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Showing NP-Card for 2,3-Diaminopropionic acid (NP0000519)

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Record Information
Version2.0
Created at2006-05-22 14:17:31 UTC
Updated at2021-06-29 00:47:19 UTC
NP-MRD IDNP0000519
Secondary Accession NumbersNone
Natural Product Identification
Common Name2,3-Diaminopropionic acid
Description2,3-Diaminopropionic acid, also known as L-2,3-diaminopropanoate or Dpr, 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. 2,3-Diaminopropionic acid is a very hydrophobic molecule, practically insoluble in water, and relatively neutral. 2,3-Diaminopropionic acid (2,3-diaminopropionate) is a non-proteinogenic amino acid found in certain secondary metabolites, including zwittermicin A and tuberactinomycin.2,3-Diaminopropionate is formed by the pyridoxal phosphate (PLP) mediated amination of serine. 2,3-Diaminopropionic acid exists in all living organisms, ranging from bacteria to humans.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0000519 (2,3-Diaminopropionic acid)


  Mrv1652305261923552D          

  7  6  0  0  1  0            999 V2000
   18.6049   -4.1579    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.8905   -2.9205    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.4615   -3.7455    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   16.4615   -5.3954    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   17.1760   -4.1579    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   17.1760   -4.9830    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.8905   -3.7455    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  7  1  0  0  0  0
  2  7  2  0  0  0  0
  5  3  1  6  0  0  0
  4  6  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  1  0  0  0  0
M  END
Download

3D MOL for NP0000519 (2,3-Diaminopropionic acid)

HMDB0002006
     RDKit          3D
2,3-Diaminopropionic acid
 15 14  0  0  0  0  0  0  0  0999 V2000
   -2.1263    0.7746    0.0996 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1365    0.0548   -0.6679 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0644   -0.1975    0.2345 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.6183    1.0462    0.6957 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.0760   -1.0447   -0.4553 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6551   -2.1609   -0.8898 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3989   -0.6584   -0.6234 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6765    1.5545    0.6144 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6233    0.0989    0.6910 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5762   -0.9022   -0.9989 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8249    0.6550   -1.5217 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2478   -0.7694    1.1413 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1846    1.5450   -0.0142 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1660    0.9407    1.5782 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0483   -0.9364    0.1164 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
  3  5  1  0
  5  6  2  0
  5  7  1  0
  1  8  1  0
  1  9  1  0
  2 10  1  0
  2 11  1  0
  3 12  1  1
  4 13  1  0
  4 14  1  0
  7 15  1  0
M  END
Download

3D SDF for NP0000519 (2,3-Diaminopropionic acid)


  Mrv1652305261923552D          

  7  6  0  0  1  0            999 V2000
   18.6049   -4.1579    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.8905   -2.9205    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.4615   -3.7455    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   16.4615   -5.3954    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   17.1760   -4.1579    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   17.1760   -4.9830    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.8905   -3.7455    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  7  1  0  0  0  0
  2  7  2  0  0  0  0
  5  3  1  6  0  0  0
  4  6  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0000519

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C3H8N2O2/c4-1-2(5)3(6)7/h2H,1,4-5H2,(H,6,7)/t2-/m0/s1

> <INCHI_KEY>
PECYZEOJVXMISF-REOHCLBHSA-N

> <FORMULA>
C3H8N2O2

> <MOLECULAR_WEIGHT>
104.1078

> <EXACT_MASS>
104.05857751

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
15

> <JCHEM_AVERAGE_POLARIZABILITY>
9.88329737678502

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-2,3-diaminopropanoic acid

> <ALOGPS_LOGP>
-3.88

> <JCHEM_LOGP>
-4.021651370053583

> <ALOGPS_LOGS>
0.53

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.1010375086495974

> <JCHEM_PKA_STRONGEST_BASIC>
9.568559967525095

> <JCHEM_POLAR_SURFACE_AREA>
89.33999999999999

> <JCHEM_REFRACTIVITY>
23.6985

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.52e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
L-2,3-diaminopropionic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0000519 (2,3-Diaminopropionic acid)

