Showing metabocard for Deoxyribose 1-phosphate (MMDBc0029628)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2021-11-17 23:35:15 UTC
Update Date2024-04-30 19:39:41 UTC
Metabolite IDMMDBc0029628
Metabolite Identification
Common NameDeoxyribose 1-phosphate
DescriptionDeoxyribose 1-phosphate is an intermediate in the metabolism of Pyrimidine. It is a substrate for Purine nucleoside phosphorylase and Thymidine phosphorylase.
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f923a4c5968>


  Mrv0541 02231219042D          

 13 13  0  0  1  0            999 V2000
    0.0984   -0.0037    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5714    0.4730    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1552   -0.7946    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8816    0.2535    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2335   -0.0037    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.9839   -0.7946    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.7028    0.2535    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0131    0.2535    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4682   -1.4568    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5239    0.2535    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6990    1.0785    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6990   -0.5676    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1834    1.0595    0.0000 O   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
  2  5  1  0  0  0  0
  3  6  1  0  0  0  0
  4  7  1  0  0  0  0
  5  8  1  1  0  0  0
  6  9  1  6  0  0  0
  7 10  1  0  0  0  0
  7 11  1  0  0  0  0
  7 12  2  0  0  0  0
  8 13  1  0  0  0  0
  5  6  1  0  0  0  0
M  END
Download

3D MOL for #<Metabolite:0x00007f923a4c5968>

HMDB0001351
     RDKit          3D
Deoxyribose 1-phosphate
 24 24  0  0  0  0  0  0  0  0999 V2000
    2.9691    0.5814    1.3196 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1814    0.3634   -0.1571 P   0  0  0  0  0  5  0  0  0  0  0  0
    4.4845   -0.7195   -0.3793 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5691    1.8441   -0.8780 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8145   -0.2814   -0.8707 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6433   -0.0040   -0.1680 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0083   -1.3359    0.1974 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4524   -0.9440    0.3091 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.2085   -2.0268   -0.0845 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5352    0.2307   -0.6192 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.1730    1.4371    0.0277 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4638    1.1478    0.4676 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2655    0.5401   -1.0440 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0978   -1.6267   -0.5220 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0520    2.5698   -0.4664 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8405    0.5892    0.7267 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1363   -2.0296   -0.6322 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4130   -1.7269    1.1513 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6187   -0.6542    1.3647 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9418   -2.1252    0.5934 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1803   -0.0747   -1.4813 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2218    2.2340   -0.7485 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5246    1.8171    0.8526 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6241    0.1942    0.3027 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
  2  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
 11 12  1  0
 10 13  1  0
 13  6  1  0
  3 14  1  0
  4 15  1  0
  6 16  1  0
  7 17  1  0
  7 18  1  0
  8 19  1  1
  9 20  1  0
 10 21  1  6
 11 22  1  0
 11 23  1  0
 12 24  1  0
M  END
Download

3D SDF for #<Metabolite:0x00007f923a4c5968>


  Mrv0541 02231219042D          

 13 13  0  0  1  0            999 V2000
    0.0984   -0.0037    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5714    0.4730    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1552   -0.7946    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8816    0.2535    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2335   -0.0037    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.9839   -0.7946    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.7028    0.2535    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0131    0.2535    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4682   -1.4568    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5239    0.2535    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6990    1.0785    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6990   -0.5676    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1834    1.0595    0.0000 O   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
  2  5  1  0  0  0  0
  3  6  1  0  0  0  0
  4  7  1  0  0  0  0
  5  8  1  1  0  0  0
  6  9  1  6  0  0  0
  7 10  1  0  0  0  0
  7 11  1  0  0  0  0
  7 12  2  0  0  0  0
  8 13  1  0  0  0  0
  5  6  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0029628

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H11O7P/c6-2-4-3(7)1-5(11-4)12-13(8,9)10/h3-7H,1-2H2,(H2,8,9,10)/t3-,4+,5?/m0/s1

> <INCHI_KEY>
KBDKAJNTYKVSEK-PYHARJCCSA-N

> <FORMULA>
C5H11O7P

> <MOLECULAR_WEIGHT>
214.1104

> <EXACT_MASS>
214.024239218

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_AVERAGE_POLARIZABILITY>
17.207710029989737

