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Showing metabocard for Glabrin A (HMDB0301777)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2021-09-22 21:01:04 UTC
Update Date2021-09-22 21:01:04 UTC
HMDB IDHMDB0301777
Secondary Accession NumbersNone
Metabolite Identification
Common NameGlabrin A
Description4,5-dihydroxy-1-methylpiperidine-2-carboxylic acid 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). Based on a literature review a significant number of articles have been published on 4,5-dihydroxy-1-methylpiperidine-2-carboxylic acid.
Structure
Thumb
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0301777 (Glabrin A)

  Mrv1533004161519322D          

 12 12  0  0  0  0            999 V2000
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 O   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
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    2.0625    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
  4  6  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  2  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 10 12  1  0  0  0  0
M  END
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3D MOL for HMDB0301777 (Glabrin A)

HMDB0301777
     RDKit          3D
Glabrin A
 25 25  0  0  0  0  0  0  0  0999 V2000
    0.8144   -1.9560    0.1099 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5297   -0.7003    0.7492 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8182   -0.6073    1.2401 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5704    0.5782    0.7635 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9452    0.2483    0.7943 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2604    1.0405   -0.6093 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3890    2.4484   -0.6208 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0886    0.6946   -1.1264 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9924    0.4398    0.0522 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4080    0.2490   -0.3325 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0322    1.1379   -0.9667 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0591   -0.9031   -0.0012 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1461   -1.8603   -0.9411 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1351   -2.5501    0.1130 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5343   -2.5071    0.7486 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7598   -0.5668    2.3542 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3893   -1.5487    1.0160 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4647    1.4059    1.5206 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1263   -0.1918   -0.0770 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0105    0.6866   -1.3742 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8273    2.7746   -1.4343 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0694   -0.1697   -1.8251 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5052    1.5431   -1.7068 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8783    1.3306    0.7290 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6385   -1.0163    0.8247 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  4  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  2  0
 10 12  1  0
  9  2  1  0
  1 13  1  0
  1 14  1  0
  1 15  1  0
  3 16  1  0
  3 17  1  0
  4 18  1  0
  5 19  1  0
  6 20  1  0
  7 21  1  0
  8 22  1  0
  8 23  1  0
  9 24  1  0
 12 25  1  0
M  END
Download

3D SDF for HMDB0301777 (Glabrin A)

  Mrv1533004161519322D          

 12 12  0  0  0  0            999 V2000
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 O   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
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    2.0625    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
  4  6  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  2  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 10 12  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0301777

> <DATABASE_NAME>
hmdb

> <SMILES>
CN1CC(O)C(O)CC1C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C7H13NO4/c1-8-3-6(10)5(9)2-4(8)7(11)12/h4-6,9-10H,2-3H2,1H3,(H,11,12)

> <INCHI_KEY>
VORPREYJNTUAGI-UHFFFAOYSA-N

> <FORMULA>
C7H13NO4

> <MOLECULAR_WEIGHT>
175.184

> <EXACT_MASS>
175.084457903

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
25

> <JCHEM_AVERAGE_POLARIZABILITY>
17.126731450851494

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
4,5-dihydroxy-1-methylpiperidine-2-carboxylic acid

> <ALOGPS_LOGP>
-2.10

> <JCHEM_LOGP>
-4.220250786432417

> <ALOGPS_LOGS>
0.75

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.659948208705725

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.4015863216231796

> <JCHEM_PKA_STRONGEST_BASIC>
8.974717971095396

> <JCHEM_POLAR_SURFACE_AREA>
81.0

> <JCHEM_REFRACTIVITY>
40.6394

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
9.81e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
4,5-dihydroxy-1-methylpiperidine-2-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0301777 (Glabrin A)

HMDB0301777
     RDKit          3D
Glabrin A
 25 25  0  0  0  0  0  0  0  0999 V2000
    0.8144   -1.9560    0.1099 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5297   -0.7003    0.7492 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8182   -0.6073    1.2401 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5704    0.5782    0.7635 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9452    0.2483    0.7943 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2604    1.0405   -0.6093 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3890    2.4484   -0.6208 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0886    0.6946   -1.1264 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9924    0.4398    0.0522 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4080    0.2490   -0.3325 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0322    1.1379   -0.9667 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0591   -0.9031   -0.0012 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1461   -1.8603   -0.9411 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1351   -2.5501    0.1130 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5343   -2.5071    0.7486 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7598   -0.5668    2.3542 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3893   -1.5487    1.0160 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4647    1.4059    1.5206 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1263   -0.1918   -0.0770 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0105    0.6866   -1.3742 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8273    2.7746   -1.4343 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0694   -0.1697   -1.8251 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5052    1.5431   -1.7068 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8783    1.3306    0.7290 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6385   -1.0163    0.8247 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  4  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  2  0
 10 12  1  0
  9  2  1  0
  1 13  1  0
  1 14  1  0
  1 15  1  0
  3 16  1  0
  3 17  1  0
  4 18  1  0
  5 19  1  0
  6 20  1  0
  7 21  1  0
  8 22  1  0
  8 23  1  0
  9 24  1  0
 12 25  1  0
M  END
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PDB for HMDB0301777 (Glabrin A)

