Showing metabocard for 2-dehydro-3-deoxy-D-arabinonate (MMDBc0054162)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2022-06-05 22:56:36 UTC
Update Date2022-09-01 02:27:37 UTC
MiMeDB IDMMDBc0054162
Metabolite Identification
Common Name2-dehydro-3-deoxy-D-arabinonate
Description
Structure
MOLSDFPDBSMILESInChI

MOL for #<Metabolite:0x0000564abf7496a8>

 
  Mrv1533006051517552D          
 
 10  9  0  0  1  0            999 V2000
    8.7037   -8.4975    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.4182   -8.9100    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.1327   -8.4975    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.8472   -8.9100    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.5616   -8.4975    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   12.2761   -8.9100    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.9906   -8.4975    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.4182   -9.7350    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.1327   -7.6725    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.5616   -7.6725    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  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  2  8  2  0  0  0  0
  3  9  2  0  0  0  0
  5 10  1  6  0  0  0
M  END
Download

3D MOL for #<Metabolite:0x0000564abf7496a8>

Download
3D SDF for #<Metabolite:0x0000564abf7496a8>
 
  Mrv1533006051517552D          
 
 10  9  0  0  1  0            999 V2000
    8.7037   -8.4975    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.4182   -8.9100    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.1327   -8.4975    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.8472   -8.9100    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.5616   -8.4975    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   12.2761   -8.9100    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.9906   -8.4975    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.4182   -9.7350    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.1327   -7.6725    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.5616   -7.6725    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  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  2  8  2  0  0  0  0
  3  9  2  0  0  0  0
  5 10  1  6  0  0  0
M  END
> <DATABASE_ID>
MMDBc0054162

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H8O5/c6-2-3(7)1-4(8)5(9)10/h3,6-7H,1-2H2,(H,9,10)/t3-/m0/s1

> <INCHI_KEY>
UQIGQRSJIKIPKZ-VKHMYHEASA-N

> <FORMULA>
C5H8O5

> <MOLECULAR_WEIGHT>
148.114

> <EXACT_MASS>
148.037173358

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
18

> <JCHEM_AVERAGE_POLARIZABILITY>
12.905738953771145

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(4S)-4,5-dihydroxy-2-oxopentanoic acid

> <ALOGPS_LOGP>
-1.62

> <JCHEM_LOGP>
-1.1446962983333338

> <ALOGPS_LOGS>
0.14

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
14.12213716943176

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.9063050280407245

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9433681969036742

> <JCHEM_POLAR_SURFACE_AREA>
94.83

> <JCHEM_REFRACTIVITY>
30.3538

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.05e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-dehydro-3-deoxy-D-pentonate

> <JCHEM_VEBER_RULE>
0

$$$$

Download
3D-SDF for #<Metabolite:0x0000564abf7496a8>
Download
PDB for #<Metabolite:0x0000564abf7496a8>
HEADER    PROTEIN                                 05-JUN-15   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   05-JUN-15         0                                  
HETATM    1  O   UNK     0      16.247 -15.862   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      17.581 -16.632   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      18.914 -15.862   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      20.248 -16.632   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      21.582 -15.862   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      22.915 -16.632   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      24.249 -15.862   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      17.581 -18.172   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      18.914 -14.322   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      21.582 -14.322   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    8                                                  
CONECT    3    2    4    9                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   10                                                  
CONECT    6    5    7                                                       
CONECT    7    6                                                            
CONECT    8    2                                                            
CONECT    9    3                                                            
CONECT   10    5                                                            
MASTER        0    0    0    0    0    0    0    0   10    0   18    0
END

Download
3D PDB for #<Metabolite:0x0000564abf7496a8>
Download
SMILES for #<Metabolite:0x0000564abf7496a8>
OC[C@@H](O)CC(=O)C(O)=O
Download
INCHI for #<Metabolite:0x0000564abf7496a8>
InChI=1S/C5H8O5/c6-2-3(7)1-4(8)5(9)10/h3,6-7H,1-2H2,(H,9,10)/t3-/m0/s1
Download
Synonyms
ValueSource
(4S)-4,5-Dihydroxy-2-oxopentanoateChEBI
2-Dehydro-3-deoxy-D-arabinonateChEBI
2-Dehydro-3-deoxy-D-pentonateChEBI
2-Dehydro-3-deoxy-D-xylonateChEBI
(4S)-4,5-Dihydroxy-2-oxopentanoic acidGenerator
2-Dehydro-3-deoxy-D-pentonic acidGenerator
2-Dehydro-3-deoxy-D-xylonic acidGenerator
2-dehydro-3-Deoxy-D-arabinonic acidGenerator
Chemical FormulaC5H8O5
Average Molecular Weight148.114
Monoisotopic Molecular Weight148.037173358
IUPAC Name(4S)-4,5-dihydroxy-2-oxopentanoic acid
Traditional Name2-dehydro-3-deoxy-D-pentonate
CAS Registry NumberNot Available
SMILES
OC[C@@H](O)CC(=O)C(O)=O
InChI Identifier
InChI=1S/C5H8O5/c6-2-3(7)1-4(8)5(9)10/h3,6-7H,1-2H2,(H,9,10)/t3-/m0/s1
InChI KeyUQIGQRSJIKIPKZ-VKHMYHEASA-N