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Showing NP-Card for 2-homoectoine (NP0332104)

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Record Information
Version2.0
Created at2023-11-12 04:00:29 UTC
Updated at2024-09-03 04:18:01 UTC
NP-MRD IDNP0332104
Natural Product DOIhttps://doi.org/10.57994/1252
Secondary Accession NumbersNone
Natural Product Identification
Common Name2-homoectoine
Description Based on a literature review very few articles have been published on ZINC39057898.
Structure
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MOLSDFPDBSMILESInChI

MOL for NP0332104 (2-homoectoine)


  Mrv2104 11122304002D          

 11 11  0  0  1  0            999 V2000
    0.0000    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    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 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 C   0  0  1  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
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 N   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
    2.8579   -0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    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  2  0  0  0  0
  5  4  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  3  8  1  0  0  0  0
  5  9  1  6  0  0  0
  9 10  1  0  0  0  0
  9 11  2  0  0  0  0
M  END
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3D MOL for NP0332104 (2-homoectoine)

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3D SDF for NP0332104 (2-homoectoine)

  Mrv2104 11122304002D          

 11 11  0  0  1  0            999 V2000
    0.0000    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    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 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 C   0  0  1  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
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 N   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
    2.8579   -0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    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  2  0  0  0  0
  5  4  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  3  8  1  0  0  0  0
  5  9  1  6  0  0  0
  9 10  1  0  0  0  0
  9 11  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0332104

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CCC1=N[C@@H](CCN1)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C7H12N2O2/c1-2-6-8-4-3-5(9-6)7(10)11/h5H,2-4H2,1H3,(H,8,9)(H,10,11)/t5-/m0/s1

> <INCHI_KEY>
UQMCNTQAZYBDRP-YFKPBYRVSA-N

> <FORMULA>
C7H12N2O2

> <MOLECULAR_WEIGHT>
156.185

> <EXACT_MASS>
156.089877634

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
23

> <JCHEM_AVERAGE_POLARIZABILITY>
16.072906485032117

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(4S)-2-ethyl-1,4,5,6-tetrahydropyrimidine-4-carboxylic acid

> <JCHEM_LOGP>
-1.8253425160873238

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.853129068627507

> <JCHEM_PKA_STRONGEST_BASIC>
10.502034430619688

> <JCHEM_POLAR_SURFACE_AREA>
61.690000000000005

> <JCHEM_REFRACTIVITY>
39.6696

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(4S)-2-ethyl-1,4,5,6-tetrahydropyrimidine-4-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for NP0332104 (2-homoectoine)
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PDB for NP0332104 (2-homoectoine)
HEADER    PROTEIN                                 12-NOV-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   12-NOV-23         0                                  
HETATM    1  C   UNK     0       0.000   4.620   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0       2.667   1.540   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.334  -0.770   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  N   UNK     0       0.000   1.540   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       5.335  -0.000   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       4.001  -2.310   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    8                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6    9                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    3                                                       
CONECT    9    5   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9                                                            
MASTER        0    0    0    0    0    0    0    0   11    0   22    0
END

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3D PDB for NP0332104 (2-homoectoine)
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SMILES for NP0332104 (2-homoectoine)
CCC1=N[C@@H](CCN1)C(O)=O
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INCHI for NP0332104 (2-homoectoine)
InChI=1S/C7H12N2O2/c1-2-6-8-4-3-5(9-6)7(10)11/h5H,2-4H2,1H3,(H,8,9)(H,10,11)/t5-/m0/s1
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View in JSmol
SynonymsNot Available
Chemical FormulaC7H12N2O2
Average Mass156.1850 Da
Monoisotopic Mass156.08988 Da
IUPAC Name(4S)-2-ethyl-1,4,5,6-tetrahydropyrimidine-4-carboxylic acid
Traditional Name(4S)-2-ethyl-1,4,5,6-tetrahydropyrimidine-4-carboxylic acid
CAS Registry NumberNot Available
SMILES
CCC1=N[C@@H](CCN1)C(O)=O
InChI Identifier
InChI=1S/C7H12N2O2/c1-2-6-8-4-3-5(9-6)7(10)11/h5H,2-4H2,1H3,(H,8,9)(H,10,11)/t5-/m0/s1
InChI KeyUQMCNTQAZYBDRP-YFKPBYRVSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
COSY NMR[1H, 1H] NMR Spectrum (2D, 500 MHz, D2O, experimental)Not AvailableFriedrich Schiller University JenaMuhaiminatul Azizah2023-11-15View Spectrum
HMBC NMR[1H, 13C] NMR Spectrum (2D, 500 MHz, D2O, experimental)Not AvailableFriedrich Schiller University JenaMuhaiminatul Azizah2023-11-15View Spectrum
HSQC NMR[1H, 13C] NMR Spectrum (2D, 500 MHz, D2O, experimental)Not AvailableFriedrich Schiller University JenaMuhaiminatul Azizah2023-11-15View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, D2O, experimental)Not AvailableFriedrich Schiller University JenaMuhaiminatul Azizah2023-11-15View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, experimental)Not AvailableFriedrich Schiller University JenaMuhaiminatul Azizah2023-11-15View Spectrum
1D_DEPT NMR13C NMR Spectrum (1D, 126 MHz, D2O, experimental)Not AvailableFriedrich Schiller University JenaMuhaiminatul Azizah2024-05-04View Spectrum
COSY NMR[1H, 1H] NMR Spectrum (2D, 500 MHz, D2O, experimental)Not AvailableFriedrich Schiller University JenaMuhaiminatul Azizah2023-11-12View Spectrum
HMBC NMR[1H, 13C] NMR Spectrum (2D, 500 MHz, D2O, experimental)Not AvailableFriedrich Schiller University JenaMuhaiminatul Azizah2023-11-12View Spectrum
HSQC NMR[1H, 13C] NMR Spectrum (2D, 500 MHz, D2O, experimental)Not AvailableFriedrich Schiller University JenaMuhaiminatul Azizah2023-11-12View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, D2O, experimental)Not AvailableFriedrich Schiller University JenaMuhaiminatul Azizah2023-11-12View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, experimental)Not AvailableFriedrich Schiller University JenaMuhaiminatul Azizah2023-11-12View Spectrum
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
Chemical Shift Submissions
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 500.18, D2O, simulated)muhaiminatul.azizah@uni-jena.deFriedrich Schiller University JenaMuhaiminatu Azizah2024-05-04View Spectrum
Species
Species of Origin
Species NameSourceReference
salina
      Not Available
Chemical Taxonomy
ClassificationNot classified
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-1.8ChemAxon
pKa (Strongest Acidic)2.85ChemAxon
pKa (Strongest Basic)10.5ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area61.69 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity39.67 m³·mol⁻¹ChemAxon
Polarizability16.07 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID115294046  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound93495276  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Azizah M, Pohnert G: 2-Homoectoine: An Additional Member of the Ectoine Family from Phyto- and Bacterioplankton Involved in Osmoadaptation. J Nat Prod. 2024 Jan 26;87(1):50-57. doi: 10.1021/acs.jnatprod.3c00766. Epub 2023  Dec 27. [PubMed:38150306  ]