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Showing NP-Card for 2,4-Diaminobutyric acid (NP0000809)

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Record Information
Version2.0
Created at2006-05-22 14:17:50 UTC
Updated at2021-10-07 20:40:48 UTC
NP-MRD IDNP0000809
Secondary Accession NumbersNone
Natural Product Identification
Common Name2,4-Diaminobutyric acid
Description2,4-Diaminobutyric acid, also known as 2,4-diaminobutanoate or Dbu, 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). 2,4-Diaminobutyric acid is a very hydrophobic molecule, practically insoluble in water, and relatively neutral. 2,4-Diaminobutyric acid exists in all living organisms, ranging from bacteria to humans. Outside of the human body, 2,4-Diaminobutyric acid has been detected, but not quantified in cow milk. This could make 2,4-diaminobutyric acid a potential biomarker for the consumption of these foods. 2,4-Diaminobutyric acid is a non-physiological, cationic amino acid analogue that is transported into cells by System A with potent antitumoral activity in vitro against human glioma cells, the result of the pronounced concentrated uptake of DAB in glioma cells to the extent that a cellular lysis could occur due to osmotic reasons.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0000809 (2,4-Diaminobutyric acid)


  Mrv1652305261923562D          

  8  7  0  0  0  0            999 V2000
    1.2375    0.7145    0.0000 C   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
    1.9520    1.1270    0.0000 C   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
   -0.1914    0.7145    0.0000 N   0  0  0  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
    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
  2  1  1  0  0  0  0
  3  1  1  0  0  0  0
  4  3  1  0  0  0  0
  5  2  1  0  0  0  0
  6  3  1  0  0  0  0
  7  4  2  0  0  0  0
  8  4  1  0  0  0  0
M  END
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3D MOL for NP0000809 (2,4-Diaminobutyric acid)

HMDB0002362
     RDKit          3D
2,4-Diaminobutyric acid
 18 17  0  0  0  0  0  0  0  0999 V2000
    2.7649    0.4925    0.0357 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.5576    0.1694   -0.6875 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4070    0.2656    0.2824 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9197   -0.0626   -0.4022 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8331   -1.4136   -0.9152 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9591   -0.0122    0.6373 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5863   -1.0591    0.9235 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2992    1.1349    1.3355 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0409   -0.3003    0.6577 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7318    1.4063    0.5079 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6568   -0.8577   -1.0891 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4071    0.8567   -1.5308 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5953   -0.4604    1.0937 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3932    1.2709    0.7340 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1014    0.6449   -1.2352 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0993   -1.9747   -0.4370 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7479   -1.8794   -0.9922 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0087    1.7787    1.0814 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  2  0
  6  8  1  0
  1  9  1  0
  1 10  1  0
  2 11  1  0
  2 12  1  0
  3 13  1  0
  3 14  1  0
  4 15  1  0
  5 16  1  0
  5 17  1  0
  8 18  1  0
M  END
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3D SDF for NP0000809 (2,4-Diaminobutyric acid)


  Mrv1652305261923562D          

  8  7  0  0  0  0            999 V2000
    1.2375    0.7145    0.0000 C   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
    1.9520    1.1270    0.0000 C   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
   -0.1914    0.7145    0.0000 N   0  0  0  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
    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
  2  1  1  0  0  0  0
  3  1  1  0  0  0  0
  4  3  1  0  0  0  0
  5  2  1  0  0  0  0
  6  3  1  0  0  0  0
  7  4  2  0  0  0  0
  8  4  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0000809

> <DATABASE_NAME>
NP-MRD

> <SMILES>
NCCC(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)

> <INCHI_KEY>
OGNSCSPNOLGXSM-UHFFFAOYSA-N

> <FORMULA>
C4H10N2O2

> <MOLECULAR_WEIGHT>
118.1344

> <EXACT_MASS>
118.074227574

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
18

> <JCHEM_AVERAGE_POLARIZABILITY>
11.790777046983148

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2,4-diaminobutanoic acid

> <ALOGPS_LOGP>
-3.66

> <JCHEM_LOGP>
-4.0127487706017835

> <ALOGPS_LOGS>
0.36

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.546541066724605

> <JCHEM_PKA_STRONGEST_BASIC>
9.952302620531269

> <JCHEM_POLAR_SURFACE_AREA>
89.33999999999999

> <JCHEM_REFRACTIVITY>
28.5639

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.70e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2,4-diaminobutanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0000809 (2,4-Diaminobutyric acid)

