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Showing metabocard for N6,N6-dimethyllysine (HMDB0341183)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2022-09-09 19:33:29 UTC
Update Date2022-09-22 18:35:05 UTC
HMDB IDHMDB0341183
Secondary Accession NumbersNone
Metabolite Identification
Common NameN6,N6-dimethyllysine
DescriptionN-Dimethyl-Lysine, also known as lys(me2) or N,N-dimethyl lysine, belongs to the class of organic compounds known as l-alpha-amino acids. These are alpha amino acids which have the L-configuration of the alpha-carbon atom. An L-lysine derivative comprising L-lysine having two methyl substituents attached to the side-chain amino group. N-Dimethyl-Lysine is a very strong basic compound (based on its pKa).
Structure
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MOLSDFPDBSMILESInChI

MOL for HMDB0341183 (N6,N6-dimethyllysine)


  Mrv0541 05041407442D          

 13 12  0  0  1  0            999 V2000
   -0.7145    0.4125    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
    2.1434    0.4125    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
    2.8579    0.0000    0.0000 C   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
    3.5724    0.4125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.2868    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    1.2375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -0.4125    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  4  3  1  0  0  0  0
  5  3  1  0  0  0  0
  6  4  1  0  0  0  0
  7  5  1  0  0  0  0
  8  7  1  0  0  0  0
  7  9  1  1  0  0  0
 10  1  1  0  0  0  0
 10  2  1  0  0  0  0
 10  6  1  0  0  0  0
 11  8  2  0  0  0  0
 12  8  1  0  0  0  0
  7 13  1  1  0  0  0
M  END
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3D MOL for HMDB0341183 (N6,N6-dimethyllysine)

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3D SDF for HMDB0341183 (N6,N6-dimethyllysine)

  Mrv0541 05041407442D          

 13 12  0  0  1  0            999 V2000
   -0.7145    0.4125    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
    2.1434    0.4125    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
    2.8579    0.0000    0.0000 C   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
    3.5724    0.4125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.2868    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    1.2375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -0.4125    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  4  3  1  0  0  0  0
  5  3  1  0  0  0  0
  6  4  1  0  0  0  0
  7  5  1  0  0  0  0
  8  7  1  0  0  0  0
  7  9  1  1  0  0  0
 10  1  1  0  0  0  0
 10  2  1  0  0  0  0
 10  6  1  0  0  0  0
 11  8  2  0  0  0  0
 12  8  1  0  0  0  0
  7 13  1  1  0  0  0
M  END
> <DATABASE_ID>
HMDB0341183

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C8H18N2O2/c1-10(2)6-4-3-5-7(9)8(11)12/h7H,3-6,9H2,1-2H3,(H,11,12)/t7-/m0/s1

> <INCHI_KEY>
XXEWFEBMSGLYBY-ZETCQYMHSA-N

> <FORMULA>
C8H18N2O2

> <MOLECULAR_WEIGHT>
174.2407

> <EXACT_MASS>
174.13682783

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
19.874208124052785

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-2-amino-6-(dimethylamino)hexanoic acid

> <ALOGPS_LOGP>
-1.60

> <JCHEM_LOGP>
-2.712961011238819

> <ALOGPS_LOGS>
-0.01

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.842087440876693

> <JCHEM_PKA_STRONGEST_BASIC>
9.979156400775684

> <JCHEM_POLAR_SURFACE_AREA>
66.56

> <JCHEM_REFRACTIVITY>
47.8788

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.70e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
lys(me2)

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for HMDB0341183 (N6,N6-dimethyllysine)
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PDB for HMDB0341183 (N6,N6-dimethyllysine)
HEADER    PROTEIN                                 04-MAY-14   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-MAY-14         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.000   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  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   10  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   11  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   13  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
CONECT    1   10                                                            
CONECT    2   10                                                            
CONECT    3    4    5                                                       
CONECT    4    3    6                                                       
CONECT    5    3    7                                                       
CONECT    6    4   10                                                       
CONECT    7    5    8    9   13                                             
CONECT    8    7   11   12                                                  
CONECT    9    7                                                            
CONECT   10    1    2    6                                                  
CONECT   11    8                                                            
CONECT   12    8                                                            
CONECT   13    7                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   24    0
END

