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Showing NP-Card for L-2,4-Diaminobutanoic acid (NP0334613)

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Record Information
Version2.0
Created at2024-09-10 19:08:45 UTC
Updated at2024-09-10 19:08:45 UTC
NP-MRD IDNP0334613
Secondary Accession NumbersNone
Natural Product Identification
Common NameL-2,4-Diaminobutanoic acid
DescriptionL-2,4-diaminobutyric acid, also known as Dbu or alpha,gamma-diaminobutyrate, 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. L-2,4-diaminobutyric acid is a very strong basic compound (based on its pKa). Outside of the human body, L-2,4-diaminobutyric acid has been detected, but not quantified in, several different foods, such as peachs, mountain yams, corianders, muscadine grapes, and mango. This could make L-2,4-diaminobutyric acid a potential biomarker for the consumption of these foods. L-2,4-Diaminobutanoic acid was first documented in 1966 (PMID: 5972321). A 2,4-diaminobutyric acid that has S-configuration (PMID: 23990652).
Structure
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MOLSDFPDBSMILESInChI

MOL for NP0334613 (L-2,4-Diaminobutanoic acid)


  Mrv0541 02231217122D          

  8  7  0  0  1  0            999 V2000
   -0.1914    0.7145    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    1.1270    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
    1.9520    1.1270    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9520    1.9520    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809    1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664   -0.1105    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  6  0  0  0
  4  6  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  2  0  0  0  0
M  END
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3D MOL for NP0334613 (L-2,4-Diaminobutanoic acid)

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3D SDF for NP0334613 (L-2,4-Diaminobutanoic acid)

  Mrv0541 02231217122D          

  8  7  0  0  1  0            999 V2000
   -0.1914    0.7145    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    1.1270    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
    1.9520    1.1270    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9520    1.9520    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809    1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664   -0.1105    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  6  0  0  0
  4  6  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0334613

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C4H10N2O2/c5-2-1-3(6)4(7)8/h3H,1-2,5-6H2,(H,7,8)/t3-/m0/s1

> <INCHI_KEY>
OGNSCSPNOLGXSM-VKHMYHEASA-N

> <FORMULA>
C4H10N2O2

> <MOLECULAR_WEIGHT>
118.1344

> <EXACT_MASS>
118.074227574

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
11.890036673420415

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-2,4-diaminobutanoic acid

> <ALOGPS_LOGP>
-3.66

> <JCHEM_LOGP>
-4.025544175769902

> <ALOGPS_LOGS>
0.36

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.5466043382409564

> <JCHEM_PKA_STRONGEST_BASIC>
10.25230176518907

> <JCHEM_POLAR_SURFACE_AREA>
89.34

> <JCHEM_REFRACTIVITY>
28.563900000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.70e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2,4-diaminobutyric acid

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for NP0334613 (L-2,4-Diaminobutanoic acid)
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PDB for NP0334613 (L-2,4-Diaminobutanoic acid)
HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  N   UNK     0      -0.357   1.334   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       0.976   2.104   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       3.644   2.104   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0       3.644   3.644   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0       4.977   1.334   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       6.311   2.104   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       4.977  -0.206   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6                                                            
MASTER        0    0    0    0    0    0    0    0    8    0   14    0
END

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3D PDB for NP0334613 (L-2,4-Diaminobutanoic acid)
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SMILES for NP0334613 (L-2,4-Diaminobutanoic acid)
NCC[C@H](N)C(O)=O
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INCHI for NP0334613 (L-2,4-Diaminobutanoic acid)
InChI=1S/C4H10N2O2/c5-2-1-3(6)4(7)8/h3H,1-2,5-6H2,(H,7,8)/t3-/m0/s1
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Synonyms
ValueSource
(S)-2,4-Diaminobutanoic acidChEBI
alpha,gamma-DiaminobutyrateChEBI
DbuChEBI
L-2,4-DiaminobutanoateChEBI
L-2,4-Diaminobutanoic acidChEBI
L-2,4-DiaminobutyrateChEBI
L-DbuChEBI
L-Diaminobutyric acidChEBI
(S)-2,4-DiaminobutanoateGenerator
a,g-DiaminobutyrateGenerator
a,g-Diaminobutyric acidGenerator
alpha,gamma-Diaminobutyric acidGenerator
Α,γ-diaminobutyrateGenerator
Α,γ-diaminobutyric acidGenerator
L-DiaminobutyrateGenerator
(S)-2,4-Diamino-butanoateHMDB
(S)-2,4-Diamino-butanoic acidHMDB
(S)-2,4-Diaminobutyric acidHMDB
L-2,4-Diamino-butyric acidHMDB
L-2,4-Diamino-N-butyric acidHMDB
L-alpha,gamma-Diaminobutyric acidHMDB
L-DABAHMDB
2,4-Diaminobutyric acid dihydrochloride, (+-)-isomerHMDB
2,4-Diaminobutyric acid monohydrochloride, (+-)-isomerHMDB
2,4-Diaminobutyric acid, (+)-isomerHMDB
2,4-Diaminobutyric acid, (+-)-isomerHMDB
2,4-Diaminobutyric acid, (R)-isomerHMDB
2,4-Diaminobutyric acid, (S)-isomerHMDB
2,4-Diaminobutyric acid dihydrochloride, (S)-isomerHMDB
2,4-Diaminobutyric acidHMDB
2,4-Diaminobutyric acid monohydrochloride, (S)-isomerHMDB
Chemical FormulaC4H10N2O2
Average Mass118.1344 Da
Monoisotopic Mass118.07423 Da
IUPAC Name(2S)-2,4-diaminobutanoic acid
Traditional Name2,4-diaminobutyric acid
CAS Registry NumberNot Available
SMILES
NCC[C@H](N)C(O)=O
InChI Identifier
InChI=1S/C4H10N2O2/c5-2-1-3(6)4(7)8/h3H,1-2,5-6H2,(H,7,8)/t3-/m0/s1
InChI KeyOGNSCSPNOLGXSM-VKHMYHEASA-N
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of OriginNot Available
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
    • 

  • Amino fatty acid
    • 

  • Fatty acid
    • 

  • Fatty acyl
    • 

  • Amino acid
    • 

  • 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
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP-3.7ALOGPS
logP-4ChemAxon
logS0.36ALOGPS
pKa (Strongest Acidic)2.55ChemAxon
pKa (Strongest Basic)10.25ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area89.34 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity28.56 m³·mol⁻¹ChemAxon
Polarizability11.89 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0006284  
DrugBank IDDB03817  
Phenol Explorer Compound IDNot Available
FoodDB IDFDB030953  
KNApSAcK IDC00001353  
Chemspider ID118548  
KEGG Compound IDC03283  
BioCyc IDCPD-470  
BiGG ID41559  
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound134490  
PDB IDDAB  
ChEBI ID48950  
Good Scents IDNot Available
References
General References
  1. Jin L, Lee HG, Kim HS, Ahn CY, Oh HM: Amnibacterium soli sp. nov., an actinobacterium isolated from grass soil. Int J Syst Evol Microbiol. 2013 Dec;63(Pt 12):4750-4753. doi:  10.1099/ijs.0.052506-0. Epub 2013 Aug 29. [PubMed:23990652  ] 
  2. Nigam SN, Ressler C: Biosynthesis of 2,4-diaminobutyric acid from L-[3H]homoserine and DL-[1-14C]aspartic acid in Lathyrus sylvestris W. Biochemistry. 1966 Nov;5(11):3426-31. doi: 10.1021/bi00875a006. [PubMed:5972321  ]