Showing metabocard for 1-Hydroxy-2-methyl-2-butenyl 4-diphosphate (MMDBc0029957)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2021-11-17 23:48:17 UTC
Update Date2022-08-31 17:37:58 UTC
Metabolite IDMMDBc0029957
Metabolite Identification
Common Name1-Hydroxy-2-methyl-2-butenyl 4-diphosphate
Description1-hydroxy-2-methyl-2-butenyl 4-diphosphate is a member of the chemical class known as Organic Pyrophosphates. These are organic compounds containing the pyrophosphate oxoanion, with the structure OP([O-])(=O)OP(O)([O-])=O.
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x0000560be2934628>

Structure #1
  Mrv0541 02241206552D          

 15 14  0  0  0  0            999 V2000
   -0.4125    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2375   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    4.2868    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    3.9849    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    3.1599    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    1.7309    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    2.5559    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500    2.8579    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    3.5724    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    2.1434    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
  1  5  1  0  0  0  0
  2  3  1  4  0  0  0
  2  5  2  0  0  0  0
  3 12  1  0  0  0  0
  4  5  1  0  0  0  0
  4  6  1  0  0  0  0
  7 14  1  0  0  0  0
  8 14  1  0  0  0  0
  9 14  2  0  0  0  0
 10 15  1  0  0  0  0
 11 15  2  0  0  0  0
 12 15  1  0  0  0  0
 13 14  1  0  0  0  0
 13 15  1  0  0  0  0
M  END
Download

3D MOL for #<Metabolite:0x0000560be2934628>

HMDB0242600
     RDKit          3D
(2E)-4-Hydroxy-3-methylbut-2-en-1-yl trihydrogen diphosphate
 27 26  0  0  0  0  0  0  0  0999 V2000
   -4.1187   -0.5513    0.2426 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7609   -0.0390   -0.1624 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8057   -0.1031    0.7253 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4068    0.3347    0.5579 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3870   -0.8199    0.7619 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9995   -0.3439    0.5751 P   0  0  0  0  0  5  0  0  0  0  0  0
    2.8591   -1.1878    1.4946 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1099    1.2577    1.1059 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4863   -0.5237   -1.0196 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1590   -0.4996   -1.1836 P   0  0  0  0  0  5  0  0  0  0  0  0
    4.5407   -0.3877   -2.6297 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8419    0.8122   -0.3464 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7846   -1.9593   -0.5867 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5942    0.4924   -1.5181 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4455    1.5958   -1.7476 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1035   -1.0241    1.2249 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7745    0.3320    0.3027 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4902   -1.2658   -0.5152 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0548   -0.5298    1.7180 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1653    1.1016    1.3266 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1968    0.8018   -0.4074 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2392    1.8246    0.2823 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6088    0.6996    0.6266 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1095   -2.4611   -0.0530 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9253   -0.2797   -2.2783 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5739    0.7864   -1.7777 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7093    1.9369   -0.8693 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  3
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  6  8  1  0
  6  9  1  0
  9 10  1  0
 10 11  2  0
 10 12  1  0
 10 13  1  0
  2 14  1  0
 14 15  1  0
  1 16  1  0
  1 17  1  0
  1 18  1  0
  3 19  1  0
  4 20  1  0
  4 21  1  0
  8 22  1  0
 12 23  1  0
 13 24  1  0
 14 25  1  0
 14 26  1  0
 15 27  1  0
M  END
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3D SDF for #<Metabolite:0x0000560be2934628>

Structure #1
  Mrv0541 02241206552D          

 15 14  0  0  0  0            999 V2000
   -0.4125    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2375   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    4.2868    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    3.9849    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    3.1599    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    1.7309    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    2.5559    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500    2.8579    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    3.5724    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    2.1434    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
  1  5  1  0  0  0  0
  2  3  1  4  0  0  0
  2  5  2  0  0  0  0
  3 12  1  0  0  0  0
  4  5  1  0  0  0  0
  4  6  1  0  0  0  0
  7 14  1  0  0  0  0
  8 14  1  0  0  0  0
  9 14  2  0  0  0  0
 10 15  1  0  0  0  0
 11 15  2  0  0  0  0
 12 15  1  0  0  0  0
 13 14  1  0  0  0  0
 13 15  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0029957