HMDB0002006
     RDKit          3D
2,3-Diaminopropionic acid
 15 14  0  0  0  0  0  0  0  0999 V2000
   -2.1263    0.7746    0.0996 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1365    0.0548   -0.6679 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0644   -0.1975    0.2345 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.6183    1.0462    0.6957 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.0760   -1.0447   -0.4553 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6551   -2.1609   -0.8898 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3989   -0.6584   -0.6234 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6765    1.5545    0.6144 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6233    0.0989    0.6910 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5762   -0.9022   -0.9989 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8249    0.6550   -1.5217 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2478   -0.7694    1.1413 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1846    1.5450   -0.0142 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1660    0.9407    1.5782 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0483   -0.9364    0.1164 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
  3  5  1  0
  5  6  2  0
  5  7  1  0
  1  8  1  0
  1  9  1  0
  2 10  1  0
  2 11  1  0
  3 12  1  1
  4 13  1  0
  4 14  1  0
  7 15  1  0
M  END
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PDB for NP0000519 (2,3-Diaminopropionic 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  O   UNK     0      34.729  -7.761   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      33.396  -5.452   0.000  0.00  0.00           O+0
HETATM    3  N   UNK     0      30.728  -6.992   0.000  0.00  0.00           N+0
HETATM    4  N   UNK     0      30.728 -10.071   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0      32.062  -7.761   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      32.062  -9.302   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      33.396  -6.992   0.000  0.00  0.00           C+0
CONECT    1    7                                                            
CONECT    2    7                                                            
CONECT    3    5                                                            
CONECT    4    6                                                            
CONECT    5    3    6    7                                                  
CONECT    6    4    5                                                       
CONECT    7    1    2    5                                                  
MASTER        0    0    0    0    0    0    0    0    7    0   12    0
END
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3D PDB for NP0000519 (2,3-Diaminopropionic acid)

COMPND    HMDB0002006
HETATM    1  N1  UNL     1      -2.126   0.775   0.100  1.00  0.00           N  
HETATM    2  C1  UNL     1      -1.137   0.055  -0.668  1.00  0.00           C  
HETATM    3  C2  UNL     1       0.064  -0.197   0.235  1.00  0.00           C  
HETATM    4  N2  UNL     1       0.618   1.046   0.696  1.00  0.00           N  
HETATM    5  C3  UNL     1       1.076  -1.045  -0.455  1.00  0.00           C  
HETATM    6  O1  UNL     1       0.655  -2.161  -0.890  1.00  0.00           O  
HETATM    7  O2  UNL     1       2.399  -0.658  -0.623  1.00  0.00           O  
HETATM    8  H1  UNL     1      -1.677   1.555   0.614  1.00  0.00           H  
HETATM    9  H2  UNL     1      -2.623   0.099   0.691  1.00  0.00           H  
HETATM   10  H3  UNL     1      -1.576  -0.902  -0.999  1.00  0.00           H  
HETATM   11  H4  UNL     1      -0.825   0.655  -1.522  1.00  0.00           H  
HETATM   12  H5  UNL     1      -0.248  -0.769   1.141  1.00  0.00           H  
HETATM   13  H6  UNL     1       1.185   1.545  -0.014  1.00  0.00           H  
HETATM   14  H7  UNL     1       1.166   0.941   1.578  1.00  0.00           H  
HETATM   15  H8  UNL     1       3.048  -0.936   0.116  1.00  0.00           H  
CONECT    1    2    8    9
CONECT    2    3   10   11
CONECT    3    4    5   12
CONECT    4   13   14
CONECT    5    6    6    7
CONECT    7   15
END
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SMILES for NP0000519 (2,3-Diaminopropionic acid)

NC[C@H](N)C(O)=O
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INCHI for NP0000519 (2,3-Diaminopropionic acid)