HMDB0002362
     RDKit          3D
2,4-Diaminobutyric acid
 18 17  0  0  0  0  0  0  0  0999 V2000
    2.7649    0.4925    0.0357 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.5576    0.1694   -0.6875 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4070    0.2656    0.2824 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9197   -0.0626   -0.4022 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8331   -1.4136   -0.9152 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9591   -0.0122    0.6373 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5863   -1.0591    0.9235 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2992    1.1349    1.3355 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0409   -0.3003    0.6577 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7318    1.4063    0.5079 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6568   -0.8577   -1.0891 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4071    0.8567   -1.5308 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5953   -0.4604    1.0937 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3932    1.2709    0.7340 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1014    0.6449   -1.2352 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0993   -1.9747   -0.4370 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7479   -1.8794   -0.9922 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0087    1.7787    1.0814 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  2  0
  6  8  1  0
  1  9  1  0
  1 10  1  0
  2 11  1  0
  2 12  1  0
  3 13  1  0
  3 14  1  0
  4 15  1  0
  5 16  1  0
  5 17  1  0
  8 18  1  0
M  END
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PDB for NP0000809 (2,4-Diaminobutyric acid)

HEADER    PROTEIN                                 26-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   26-MAY-19         0                                  
HETATM    1  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.976   2.104   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       3.644   2.104   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.977   1.334   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0      -0.357   1.334   0.000  0.00  0.00           N+0
HETATM    6  N   UNK     0       3.644   3.644   0.000  0.00  0.00           N+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    3                                                       
CONECT    2    1    5                                                       
CONECT    3    1    4    6                                                  
CONECT    4    3    7    8                                                  
CONECT    5    2                                                            
CONECT    6    3                                                            
CONECT    7    4                                                            
CONECT    8    4                                                            
MASTER        0    0    0    0    0    0    0    0    8    0   14    0
END
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3D PDB for NP0000809 (2,4-Diaminobutyric acid)

COMPND    HMDB0002362
HETATM    1  N1  UNL     1       2.765   0.492   0.036  1.00  0.00           N  
HETATM    2  C1  UNL     1       1.558   0.169  -0.687  1.00  0.00           C  
HETATM    3  C2  UNL     1       0.407   0.266   0.282  1.00  0.00           C  
HETATM    4  C3  UNL     1      -0.920  -0.063  -0.402  1.00  0.00           C  
HETATM    5  N2  UNL     1      -0.833  -1.414  -0.915  1.00  0.00           N  
HETATM    6  C4  UNL     1      -1.959  -0.012   0.637  1.00  0.00           C  
HETATM    7  O1  UNL     1      -2.586  -1.059   0.924  1.00  0.00           O  
HETATM    8  O2  UNL     1      -2.299   1.135   1.335  1.00  0.00           O  
HETATM    9  H1  UNL     1       3.041  -0.300   0.658  1.00  0.00           H  
HETATM   10  H2  UNL     1       2.732   1.406   0.508  1.00  0.00           H  
HETATM   11  H3  UNL     1       1.657  -0.858  -1.089  1.00  0.00           H  
HETATM   12  H4  UNL     1       1.407   0.857  -1.531  1.00  0.00           H  
HETATM   13  H5  UNL     1       0.595  -0.460   1.094  1.00  0.00           H  
HETATM   14  H6  UNL     1       0.393   1.271   0.734  1.00  0.00           H  
HETATM   15  H7  UNL     1      -1.101   0.645  -1.235  1.00  0.00           H  
HETATM   16  H8  UNL     1      -0.099  -1.975  -0.437  1.00  0.00           H  
HETATM   17  H9  UNL     1      -1.748  -1.879  -0.992  1.00  0.00           H  
HETATM   18  H10 UNL     1      -3.009   1.779   1.081  1.00  0.00           H  
CONECT    1    2    9   10
CONECT    2    3   11   12
CONECT    3    4   13   14
CONECT    4    5    6   15
CONECT    5   16   17
CONECT    6    7    7    8
CONECT    8   18
END
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SMILES for NP0000809 (2,4-Diaminobutyric acid)

NCCC(N)C(O)=O
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INCHI for NP0000809 (2,4-Diaminobutyric acid)