> <DATABASE_NAME>
MIME

> <SMILES>
CC(CO)=CCOP(O)(=O)OP(O)(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C5H12O8P2/c1-5(4-6)2-3-12-15(10,11)13-14(7,8)9/h2,6H,3-4H2,1H3,(H,10,11)(H2,7,8,9)

> <INCHI_KEY>
MDSIZRKJVDMQOQ-UHFFFAOYSA-N

> <FORMULA>
C5H12O8P2

> <MOLECULAR_WEIGHT>
262.0915

> <EXACT_MASS>
262.000740384

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_AVERAGE_POLARIZABILITY>
20.302484183385786

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
({hydroxy[(4-hydroxy-3-methylbut-2-en-1-yl)oxy]phosphoryl}oxy)phosphonic acid

> <ALOGPS_LOGP>
-0.31

> <JCHEM_LOGP>
-0.9834666459999992

> <ALOGPS_LOGS>
-1.56

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.184335387773854

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.767214908380022

> <JCHEM_PKA_STRONGEST_BASIC>
-2.730459729715264

> <JCHEM_POLAR_SURFACE_AREA>
133.52

> <JCHEM_REFRACTIVITY>
50.9

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.16e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[hydroxy(4-hydroxy-3-methylbut-2-en-1-yl)oxyphosphoryl]oxyphosphonic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for #<Metabolite:0x0000560be2934628>

HMDB0242600
     RDKit          3D
(2E)-4-Hydroxy-3-methylbut-2-en-1-yl trihydrogen diphosphate
 27 26  0  0  0  0  0  0  0  0999 V2000
   -4.1187   -0.5513    0.2426 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7609   -0.0390   -0.1624 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8057   -0.1031    0.7253 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4068    0.3347    0.5579 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3870   -0.8199    0.7619 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9995   -0.3439    0.5751 P   0  0  0  0  0  5  0  0  0  0  0  0
    2.8591   -1.1878    1.4946 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1099    1.2577    1.1059 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4863   -0.5237   -1.0196 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1590   -0.4996   -1.1836 P   0  0  0  0  0  5  0  0  0  0  0  0
    4.5407   -0.3877   -2.6297 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8419    0.8122   -0.3464 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7846   -1.9593   -0.5867 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5942    0.4924   -1.5181 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4455    1.5958   -1.7476 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1035   -1.0241    1.2249 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7745    0.3320    0.3027 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4902   -1.2658   -0.5152 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0548   -0.5298    1.7180 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1653    1.1016    1.3266 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1968    0.8018   -0.4074 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2392    1.8246    0.2823 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6088    0.6996    0.6266 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1095   -2.4611   -0.0530 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9253   -0.2797   -2.2783 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5739    0.7864   -1.7777 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7093    1.9369   -0.8693 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  3
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  6  8  1  0
  6  9  1  0
  9 10  1  0
 10 11  2  0
 10 12  1  0
 10 13  1  0
  2 14  1  0
 14 15  1  0
  1 16  1  0
  1 17  1  0
  1 18  1  0
  3 19  1  0
  4 20  1  0
  4 21  1  0
  8 22  1  0
 12 23  1  0
 13 24  1  0
 14 25  1  0
 14 26  1  0
 15 27  1  0
M  END
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PDB for #<Metabolite:0x0000560be2934628>

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: Structure #1                                      
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0      -0.770   1.334   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.770  -1.334   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -2.310  -1.334   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       1.540   8.002   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       3.644   7.438   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       0.976   5.898   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       3.644   3.231   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       0.976   4.771   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       1.540   2.667   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       3.080   5.335   0.000  0.00  0.00           O+0
HETATM   14  P   UNK     0       2.310   6.668   0.000  0.00  0.00           P+0
HETATM   15  P   UNK     0       2.310   4.001   0.000  0.00  0.00           P+0
CONECT    1    5                                                            
CONECT    2    3    5                                                       
CONECT    3    2   12                                                       
CONECT    4    5    6                                                       
CONECT    5    1    2    4                                                  
CONECT    6    4                                                            
CONECT    7   14                                                            
CONECT    8   14                                                            
CONECT    9   14                                                            
CONECT   10   15                                                            
CONECT   11   15                                                            
CONECT   12    3   15                                                       
CONECT   13   14   15                                                       
CONECT   14    7    8    9   13                                             
CONECT   15   10   11   12   13                                             
MASTER        0    0    0    0    0    0    0    0   15    0   28    0
END
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3D PDB for #<Metabolite:0x0000560be2934628>