InChI=1S/C3H8N2O2/c4-1-2(5)3(6)7/h2H,1,4-5H2,(H,6,7)/t2-/m0/s1
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View in JSmol
Synonyms
ValueSource
DprChEBI
L-2,3-DiaminopropanoateChEBI
L-2,3-Diaminopropanoic acidChEBI
L-2,3-DiaminopropionateChEBI
L-2,3-Diaminopropionic acidChEBI
3-Amino-L-alanineKegg
(S)-2,3-DiaminopropanoateKegg
(S)-2,3-Diaminopropanoic acidGenerator
2,3-DiaminopropionateGenerator
(2S)-2,3-DiaminopropanoateHMDB
(2S)-2,3-Diaminopropanoic acidHMDB
2,3-Diaminopropionic acid, (D)-isomerHMDB
2,3-Diaminopropionic acid, (DL)-isomer, monohydrochlorideHMDB
2,3-Diaminopropionic acid, (L)-isomerHMDB
3-AminoalanineHMDB
2,3-Diaminopropionic acid, (DL)-isomerHMDB
2,3-Diaminopropionic acid, (L)-isomer, monohydrochlorideHMDB
alpha,beta-Diaminopropionic acidHMDB
beta-AminoalanineHMDB
2,3-Diaminopropanoic acidHMDB
2-Amino-beta-alanineHMDB
2,3-Diamino-propionateHMDB
2,3-Diaminopropionic acidMeSH
Chemical FormulaC3H8N2O2
Average Mass104.1078 Da
Monoisotopic Mass104.05858 Da
IUPAC Name(2S)-2,3-diaminopropanoic acid
Traditional NameL-2,3-diaminopropionic acid
CAS Registry Number4033-39-0
SMILES
NC[C@H](N)C(O)=O
InChI Identifier
InChI=1S/C3H8N2O2/c4-1-2(5)3(6)7/h2H,1,4-5H2,(H,6,7)/t2-/m0/s1
InChI KeyPECYZEOJVXMISF-REOHCLBHSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
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
Not Available
Species
Species of Origin
Species NameSourceReference
Anas platyrhynchosFooDB
AnatidaeFooDB
Anser anserFooDB
Bison bisonFooDB
Bos taurusFooDB
Bos taurus X Bison bisonFooDB
Bubalus bubalisFooDB
Capra aegagrus hircusFooDB
CervidaeFooDB
Cervus canadensisFooDB
ColumbaFooDB
ColumbidaeFooDB
Coniophora puteanaLOTUS Database
Dromaius novaehollandiaeFooDB
Equus caballusFooDB
Gallus gallusFooDB
Lagopus mutaFooDB
LeporidaeFooDB
Lepus timidusFooDB
Melanitta fuscaFooDB
Meleagris gallopavoFooDB
Numida meleagrisFooDB
OdocoileusFooDB
OryctolagusFooDB
Ovis ariesFooDB
PhasianidaeFooDB
Phasianus colchicusFooDB
Struthio camelusFooDB
Sus scrofaFooDB
Sus scrofa domesticaFooDB
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 acid
  • Carboxylic acid
  • Monocarboxylic acid or derivatives
  • Amine
  • Organic oxide
  • Hydrocarbon derivative
  • Organopnictogen compound
  • Primary amine
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxygen compound
  • Primary aliphatic amine
  • Organic nitrogen compound
  • Carbonyl group
  • 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
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility352 g/LALOGPS
logP-3.9ALOGPS
logP-4ChemAxon
logS0.53ALOGPS
pKa (Strongest Acidic)2.1ChemAxon
pKa (Strongest Basic)9.57ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area89.34 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity23.7 m³·mol⁻¹ChemAxon
Polarizability9.88 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0002006
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB022790
KNApSAcK IDNot Available
Chemspider ID87849
KEGG Compound IDC03401
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia Link2,3-Diaminopropionic_acid
METLIN ID6429
PubChem Compound97328
PDB IDNot Available
ChEBI ID16303
