl-1-amineHMDB
Molecular FormulaC5H12NO7P
Average Mass229.125
Monoisotopic Mass229.035138255
IUPAC Name{[(2R,3S,4R,5R)-5-amino-3,4-dihydroxyoxolan-2-yl]methoxy}phosphonic acid
Traditional Name5-phospho-β-D-ribosylamine
CAS Registry NumberNot Available
SMILES
N[C@@H]1O[C@H](COP(O)(O)=O)[C@@H](O)[C@H]1O
InChI Identifier
InChI=1S/C5H12NO7P/c6-5-4(8)3(7)2(13-5)1-12-14(9,10)11/h2-5,7-8H,1,6H2,(H2,9,10,11)/t2-,3-,4-,5-/m1/s1
InChI KeySKCBPEVYGOQGJN-TXICZTDVSA-N