COMPND    HMDB0242600
HETATM    1  C1  UNL     1      -4.119  -0.551   0.243  1.00  0.00           C  
HETATM    2  C2  UNL     1      -2.761  -0.039  -0.162  1.00  0.00           C  
HETATM    3  C3  UNL     1      -1.806  -0.103   0.725  1.00  0.00           C  
HETATM    4  C4  UNL     1      -0.407   0.335   0.558  1.00  0.00           C  
HETATM    5  O1  UNL     1       0.387  -0.820   0.762  1.00  0.00           O  
HETATM    6  P1  UNL     1       2.000  -0.344   0.575  1.00  0.00           P  
HETATM    7  O2  UNL     1       2.859  -1.188   1.495  1.00  0.00           O  
HETATM    8  O3  UNL     1       2.110   1.258   1.106  1.00  0.00           O  
HETATM    9  O4  UNL     1       2.486  -0.524  -1.020  1.00  0.00           O  
HETATM   10  P2  UNL     1       4.159  -0.500  -1.184  1.00  0.00           P  
HETATM   11  O5  UNL     1       4.541  -0.388  -2.630  1.00  0.00           O  
HETATM   12  O6  UNL     1       4.842   0.812  -0.346  1.00  0.00           O  
HETATM   13  O7  UNL     1       4.785  -1.959  -0.587  1.00  0.00           O  
HETATM   14  C5  UNL     1      -2.594   0.492  -1.518  1.00  0.00           C  
HETATM   15  O8  UNL     1      -3.446   1.596  -1.748  1.00  0.00           O  
HETATM   16  H1  UNL     1      -4.103  -1.024   1.225  1.00  0.00           H  
HETATM   17  H2  UNL     1      -4.775   0.332   0.303  1.00  0.00           H  
HETATM   18  H3  UNL     1      -4.490  -1.266  -0.515  1.00  0.00           H  
HETATM   19  H4  UNL     1      -2.055  -0.530   1.718  1.00  0.00           H  
HETATM   20  H5  UNL     1      -0.165   1.102   1.327  1.00  0.00           H  
HETATM   21  H6  UNL     1      -0.197   0.802  -0.407  1.00  0.00           H  
HETATM   22  H7  UNL     1       2.239   1.825   0.282  1.00  0.00           H  
HETATM   23  H8  UNL     1       4.609   0.700   0.627  1.00  0.00           H  
HETATM   24  H9  UNL     1       4.110  -2.461  -0.053  1.00  0.00           H  
HETATM   25  H10 UNL     1      -2.925  -0.280  -2.278  1.00  0.00           H  
HETATM   26  H11 UNL     1      -1.574   0.786  -1.778  1.00  0.00           H  
HETATM   27  H12 UNL     1      -3.709   1.937  -0.869  1.00  0.00           H  
CONECT    1    2   16   17   18
CONECT    2    3    3   14
CONECT    3    4   19
CONECT    4    5   20   21
CONECT    5    6
CONECT    6    7    7    8    9
CONECT    8   22
CONECT    9   10
CONECT   10   11   11   12   13
CONECT   12   23
CONECT   13   24
CONECT   14   15   25   26
CONECT   15   27
END
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SMILES for #<Metabolite:0x0000560be2934628>

CC(CO)=CCOP(O)(=O)OP(O)(O)=O
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INCHI for #<Metabolite:0x0000560be2934628>

InChI=1S/C5H12O8P2/c1-5(4-6)2-3-12-15(10,11)13-14(7,8)9/h2,6H,3-4H2,1H3,(H,10,11)(H2,7,8,9)
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SynonymsNot Available
Molecular FormulaC5H12O8P2
Average Mass262.0915
Monoisotopic Mass262.000740384
IUPAC Name({hydroxy[(4-hydroxy-3-methylbut-2-en-1-yl)oxy]phosphoryl}oxy)phosphonic acid
Traditional Name[hydroxy(4-hydroxy-3-methylbut-2-en-1-yl)oxyphosphoryl]oxyphosphonic acid
CAS Registry NumberNot Available
SMILES
CC(CO)=CCOP(O)(=O)OP(O)(O)=O
InChI Identifier
InChI=1S/C5H12O8P2/c1-5(4-6)2-3-12-15(10,11)13-14(7,8)9/h2,6H,3-4H2,1H3,(H,10,11)(H2,7,8,9)
InChI KeyMDSIZRKJVDMQOQ-UHFFFAOYSA-N