HEADER    PROTEIN                                 16-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   16-APR-15         0                                  
HETATM    1  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0       1.334   2.310   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       4.001  -0.770   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -1.334   2.310   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -2.667   1.540   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      -1.334   3.850   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    9                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9                                                       
CONECT    9    8    2   10                                                  
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   24    0
END
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3D PDB for HMDB0301777 (Glabrin A)

COMPND    HMDB0301777
HETATM    1  C1  UNL     1       0.814  -1.956   0.110  1.00  0.00           C  
HETATM    2  N1  UNL     1       0.530  -0.700   0.749  1.00  0.00           N  
HETATM    3  C2  UNL     1      -0.818  -0.607   1.240  1.00  0.00           C  
HETATM    4  C3  UNL     1      -1.570   0.578   0.764  1.00  0.00           C  
HETATM    5  O1  UNL     1      -2.945   0.248   0.794  1.00  0.00           O  
HETATM    6  C4  UNL     1      -1.260   1.040  -0.609  1.00  0.00           C  
HETATM    7  O2  UNL     1      -1.389   2.448  -0.621  1.00  0.00           O  
HETATM    8  C5  UNL     1       0.089   0.695  -1.126  1.00  0.00           C  
HETATM    9  C6  UNL     1       0.992   0.440   0.052  1.00  0.00           C  
HETATM   10  C7  UNL     1       2.408   0.249  -0.332  1.00  0.00           C  
HETATM   11  O3  UNL     1       3.032   1.138  -0.967  1.00  0.00           O  
HETATM   12  O4  UNL     1       3.059  -0.903  -0.001  1.00  0.00           O  
HETATM   13  H1  UNL     1       1.146  -1.860  -0.941  1.00  0.00           H  
HETATM   14  H2  UNL     1      -0.135  -2.550   0.113  1.00  0.00           H  
HETATM   15  H3  UNL     1       1.534  -2.507   0.749  1.00  0.00           H  
HETATM   16  H4  UNL     1      -0.760  -0.567   2.354  1.00  0.00           H  
HETATM   17  H5  UNL     1      -1.389  -1.549   1.016  1.00  0.00           H  
HETATM   18  H6  UNL     1      -1.465   1.406   1.521  1.00  0.00           H  
HETATM   19  H7  UNL     1      -3.126  -0.192  -0.077  1.00  0.00           H  
HETATM   20  H8  UNL     1      -2.010   0.687  -1.374  1.00  0.00           H  
HETATM   21  H9  UNL     1      -1.827   2.775  -1.434  1.00  0.00           H  
HETATM   22  H10 UNL     1       0.069  -0.170  -1.825  1.00  0.00           H  
HETATM   23  H11 UNL     1       0.505   1.543  -1.707  1.00  0.00           H  
HETATM   24  H12 UNL     1       0.878   1.331   0.729  1.00  0.00           H  
HETATM   25  H13 UNL     1       3.639  -1.016   0.825  1.00  0.00           H  
CONECT    1    2   13   14   15
CONECT    2    3    9
CONECT    3    4   16   17
CONECT    4    5    6   18
CONECT    5   19
CONECT    6    7    8   20
CONECT    7   21
CONECT    8    9   22   23
CONECT    9   10   24
CONECT   10   11   11   12
CONECT   12   25
END
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SMILES for HMDB0301777 (Glabrin A)

CN1CC(O)C(O)CC1C(O)=O
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INCHI for HMDB0301777 (Glabrin A)

InChI=1S/C7H13NO4/c1-8-3-6(10)5(9)2-4(8)7(11)12/h4-6,9-10H,2-3H2,1H3,(H,11,12)
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View in JSmolView Stereo Labels
Synonyms
ValueSource
4,5-Dihydroxy-1-methylpiperidine-2-carboxylateGenerator
GlabrinMeSH
Chemical FormulaC7H13NO4
Average Molecular Weight175.184
Monoisotopic Molecular Weight175.084457903
IUPAC Name4,5-dihydroxy-1-methylpiperidine-2-carboxylic acid
Traditional Name4,5-dihydroxy-1-methylpiperidine-2-carboxylic acid
CAS Registry Number162157-00-8
SMILES
CN1CC(O)C(O)CC1C(O)=O
InChI Identifier
InChI=1S/C7H13NO4/c1-8-3-6(10)5(9)2-4(8)7(11)12/h4-6,9-10H,2-3H2,1H3,(H,11,12)
InChI KeyVORPREYJNTUAGI-UHFFFAOYSA-N
Chemical Taxonomy
Description 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).
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct ParentAlpha amino acids
Alternative Parents
Substituents
  • Alpha-amino acid
  • Piperidinecarboxylic acid
  • Piperidine
  • 1,2-aminoalcohol
  • 1,2-diol
  • Amino acid
  • Tertiary aliphatic amine
  • Tertiary amine
  • Secondary alcohol
  • Carboxylic acid
  • Monocarboxylic acid or derivatives
  • Azacycle
  • Organoheterocyclic compound
  • Organic nitrogen compound
  • Organooxygen compound
  • Organonitrogen compound
  • Hydrocarbon derivative
  • Organic oxide
  • Carbonyl group
  • Amine
  • Organopnictogen compound
  • Alcohol
  • Organic oxygen compound
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Source
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB001286
KNApSAcK IDNot Available
Chemspider ID142147
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound161850
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available