Showing metabocard for D-Arabinose 5-phosphate (MMDBc0029914)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2021-11-17 23:46:39 UTC
Update Date2024-10-15 18:44:50 UTC
Metabolite IDMMDBc0029914
Metabolite Identification
Common NameD-Arabinose 5-phosphate
DescriptionD-Arabinose 5-phosphate is an intermediate in biosynthesis of lipopolysaccharide.
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f922886e4c8>


  Mrv1652309042000342D          

 14 13  0  0  1  0            999 V2000
   12.4149  -18.4154    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   11.7005  -18.8279    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.8274  -19.1299    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.0024  -17.7009    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.8439  -18.4154    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.5583  -18.0029    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   15.2728  -18.4154    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   15.9873  -18.0029    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   16.7018  -18.4154    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.1294  -18.0029    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.7018  -19.2404    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.9873  -17.1779    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.2728  -19.2404    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.5583  -17.1779    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  3  1  1  0  0  0  0
  4  1  1  0  0  0  0
  6  5  1  0  0  0  0
  7  6  1  0  0  0  0
  8  7  1  0  0  0  0
  9  8  1  0  0  0  0
 10  5  1  0  0  0  0
 11  9  2  0  0  0  0
  8 12  1  6  0  0  0
  7 13  1  6  0  0  0
  6 14  1  1  0  0  0
  1 10  1  0  0  0  0
M  END
Download

3D MOL for #<Metabolite:0x00007f922886e4c8>

HMDB0011734
     RDKit          3D
D-Arabinose 5-phosphate
 25 24  0  0  0  0  0  0  0  0999 V2000
   -2.4512    2.2362   -0.9198 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0515    1.2661   -0.5367 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6331    0.3730    0.5478 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.7113   -0.4982    0.8876 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4574   -0.5011    0.1231 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.2114   -1.3356    1.2509 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2757    0.3270   -0.1757 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.3091    1.1291   -1.2786 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0207   -0.4957   -0.2355 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0499    0.4256   -0.2388 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5721   -0.2400   -0.3005 P   0  0  0  0  0  5  0  0  0  0  0  0
    3.6828   -1.4353   -1.1976 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6330    0.9573   -0.9109 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1743   -0.6529    1.2352 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9924    1.0634   -1.0708 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3212    0.9175    1.4523 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5648   -0.7284    1.8404 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7474   -1.1135   -0.7375 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6160   -2.2139    1.0436 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0861    1.0166    0.7095 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4485    0.5895   -2.0830 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0724   -1.1722    0.6468 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9635   -1.0766   -1.1833 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2389    1.8609   -0.7799 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4694   -0.6986    1.9113 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  3  5  1  0
  5  6  1  0
  5  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  2  0
 11 13  1  0
 11 14  1  0
  2 15  1  0
  3 16  1  1
  4 17  1  0
  5 18  1  6
  6 19  1  0
  7 20  1  1
  8 21  1  0
  9 22  1  0
  9 23  1  0
 13 24  1  0
 14 25  1  0
M  END
Download

3D SDF for #<Metabolite:0x00007f922886e4c8>


  Mrv1652309042000342D          

 14 13  0  0  1  0            999 V2000
   12.4149  -18.4154    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   11.7005  -18.8279    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.8274  -19.1299    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.0024  -17.7009    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.8439  -18.4154    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.5583  -18.0029    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   15.2728  -18.4154    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   15.9873  -18.0029    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   16.7018  -18.4154    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.1294  -18.0029    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.7018  -19.2404    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.9873  -17.1779    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.2728  -19.2404    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.5583  -17.1779    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  3  1  1  0  0  0  0
  4  1  1  0  0  0  0
  6  5  1  0  0  0  0
  7  6  1  0  0  0  0
  8  7  1  0  0  0  0
  9  8  1  0  0  0  0
 10  5  1  0  0  0  0
 11  9  2  0  0  0  0
  8 12  1  6  0  0  0
  7 13  1  6  0  0  0
  6 14  1  1  0  0  0
  1 10  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0029914

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H11O8P/c6-1-3(7)5(9)4(8)2-13-14(10,11)12/h1,3-5,7-9H,2H2,(H2,10,11,12)/t3-,4-,5+/m1/s1