InChI=1S/C4H10N2O2/c5-2-1-3(6)4(7)8/h3H,1-2,5-6H2,(H,7,8)
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View in JSmol
Synonyms
ValueSource
2,4-Diaminobutanoic acidChEBI
alpha,gamma-Diaminobutanoic acidChEBI
alpha,gamma-Diaminobutyric acidChEBI
DbuChEBI
2,4-DiaminobutanoateGenerator
a,g-DiaminobutanoateGenerator
a,g-Diaminobutanoic acidGenerator
alpha,gamma-DiaminobutanoateGenerator
Α,γ-diaminobutanoateGenerator
Α,γ-diaminobutanoic acidGenerator
a,g-DiaminobutyrateGenerator
a,g-Diaminobutyric acidGenerator
alpha,gamma-DiaminobutyrateGenerator
Α,γ-diaminobutyrateGenerator
Α,γ-diaminobutyric acidGenerator
2,4-DiaminobutyrateGenerator
(RS)-2,4-Diaminobutyric acidHMDB
2,4-Diamino-butanoateHMDB
2,4-Diamino-butanoic acidHMDB
2,4-Diamino-butyric acidHMDB
2,4-Diamino-N-butyric acidHMDB
DL-2,4-Diamino-N-butyric acidHMDB
DL-2,4-DiaminobutanoateHMDB
DL-2,4-Diaminobutanoic acidHMDB
DL-2,4-Diaminobutyric acidHMDB
DL-alpha,gamma-Diaminobutyric acidHMDB
2,4-Diaminobutyric acid dihydrochloride, (+-)-isomerHMDB
2,4-Diaminobutyric acid monohydrochloride, (S)-isomerHMDB
2,4-Diaminobutyric acid, (+)-isomerHMDB
2,4-Diaminobutyric acid, (+-)-isomerHMDB
2,4-Diaminobutyric acid, (R)-isomerHMDB
2,4-Diaminobutyric acid, (S)-isomerHMDB
L-2,4-Diaminobutyric acidHMDB
2,4-Diaminobutyric acid dihydrochloride, (S)-isomerHMDB
2,4-Diaminobutyric acid monohydrochloride, (+-)-isomerHMDB
2,4-Diamino-butyrateHMDB
2,4-Diaminobutyric acidMeSH
Chemical FormulaC4H10N2O2
Average Mass118.1344 Da
Monoisotopic Mass118.07423 Da
IUPAC Name2,4-diaminobutanoic acid
Traditional Name2,4-diaminobutanoic acid
CAS Registry Number305-62-4
SMILES
NCCC(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)
InChI KeyOGNSCSPNOLGXSM-UHFFFAOYSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Not Available
Chemical Shift Submissions
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, simulated)v.dorna83@yahoo.comNot AvailableNot Available2021-08-08View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, simulated)varshavi.d26@gmail.comNot AvailableNot Available2021-08-08View Spectrum
Species
Species of Origin
Species NameSourceReference
Bos taurusMilk
Lathrism latifolius-
Lathrism sylvestris-
Lathyrus latifoliusLOTUS Database
Streptomyces coelicolorLOTUS Database
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
  • Amino fatty acid
  • Fatty acid
  • Fatty acyl
  • Amino acid
  • Carboxylic acid
  • Monocarboxylic acid or derivatives
  • Organic nitrogen compound
  • Hydrocarbon derivative
  • Primary amine
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxide
  • Primary aliphatic amine
  • Organopnictogen compound
  • Carbonyl group
  • Organic oxygen compound
  • Amine
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogP-4.64Hansch CH, Leo A and Hoekman DH. "Exploring QSAR: Hydrophobic, Electronic, and Steric Constraints. Volume 1" ACS Publications (1995).
Predicted Properties
PropertyValueSource
Water Solubility270 g/LALOGPS
logP-3.7ALOGPS
logP-4ChemAxon
logS0.36ALOGPS
pKa (Strongest Acidic)2.55ChemAxon
pKa (Strongest Basic)9.95ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area89.34 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity28.56 m³·mol⁻¹ChemAxon
Polarizability11.79 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0002362
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB022978
KNApSAcK IDC00034868
Chemspider ID457
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound470
PDB IDNot Available
ChEBI ID64307
Good Scents IDNot Available
References
General References
  1. Xu M, Dai Y, Huang Y, Yang J, Lai XH, Jin D, Lu S, Zhou J, Zhang S, Bai Y, Jiao Y, Qiao L, Jiang Y, Xu J: Identification of Haloactinobacterium kanbiaonis sp. nov. and Ruania zhangjianzhongii sp. nov., two novel species of the family Ruaniaceae isolated from faeces of bats (Hipposideros spp.). Int J Syst Evol Microbiol. 2021 Aug;71(8). doi: 10.1099/ijsem.0.004953. [PubMed:34388085 ]
  2. Xu Z, Li X, Tian J, Gan L, Tian Y: Leucobacter chromiisoli sp. nov., isolated from chromium-containing chemical plant soil. Int J Syst Evol Microbiol. 2021 Jul;71(7). doi: 10.1099/ijsem.0.004923. [PubMed:34319867 ]
  3. Yamanaka K, Ozaki R, Hamano Y, Oikawa T: Molecular and Mechanistic Characterization of PddB, the First PLP-Independent 2,4-Diaminobutyric Acid Racemase Discovered in an Actinobacterial D-Amino Acid Homopolymer Biosynthesis. Front Microbiol. 2021 Jun 10;12:686023. doi: 10.3389/fmicb.2021.686023. eCollection 2021. [PubMed:34177872 ]