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{[(4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy}phosphonic acid

> <ALOGPS_LOGP>
-2.14

> <JCHEM_LOGP>
-1.5251322443333333

> <ALOGPS_LOGS>
-0.76

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.425838614205934

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.3651983750806824

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9789480049262043

> <JCHEM_POLAR_SURFACE_AREA>
116.45

> <JCHEM_REFRACTIVITY>
39.3231

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.76e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
deoxyribose-1-phosphate

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for #<Metabolite:0x00007f923a4c5968>

HMDB0001351
     RDKit          3D
Deoxyribose 1-phosphate
 24 24  0  0  0  0  0  0  0  0999 V2000
    2.9691    0.5814    1.3196 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1814    0.3634   -0.1571 P   0  0  0  0  0  5  0  0  0  0  0  0
    4.4845   -0.7195   -0.3793 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5691    1.8441   -0.8780 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8145   -0.2814   -0.8707 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6433   -0.0040   -0.1680 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0083   -1.3359    0.1974 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4524   -0.9440    0.3091 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.2085   -2.0268   -0.0845 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5352    0.2307   -0.6192 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.1730    1.4371    0.0277 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4638    1.1478    0.4676 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2655    0.5401   -1.0440 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0978   -1.6267   -0.5220 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0520    2.5698   -0.4664 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8405    0.5892    0.7267 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1363   -2.0296   -0.6322 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4130   -1.7269    1.1513 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6187   -0.6542    1.3647 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9418   -2.1252    0.5934 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1803   -0.0747   -1.4813 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2218    2.2340   -0.7485 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5246    1.8171    0.8526 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6241    0.1942    0.3027 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
  2  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
 11 12  1  0
 10 13  1  0
 13  6  1  0
  3 14  1  0
  4 15  1  0
  6 16  1  0
  7 17  1  0
  7 18  1  0
  8 19  1  1
  9 20  1  0
 10 21  1  6
 11 22  1  0
 11 23  1  0
 12 24  1  0
M  END
Download

PDB for #<Metabolite:0x00007f923a4c5968>

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  C   UNK     0       0.184  -0.007   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0      -1.067   0.883   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0      -0.290  -1.483   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       1.646   0.473   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0      -2.303  -0.007   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.837  -1.483   0.000  0.00  0.00           C+0
HETATM    7  P   UNK     0       3.179   0.473   0.000  0.00  0.00           P+0
HETATM    8  C   UNK     0      -3.758   0.473   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -2.741  -2.719   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       4.711   0.473   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       3.171   2.013   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       3.171  -1.060   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      -4.076   1.978   0.000  0.00  0.00           O+0
CONECT    1    2    3    4                                                  
CONECT    2    1    5                                                       
CONECT    3    1    6                                                       
CONECT    4    1    7                                                       
CONECT    5    2    8    6                                                  
CONECT    6    3    9    5                                                  
CONECT    7    4   10   11   12                                             
CONECT    8    5   13                                                       
CONECT    9    6                                                            
CONECT   10    7                                                            
CONECT   11    7                                                            
CONECT   12    7                                                            
CONECT   13    8                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   26    0
END
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3D PDB for #<Metabolite:0x00007f923a4c5968>