> <INCHI_KEY>
PPQRONHOSHZGFQ-WDCZJNDASA-N

> <FORMULA>
C5H11O8P

> <MOLECULAR_WEIGHT>
230.1098

> <EXACT_MASS>
230.01915384

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
25

> <JCHEM_AVERAGE_POLARIZABILITY>
17.998594047608492

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{[(2R,3R,4S)-2,3,4-trihydroxy-5-oxopentyl]oxy}phosphonic acid

> <ALOGPS_LOGP>
-1.64

> <JCHEM_LOGP>
-3.0615916523333335

> <ALOGPS_LOGS>
-1.08

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.51682044808608

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.4910102081094525

> <JCHEM_PKA_STRONGEST_BASIC>
-3.544450846242131

> <JCHEM_POLAR_SURFACE_AREA>
144.52

> <JCHEM_REFRACTIVITY>
42.256

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.93e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
arabinose 5-phosphate

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for #<Metabolite:0x00007f922886e4c8>

HMDB0011734
     RDKit          3D
D-Arabinose 5-phosphate
 25 24  0  0  0  0  0  0  0  0999 V2000
   -2.4512    2.2362   -0.9198 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0515    1.2661   -0.5367 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6331    0.3730    0.5478 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.7113   -0.4982    0.8876 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4574   -0.5011    0.1231 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.2114   -1.3356    1.2509 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2757    0.3270   -0.1757 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.3091    1.1291   -1.2786 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0207   -0.4957   -0.2355 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0499    0.4256   -0.2388 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5721   -0.2400   -0.3005 P   0  0  0  0  0  5  0  0  0  0  0  0
    3.6828   -1.4353   -1.1976 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6330    0.9573   -0.9109 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1743   -0.6529    1.2352 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9924    1.0634   -1.0708 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3212    0.9175    1.4523 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5648   -0.7284    1.8404 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7474   -1.1135   -0.7375 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6160   -2.2139    1.0436 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0861    1.0166    0.7095 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4485    0.5895   -2.0830 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0724   -1.1722    0.6468 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9635   -1.0766   -1.1833 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2389    1.8609   -0.7799 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4694   -0.6986    1.9113 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  3  5  1  0
  5  6  1  0
  5  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  2  0
 11 13  1  0
 11 14  1  0
  2 15  1  0
  3 16  1  1
  4 17  1  0
  5 18  1  6
  6 19  1  0
  7 20  1  1
  8 21  1  0
  9 22  1  0
  9 23  1  0
 13 24  1  0
 14 25  1  0
M  END
Download

PDB for #<Metabolite:0x00007f922886e4c8>

HEADER    PROTEIN                                 04-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-20         0                                  
HETATM    1  P   UNK     0      23.174 -34.375   0.000  0.00  0.00           P+0
HETATM    2  O   UNK     0      21.841 -35.145   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      23.944 -35.709   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      22.404 -33.042   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0      25.842 -34.375   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      27.175 -33.605   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      28.509 -34.375   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      29.843 -33.605   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      31.177 -34.375   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      24.508 -33.605   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0      31.177 -35.915   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      29.843 -32.065   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      28.509 -35.915   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0      27.175 -32.065   0.000  0.00  0.00           O+0
CONECT    1    2    3    4   10                                             
CONECT    2    1                                                            
CONECT    3    1                                                            
CONECT    4    1                                                            
CONECT    5    6   10                                                       
CONECT    6    5    7   14                                                  
CONECT    7    6    8   13                                                  
CONECT    8    7    9   12                                                  
CONECT    9    8   11                                                       
CONECT   10    5    1                                                       
CONECT   11    9                                                            
CONECT   12    8                                                            
CONECT   13    7                                                            
CONECT   14    6                                                            
MASTER        0    0    0    0    0    0    0    0   14    0   26    0
END
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3D PDB for #<Metabolite:0x00007f922886e4c8>