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3D PDB for HMDB0341183 (N6,N6-dimethyllysine)
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SMILES for HMDB0341183 (N6,N6-dimethyllysine)
[H][C@](N)(CCCCN(C)C)C(O)=O
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INCHI for HMDB0341183 (N6,N6-dimethyllysine)
InChI=1S/C8H18N2O2/c1-10(2)6-4-3-5-7(9)8(11)12/h7H,3-6,9H2,1-2H3,(H,11,12)/t7-/m0/s1
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View in JSmolView Stereo Labels
Synonyms
ValueSource
(S)-2-Amino-6-dimethylaminohexanoic acidChEBI
Epsilon N-DimethyllysineChEBI
Lys(me2)ChEBI
N(6),N(6)-DimethyllysineChEBI
N(epsilon),N(epsilon)-Dimethyl-L-lysineChEBI
N(epsilon),N(epsilon)-DimethyllysineChEBI
N(epsilon)-Dimethyl-L-lysineChEBI
N(epsilon)-DimethyllysineChEBI
(S)-2-Amino-6-dimethylaminohexanoateGenerator
N,N-Dimethyl lysineMeSH
Chemical FormulaC8H18N2O2
Average Molecular Weight174.2407
Monoisotopic Molecular Weight174.13682783
IUPAC Name(2S)-2-amino-6-(dimethylamino)hexanoic acid
Traditional Namelys(me2)
CAS Registry NumberNot Available
SMILES
[H][C@](N)(CCCCN(C)C)C(O)=O
InChI Identifier
InChI=1S/C8H18N2O2/c1-10(2)6-4-3-5-7(9)8(11)12/h7H,3-6,9H2,1-2H3,(H,11,12)/t7-/m0/s1
InChI KeyXXEWFEBMSGLYBY-ZETCQYMHSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as l-alpha-amino acids. These are alpha amino acids which have the L-configuration of the alpha-carbon atom.
KingdomOrganic compounds  
Super ClassOrganic acids and derivatives  
ClassCarboxylic acids and derivatives  
Sub ClassAmino acids, peptides, and analogues  
Direct ParentL-alpha-amino acids  
Alternative Parents
Substituents
  • L-alpha-amino acid
    • 

  • Medium-chain fatty acid
    • 

  • Amino fatty acid
    • 

  • Fatty acyl
    • 

  • Fatty acid
    • 

  • Tertiary amine
    • 

  • Amino acid
    • 

  • Tertiary aliphatic amine
    • 

  • Carboxylic acid
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Amine
    • 

  • Hydrocarbon derivative
    • 

  • Organic oxide
    • 

  • Primary amine
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Organopnictogen compound
    • 

  • Primary aliphatic amine
    • 

  • Organic oxygen compound
    • 

  • Carbonyl group
    • 

  • Organic nitrogen compound
    • 

  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Not AvailableNot 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
PropertyValueSource
logP-1.6ALOGPS
logP-2.7ChemAxon
logS-0.01ALOGPS
pKa (Strongest Acidic)2.84ChemAxon
pKa (Strongest Basic)9.98ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area66.56 ŲChemAxon
Rotatable Bond Count6ChemAxon
Refractivity47.88 m³·mol⁻¹ChemAxon
Polarizability19.87 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties
Predicted Retention Times 
Not Available
Predicted Kovats Retention Indices
Not Available
Spectra
GC-MS Spectra
Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - N6,N6-dimethyllysine GC-MS (Non-derivatized) - 70eV, Positivesplash10-0abc-9100000000-41255d563e866d5cb7f32017-08-28Wishart LabView Spectrum
MS/MS Spectra
Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - N6,N6-dimethyllysine  10V, Positive-QTOFsplash10-004i-0900000000-4d854a4fabf1dbec18f22017-07-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - N6,N6-dimethyllysine  20V, Positive-QTOFsplash10-004i-2900000000-2596dea2eca09a88b0562017-07-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - N6,N6-dimethyllysine  40V, Positive-QTOFsplash10-0kgx-9200000000-87b5a48f3441c87f64e22017-07-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - N6,N6-dimethyllysine  10V, Negative-QTOFsplash10-00di-0900000000-84ed2802653995b73aa92017-07-26Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - N6,N6-dimethyllysine  20V, Negative-QTOFsplash10-00di-1900000000-6306fa46894775e1c4da2017-07-26Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - N6,N6-dimethyllysine  40V, Negative-QTOFsplash10-00e9-9300000000-cf6df2a9a0fe013ba32d2017-07-26Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
    • 

  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal  details
UrineDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal  details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDDB03362  
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound193344  
PDB IDNot Available
ChEBI ID43997  
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 References
  1. Neto FC, Raftery D: Expanding Urinary Metabolite Annotation through Integrated Mass Spectral Similarity Networking. Anal Chem. 2021 Sep 7;93(35):12001-12010. doi: 10.1021/acs.analchem.1c02041. Epub 2021 Aug 26. [PubMed:34436864  ]