Good Scents IDNot Available
References
General References
  1. Maletinska L, Pychova M, Holubova M, Blechova M, Demianova Z, Elbert T, Zelezna B: Characterization of new stable ghrelin analogs with prolonged orexigenic potency. J Pharmacol Exp Ther. 2012 Mar;340(3):781-6. doi: 10.1124/jpet.111.185371. Epub 2011 Dec 19. [PubMed:22182933 ]
  2. Theetharappan M, Neelakantan MA: A Water-Soluble Schiff Base Turn-on Fluorescent Chemosensor for the Detection of Al(3+) and Zn(2+) Ions at the Nanomolar Level: Application in Live-Cell Imaging. J Fluoresc. 2021 May 29. pii: 10.1007/s10895-021-02756-7. doi: 10.1007/s10895-021-02756-7. [PubMed:34050881 ]
  3. Romanowska A, Wegrzyn K, Bury K, Sikorska E, Gnatek A, Piwkowska A, Konieczny I, Lesner A, Wysocka M: Novel Cell Permeable Polymers of N-Substituted L-2,3-Diaminopropionic Acid (DAPEGs) and Cellular Consequences of Their Interactions with Nucleic Acids. Int J Mol Sci. 2021 Mar 4;22(5). pii: ijms22052571. doi: 10.3390/ijms22052571. [PubMed:33806461 ]
  4. Hsu SH, Zhang S, Huang SC, Wu TK, Xu Z, Chang CY: Characterization of Enzymes Catalyzing the Formation of the Nonproteinogenic Amino Acid l-Dap in Capreomycin Biosynthesis. Biochemistry. 2021 Jan 12;60(1):77-84. doi: 10.1021/acs.biochem.0c00808. Epub 2020 Dec 23. [PubMed:33356147 ]
  5. Lu J, Xu H, Xia J, Ma J, Xu J, Li Y, Feng J: D- and Unnatural Amino Acid Substituted Antimicrobial Peptides With Improved Proteolytic Resistance and Their Proteolytic Degradation Characteristics. Front Microbiol. 2020 Nov 12;11:563030. doi: 10.3389/fmicb.2020.563030. eCollection 2020. [PubMed:33281761 ]
  6. Emmrich PMF, Rejzek M, Hill L, Brett P, Edwards A, Sarkar A, Field RA, Martin C, Wang TL: Linking a rapid throughput plate-assay with high-sensitivity stable-isotope label LCMS quantification permits the identification and characterisation of low beta-L-ODAP grass pea lines. BMC Plant Biol. 2019 Nov 12;19(1):489. doi: 10.1186/s12870-019-2091-5. [PubMed:31718544 ]
  7. Arokianathan JF, Ramya KA, Janeena A, Deshpande AP, Ayyadurai N, Leemarose A, Shanmugam G: Non-proteinogenic amino acid based supramolecular hydrogel material for enhanced cell proliferation. Colloids Surf B Biointerfaces. 2020 Jan 1;185:110581. doi: 10.1016/j.colsurfb.2019.110581. Epub 2019 Oct 16. [PubMed:31677412 ]
  8. Stachurski O, Neubauer D, Maluch I, Wyrzykowski D, Bauer M, Bartoszewska S, Kamysz W, Sikorska E: Effect of self-assembly on antimicrobial activity of double-chain short cationic lipopeptides. Bioorg Med Chem. 2019 Dec 1;27(23):115129. doi: 10.1016/j.bmc.2019.115129. Epub 2019 Oct 17. [PubMed:31668583 ]
  9. Ng TL, McCallum ME, Zheng CR, Wang JX, Wu KJY, Balskus EP: The l-Alanosine Gene Cluster Encodes a Pathway for Diazeniumdiolate Biosynthesis. Chembiochem. 2020 Apr 17;21(8):1155-1160. doi: 10.1002/cbic.201900565. Epub 2019 Dec 19. [PubMed:31643127 ]
  10. Tang J, Ju Y, Gu Q, Xu J, Zhou H: Structural Insights into Substrate Recognition and Activity Regulation of the Key Decarboxylase SbnH in Staphyloferrin B Biosynthesis. J Mol Biol. 2019 Dec 6;431(24):4868-4881. doi: 10.1016/j.jmb.2019.10.009. Epub 2019 Oct 18. [PubMed:31634470 ]