COMPND    HMDB0011734
HETATM    1  O1  UNL     1      -2.451   2.236  -0.920  1.00  0.00           O  
HETATM    2  C1  UNL     1      -3.052   1.266  -0.537  1.00  0.00           C  
HETATM    3  C2  UNL     1      -2.633   0.373   0.548  1.00  0.00           C  
HETATM    4  O2  UNL     1      -3.711  -0.498   0.888  1.00  0.00           O  
HETATM    5  C3  UNL     1      -1.457  -0.501   0.123  1.00  0.00           C  
HETATM    6  O3  UNL     1      -1.211  -1.336   1.251  1.00  0.00           O  
HETATM    7  C4  UNL     1      -0.276   0.327  -0.176  1.00  0.00           C  
HETATM    8  O4  UNL     1      -0.309   1.129  -1.279  1.00  0.00           O  
HETATM    9  C5  UNL     1       1.021  -0.496  -0.235  1.00  0.00           C  
HETATM   10  O5  UNL     1       2.050   0.426  -0.239  1.00  0.00           O  
HETATM   11  P1  UNL     1       3.572  -0.240  -0.300  1.00  0.00           P  
HETATM   12  O6  UNL     1       3.683  -1.435  -1.198  1.00  0.00           O  
HETATM   13  O7  UNL     1       4.633   0.957  -0.911  1.00  0.00           O  
HETATM   14  O8  UNL     1       4.174  -0.653   1.235  1.00  0.00           O  
HETATM   15  H1  UNL     1      -3.992   1.063  -1.071  1.00  0.00           H  
HETATM   16  H2  UNL     1      -2.321   0.917   1.452  1.00  0.00           H  
HETATM   17  H3  UNL     1      -3.565  -0.728   1.840  1.00  0.00           H  
HETATM   18  H4  UNL     1      -1.747  -1.113  -0.737  1.00  0.00           H  
HETATM   19  H5  UNL     1      -1.616  -2.214   1.044  1.00  0.00           H  
HETATM   20  H6  UNL     1      -0.086   1.017   0.710  1.00  0.00           H  
HETATM   21  H7  UNL     1      -0.449   0.589  -2.083  1.00  0.00           H  
HETATM   22  H8  UNL     1       1.072  -1.172   0.647  1.00  0.00           H  
HETATM   23  H9  UNL     1       0.963  -1.077  -1.183  1.00  0.00           H  
HETATM   24  H10 UNL     1       4.239   1.861  -0.780  1.00  0.00           H  
HETATM   25  H11 UNL     1       3.469  -0.699   1.911  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3   15
CONECT    3    4    5   16
CONECT    4   17
CONECT    5    6    7   18
CONECT    6   19
CONECT    7    8    9   20
CONECT    8   21
CONECT    9   10   22   23
CONECT   10   11
CONECT   11   12   12   13   14
CONECT   13   24
CONECT   14   25
END
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SMILES for #<Metabolite:0x00007f922886e4c8>

O[C@H](COP(O)(O)=O)[C@@H](O)[C@H](O)C=O
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INCHI for #<Metabolite:0x00007f922886e4c8>

InChI=1S/C5H11O8P/c6-1-3(7)5(9)4(8)2-13-14(10,11)12/h1,3-5,7-9H,2H2,(H2,10,11,12)/t3-,4-,5+/m1/s1
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Synonyms
ValueSource
5-O-Phosphono-D-arabinoseChEBI
D-a-5-pChEBI
D-Arabinose 5-phosphoric acidGenerator
Arabinose-5-PHMDB
Arabinose-5PHMDB
Arabinose 5-phosphate, di-li saltMeSH, HMDB
Arabinose 5-phosphateMeSH, HMDB
Arabinose 5-phosphate, (beta-D)-isomerMeSH, HMDB
Molecular FormulaC5H11O8P
Average Mass230.1098
Monoisotopic Mass230.01915384
IUPAC Name{[(2R,3R,4S)-2,3,4-trihydroxy-5-oxopentyl]oxy}phosphonic acid
Traditional Namearabinose 5-phosphate
CAS Registry Number13137-52-5
SMILES
O[C@H](COP(O)(O)=O)[C@@H](O)[C@H](O)C=O
InChI Identifier
InChI=1S/C5H11O8P/c6-1-3(7)5(9)4(8)2-13-14(10,11)12/h1,3-5,7-9H,2H2,(H2,10,11,12)/t3-,4-,5+/m1/s1
InChI KeyPPQRONHOSHZGFQ-WDCZJNDASA-N