Showing metabocard for Ectoine (MMDBc0000763)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2020-12-10 18:54:25 UTC
Update Date2024-04-30 19:33:38 UTC
Metabolite IDMMDBc0000763
Metabolite Identification
Common NameEctoine
DescriptionEctoine belongs to the class of organic compounds known as alpha-amino acids. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon). Ectoine has been identified in urine (PMID: 22409530 ).
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007fd0f40c0c70>


  Mrv1652306032018232D          

 10 10  0  0  0  0            999 V2000
10000.7109 9999.1847    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.4247 9999.5984    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.7109 9998.3597    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9999.281710001.6602    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.280610000.8352    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.566110000.4227    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9998.5661 9999.5976    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.2806 9999.1852    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.9951 9999.5976    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
 9999.995110000.4227    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  5 10  1  0  0  0  0
  9 10  1  0  0  0  0
  9  1  1  6  0  0  0
  5  4  1  0  0  0  0
M  END
Download

3D MOL for #<Metabolite:0x00007fd0f40c0c70>

HMDB0240650
     RDKit          3D
Ectoine
 20 20  0  0  0  0  0  0  0  0999 V2000
    2.8339    0.4416   -0.2827 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5138   -0.2037   -0.1334 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2879   -1.4313   -0.4163 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0453   -1.9143   -0.1923 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1492   -1.0264   -0.5956 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8797    0.4733   -0.4281 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.0535    1.0153    0.3312 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0210    0.4543    0.6001 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8249    2.3825    0.6656 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3683    0.5641    0.2923 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.0985    0.8853    0.7289 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8915    1.1166   -1.0891 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5699   -0.4048   -0.4496 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1206   -2.0854    0.9631 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1488   -2.9200   -0.6313 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0544   -1.3210    0.0198 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4156   -1.2562   -1.6266 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8176    0.9448   -1.4042 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5267    3.0598    0.6315 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4935    1.2256    1.0991 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  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
  6 10  1  0
 10  2  1  0
  1 11  1  0
  1 12  1  0
  1 13  1  0
  4 14  1  0
  4 15  1  0
  5 16  1  0
  5 17  1  0
  6 18  1  6
  9 19  1  0
 10 20  1  0
M  END
Download

3D SDF for #<Metabolite:0x00007fd0f40c0c70>


  Mrv1652306032018232D          

 10 10  0  0  0  0            999 V2000
10000.7109 9999.1847    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.4247 9999.5984    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.7109 9998.3597    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9999.281710001.6602    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.280610000.8352    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.566110000.4227    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9998.5661 9999.5976    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.2806 9999.1852    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.9951 9999.5976    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
 9999.995110000.4227    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  5 10  1  0  0  0  0
  9 10  1  0  0  0  0
  9  1  1  6  0  0  0
  5  4  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0000763

> <DATABASE_NAME>
MIME

> <SMILES>
CC1=NCC[C@H](N1)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C6H10N2O2/c1-4-7-3-2-5(8-4)6(9)10/h5H,2-3H2,1H3,(H,7,8)(H,9,10)/t5-/m0/s1

> <INCHI_KEY>
WQXNXVUDBPYKBA-YFKPBYRVSA-N

> <FORMULA>
C6H10N2O2

> <MOLECULAR_WEIGHT>
142.1558

> <EXACT_MASS>
142.074227574

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
20

> <JCHEM_AVERAGE_POLARIZABILITY>
14.253895179555728

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(4S)-2-methyl-1,4,5,6-tetrahydropyrimidine-4-carboxylic acid

> <ALOGPS_LOGP>
-0.23

> <JCHEM_LOGP>
-2.525868016561477

> <ALOGPS_LOGS>
-1.14

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.746020462418522

> <JCHEM_PKA_STRONGEST_BASIC>
10.525331945460499

> <JCHEM_POLAR_SURFACE_AREA>
61.690000000000005

> <JCHEM_REFRACTIVITY>
35.0427

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.03e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
ectoine

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for #<Metabolite:0x00007fd0f40c0c70>

HMDB0240650
     RDKit          3D
Ectoine
 20 20  0  0  0  0  0  0  0  0999 V2000
    2.8339    0.4416   -0.2827 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5138   -0.2037   -0.1334 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2879   -1.4313   -0.4163 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0453   -1.9143   -0.1923 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1492   -1.0264   -0.5956 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8797    0.4733   -0.4281 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.0535    1.0153    0.3312 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0210    0.4543    0.6001 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8249    2.3825    0.6656 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3683    0.5641    0.2923 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.0985    0.8853    0.7289 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8915    1.1166   -1.0891 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5699   -0.4048   -0.4496 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1206   -2.0854    0.9631 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1488   -2.9200   -0.6313 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0544   -1.3210    0.0198 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4156   -1.2562   -1.6266 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8176    0.9448   -1.4042 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5267    3.0598    0.6315 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4935    1.2256    1.0991 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  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
  6 10  1  0
 10  2  1  0
  1 11  1  0
  1 12  1  0
  1 13  1  0
  4 14  1  0
  4 15  1  0
  5 16  1  0
  5 17  1  0
  6 18  1  6
  9 19  1  0
 10 20  1  0
M  END
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PDB for #<Metabolite:0x00007fd0f40c0c70>