COMPND    HMDB0001351
HETATM    1  O1  UNL     1       2.969   0.581   1.320  1.00  0.00           O  
HETATM    2  P1  UNL     1       3.181   0.363  -0.157  1.00  0.00           P  
HETATM    3  O2  UNL     1       4.485  -0.719  -0.379  1.00  0.00           O  
HETATM    4  O3  UNL     1       3.569   1.844  -0.878  1.00  0.00           O  
HETATM    5  O4  UNL     1       1.815  -0.281  -0.871  1.00  0.00           O  
HETATM    6  C1  UNL     1       0.643  -0.004  -0.168  1.00  0.00           C  
HETATM    7  C2  UNL     1       0.008  -1.336   0.197  1.00  0.00           C  
HETATM    8  C3  UNL     1      -1.452  -0.944   0.309  1.00  0.00           C  
HETATM    9  O5  UNL     1      -2.208  -2.027  -0.085  1.00  0.00           O  
HETATM   10  C4  UNL     1      -1.535   0.231  -0.619  1.00  0.00           C  
HETATM   11  C5  UNL     1      -2.173   1.437   0.028  1.00  0.00           C  
HETATM   12  O6  UNL     1      -3.464   1.148   0.468  1.00  0.00           O  
HETATM   13  O7  UNL     1      -0.265   0.540  -1.044  1.00  0.00           O  
HETATM   14  H1  UNL     1       4.098  -1.627  -0.522  1.00  0.00           H  
HETATM   15  H2  UNL     1       3.052   2.570  -0.466  1.00  0.00           H  
HETATM   16  H3  UNL     1       0.840   0.589   0.727  1.00  0.00           H  
HETATM   17  H4  UNL     1       0.136  -2.030  -0.632  1.00  0.00           H  
HETATM   18  H5  UNL     1       0.413  -1.727   1.151  1.00  0.00           H  
HETATM   19  H6  UNL     1      -1.619  -0.654   1.365  1.00  0.00           H  
HETATM   20  H7  UNL     1      -2.942  -2.125   0.593  1.00  0.00           H  
HETATM   21  H8  UNL     1      -2.180  -0.075  -1.481  1.00  0.00           H  
HETATM   22  H9  UNL     1      -2.222   2.234  -0.749  1.00  0.00           H  
HETATM   23  H10 UNL     1      -1.525   1.817   0.853  1.00  0.00           H  
HETATM   24  H11 UNL     1      -3.624   0.194   0.303  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4    5
CONECT    3   14
CONECT    4   15
CONECT    5    6
CONECT    6    7   13   16
CONECT    7    8   17   18
CONECT    8    9   10   19
CONECT    9   20
CONECT   10   11   13   21
CONECT   11   12   22   23
CONECT   12   24
END
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SMILES for #<Metabolite:0x00007f923a4c5968>

OC[C@H]1OC(C[C@@H]1O)OP(O)(O)=O
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INCHI for #<Metabolite:0x00007f923a4c5968>

InChI=1S/C5H11O7P/c6-2-4-3(7)1-5(11-4)12-13(8,9)10/h3-7H,1-2H2,(H2,8,9,10)/t3-,4+,5?/m0/s1
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Synonyms
ValueSource
2-Deoxy-1-O-phosphono-D-erythro-pentofuranoseChEBI
2-Deoxy-1-O-phosphono-D-ribofuranoseChEBI
2-Deoxy-D-ribose 1-phosphateChEBI
2-Deoxy-D-ribose 1-phosphoric acidGenerator
Deoxyribose 1-phosphoric acidGenerator
2-Deoxy-alpha-D-ribose 1-phosphateHMDB
2-Deoxy-alpha-delta-ribose 1-phosphateHMDB
2-Deoxy-D-erythro-pentofuranose 1-phosphateHMDB
2-Deoxy-D-ribose-1-phosphateHMDB
2-Deoxy-delta-erythro-pentofuranose 1-phosphateHMDB
2-Deoxy-delta-ribose 1-phosphateHMDB
2-Deoxy-delta-ribose-1-phosphateHMDB
2-Deoxyribofuranose 1-phosphateHMDB
D-2-Deoxy-ribofuranose 1-phosphateHMDB
delta-2-Deoxy-ribofuranose 1-phosphateHMDB
Deoxyribose-1-phosphateHMDB
2-Deoxyribose 1-phosphateHMDB
2-Deoxyribose 1-phosphate, (alpha-D-erythro)-isomerHMDB
2-Deoxyribose 1-phosphate, (beta-D-erythro)-isomerHMDB
Molecular FormulaC5H11O7P
Average Mass214.1104
Monoisotopic Mass214.024239218
IUPAC Name{[(4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy}phosphonic acid
Traditional Namedeoxyribose-1-phosphate
CAS Registry Number17210-42-3
SMILES
OC[C@H]1OC(C[C@@H]1O)OP(O)(O)=O
InChI Identifier
InChI=1S/C5H11O7P/c6-2-4-3(7)1-5(11-4)12-13(8,9)10/h3-7H,1-2H2,(H2,8,9,10)/t3-,4+,5?/m0/s1
InChI KeyKBDKAJNTYKVSEK-PYHARJCCSA-N