HEADER    PROTEIN                                 03-JUN-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-JUN-20         0                                  
HETATM    1  C   UNK     0    8667.9948665.145   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0    8669.3268665.917   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0    8667.9948663.605   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0    8665.3268669.766   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0    8665.3248668.226   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0    8663.9908667.456   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0    8663.9908665.916   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0    8665.3248665.146   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0    8666.6588665.916   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0    8666.6588667.456   0.000  0.00  0.00           N+0
CONECT    1    2    3    9                                                  
CONECT    2    1                                                            
CONECT    3    1                                                            
CONECT    4    5                                                            
CONECT    5    6   10    4                                                  
CONECT    6    5    7                                                       
CONECT    7    8    6                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10    1                                                  
CONECT   10    5    9                                                       
MASTER        0    0    0    0    0    0    0    0   10    0   20    0
END
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3D PDB for #<Metabolite:0x00007fd0f40c0c70>

COMPND    HMDB0240650
HETATM    1  C1  UNL     1       2.834   0.442  -0.283  1.00  0.00           C  
HETATM    2  C2  UNL     1       1.514  -0.204  -0.133  1.00  0.00           C  
HETATM    3  N1  UNL     1       1.288  -1.431  -0.416  1.00  0.00           N  
HETATM    4  C3  UNL     1      -0.045  -1.914  -0.192  1.00  0.00           C  
HETATM    5  C4  UNL     1      -1.149  -1.026  -0.596  1.00  0.00           C  
HETATM    6  C5  UNL     1      -0.880   0.473  -0.428  1.00  0.00           C  
HETATM    7  C6  UNL     1      -2.054   1.015   0.331  1.00  0.00           C  
HETATM    8  O1  UNL     1      -3.021   0.454   0.600  1.00  0.00           O  
HETATM    9  O2  UNL     1      -1.825   2.382   0.666  1.00  0.00           O  
HETATM   10  N2  UNL     1       0.368   0.564   0.292  1.00  0.00           N  
HETATM   11  H1  UNL     1       3.098   0.885   0.729  1.00  0.00           H  
HETATM   12  H2  UNL     1       2.892   1.117  -1.089  1.00  0.00           H  
HETATM   13  H3  UNL     1       3.570  -0.405  -0.450  1.00  0.00           H  
HETATM   14  H4  UNL     1      -0.121  -2.085   0.963  1.00  0.00           H  
HETATM   15  H5  UNL     1      -0.149  -2.920  -0.631  1.00  0.00           H  
HETATM   16  H6  UNL     1      -2.054  -1.321   0.020  1.00  0.00           H  
HETATM   17  H7  UNL     1      -1.416  -1.256  -1.627  1.00  0.00           H  
HETATM   18  H8  UNL     1      -0.818   0.945  -1.404  1.00  0.00           H  
HETATM   19  H9  UNL     1      -2.527   3.060   0.631  1.00  0.00           H  
HETATM   20  H10 UNL     1       0.493   1.226   1.099  1.00  0.00           H  
CONECT    1    2   11   12   13
CONECT    2    3    3   10
CONECT    3    4
CONECT    4    5   14   15
CONECT    5    6   16   17
CONECT    6    7   10   18
CONECT    7    8    8    9
CONECT    9   19
CONECT   10   20
END
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SMILES for #<Metabolite:0x00007fd0f40c0c70>

CC1=NCC[C@H](N1)C(O)=O
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INCHI for #<Metabolite:0x00007fd0f40c0c70>

InChI=1S/C6H10N2O2/c1-4-7-3-2-5(8-4)6(9)10/h5H,2-3H2,1H3,(H,7,8)(H,9,10)/t5-/m0/s1
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Synonyms
ValueSource
(+)-1,4,5,6-Tetrahydro-2-methyl-4-pyrimidinecarboxylic acidChEBI
L-EctoineChEBI
(4S)-2-Methyl-1,4,5,6-tetrahydropyrimidine-4-carboxylateKegg
(+)-1,4,5,6-Tetrahydro-2-methyl-4-pyrimidinecarboxylateGenerator
(4S)-2-Methyl-1,4,5,6-tetrahydropyrimidine-4-carboxylic acidGenerator
1,4,5,6-tetrahydro-2-Methyl-4-pyrimidinecarboxylic acidMeSH, HMDB
EctoinMeSH, HMDB
(4S)-2-Methyl-3,4,5,6-tetrahydropyrimidine-4-carboxylic acidHMDB
(4S)-3,4,5,6-Tetrahydro-2-methyl-4-pyrimidinecarboxylic acidHMDB
(S)-2-methyl-1,4,5,6-tetrahydropyrimidine-4-carboxylic acidHMDB
EctoineHMDB
Pyrostatin BHMDB
Pyrostatine BHMDB
Molecular FormulaC6H10N2O2
Average Mass142.1558
Monoisotopic Mass142.074227574
IUPAC Name(4S)-2-methyl-1,4,5,6-tetrahydropyrimidine-4-carboxylic acid
Traditional Nameectoine
CAS Registry NumberNot Available
SMILES
CC1=NCC[C@H](N1)C(O)=O
InChI Identifier
InChI=1S/C6H10N2O2/c1-4-7-3-2-5(8-4)6(9)10/h5H,2-3H2,1H3,(H,7,8)(H,9,10)/t5-/m0/s1
InChI KeyWQXNXVUDBPYKBA-YFKPBYRVSA-N