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Showing NP-Card for L-2,3-Dihydrodipicolinate (NP0334808)

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Record Information
Version2.0
Created at2024-09-10 20:03:11 UTC
Updated at2024-09-10 20:03:11 UTC
NP-MRD IDNP0334808
Secondary Accession NumbersNone
Natural Product Identification
Common NameL-2,3-Dihydrodipicolinate
DescriptionL-2,3-Dihydrodipicolinate belongs to the class of organic compounds known as alpha amino acids and derivatives. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon), or a derivative thereof. L-2,3-Dihydrodipicolinate was first documented in 2016 (PMID: 26750477). Based on a literature review a small amount of articles have been published on L-2,3-Dihydrodipicolinate (PMID: 37875653).
Structure
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MOLSDFPDBSMILESInChI

MOL for NP0334808 (L-2,3-Dihydrodipicolinate)


  Mrv2104 05252322352D          

 12 12  0  0  0  0            999 V2000
   15.9805  -11.6086    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.5680  -12.3225    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.8055  -11.6086    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.5680  -10.8939    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.9805  -10.1795    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.5680   -9.4648    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.7430   -9.4648    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.3305  -10.1795    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.7430  -10.8939    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   13.5055  -10.1795    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.0931   -9.4648    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.0931  -10.8939    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  0  0  0
  4  5  1  0  0  0  0
  4  9  2  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 10  1  0  0  0  0
 10 11  2  0  0  0  0
 10 12  1  0  0  0  0
M  END
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3D MOL for NP0334808 (L-2,3-Dihydrodipicolinate)

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3D SDF for NP0334808 (L-2,3-Dihydrodipicolinate)

  Mrv2104 05252322352D          

 12 12  0  0  0  0            999 V2000
   15.9805  -11.6086    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.5680  -12.3225    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.8055  -11.6086    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.5680  -10.8939    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.9805  -10.1795    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.5680   -9.4648    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.7430   -9.4648    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.3305  -10.1795    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.7430  -10.8939    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   13.5055  -10.1795    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.0931   -9.4648    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.0931  -10.8939    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  0  0  0
  4  5  1  0  0  0  0
  4  9  2  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 10  1  0  0  0  0
 10 11  2  0  0  0  0
 10 12  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0334808

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC(=O)C1CC=CC(=N1)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1/C7H7NO4/c9-6(10)4-2-1-3-5(8-4)7(11)12/h1-2,5H,3H2,(H,9,10)(H,11,12)

> <INCHI_KEY>
UWOCFOFVIBZJGH-UHFFFAOYNA-N

> <FORMULA>
C7H7NO4

> <MOLECULAR_WEIGHT>
169.136

> <EXACT_MASS>
169.037507709

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
19

> <JCHEM_AVERAGE_POLARIZABILITY>
14.977946790840875

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2,3-dihydropyridine-2,6-dicarboxylic acid

> <JCHEM_LOGP>
0.661546247

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.8800335549347

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.1230671257870535

> <JCHEM_PKA_STRONGEST_BASIC>
-1.0507401461431112

> <JCHEM_POLAR_SURFACE_AREA>
86.96

> <JCHEM_REFRACTIVITY>
39.363

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
2,3-dihydrodipicolinic acid

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for NP0334808 (L-2,3-Dihydrodipicolinate)
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PDB for NP0334808 (L-2,3-Dihydrodipicolinate)
HEADER    PROTEIN                                 25-MAY-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   25-MAY-23         0                                  
HETATM    1  C   UNK     0      29.830 -21.669   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0      29.060 -23.002   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      31.370 -21.669   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      29.060 -20.335   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      29.830 -19.002   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      29.060 -17.668   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      27.520 -17.668   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      26.750 -19.002   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0      27.520 -20.335   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0      25.210 -19.002   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      24.440 -17.668   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      24.440 -20.335   0.000  0.00  0.00           O+0
CONECT    1    2    3    4                                                  
CONECT    2    1                                                            
CONECT    3    1                                                            
CONECT    4    1    5    9                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   10                                                  
CONECT    9    4    8                                                       
CONECT   10    8   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   24    0
END

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3D PDB for NP0334808 (L-2,3-Dihydrodipicolinate)
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SMILES for NP0334808 (L-2,3-Dihydrodipicolinate)
OC(=O)C1CC=CC(=N1)C(O)=O
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INCHI for NP0334808 (L-2,3-Dihydrodipicolinate)
InChI=1/C7H7NO4/c9-6(10)4-2-1-3-5(8-4)7(11)12/h1-2,5H,3H2,(H,9,10)(H,11,12)
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View in JSmol
Synonyms
ValueSource
L-2,3-Dihydrodipicolinic acidGenerator
Chemical FormulaC7H7NO4
Average Mass169.1360 Da
Monoisotopic Mass169.03751 Da
IUPAC Name2,3-dihydropyridine-2,6-dicarboxylic acid
Traditional Name2,3-dihydrodipicolinic acid
CAS Registry NumberNot Available
SMILES
OC(=O)C1CC=CC(=N1)C(O)=O
InChI Identifier
InChI=1/C7H7NO4/c9-6(10)4-2-1-3-5(8-4)7(11)12/h1-2,5H,3H2,(H,9,10)(H,11,12)
InChI KeyUWOCFOFVIBZJGH-UHFFFAOYNA-N
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of OriginNot Available
Chemical Taxonomy
DescriptionThis compound belongs to the class of organic compounds known as alpha amino acids and derivatives. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon), or a derivative thereof.
KingdomOrganic compounds  
Super ClassOrganic acids and derivatives  
ClassCarboxylic acids and derivatives  
Sub ClassAmino acids, peptides, and analogues  
Direct ParentAlpha amino acids and derivatives  
Alternative Parents
Substituents
  • Alpha-amino acid or derivatives
    • 

  • Dihydropyridinecarboxylic acid derivative
    • 

  • Dihydropyridine
    • 

  • Dicarboxylic acid or derivatives
    • 

  • Hydropyridine
    • 

  • Ketimine
    • 

  • Carboxylic acid
    • 

  • Azacycle
    • 

  • Propargyl-type 1,3-dipolar organic compound
    • 

  • Organic 1,3-dipolar compound
    • 

  • Organoheterocyclic compound
    • 

  • Organic nitrogen compound
    • 

  • Imine
    • 

  • Hydrocarbon derivative
    • 

  • Organic oxide
    • 

  • Organopnictogen compound
    • 

  • Organonitrogen compound
    • 

  • Organooxygen compound
    • 

  • Carbonyl group
    • 

  • Organic oxygen compound
    • 

  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic 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
logP0.66ChemAxon
pKa (Strongest Acidic)3.12ChemAxon
pKa (Strongest Basic)-1.1ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area86.96 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity39.36 m³·mol⁻¹ChemAxon
Polarizability14.98 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 IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Chen Y, Chen S, Xu C, Yu L, Chu S, Bao J, Wang J, Wang J: Identification of Diagnostic Biomarkers for Compensatory Liver Cirrhosis Based on Gut Microbiota and Urine Metabolomics Analyses. Mol Biotechnol. 2023 Oct 24. doi: 10.1007/s12033-023-00922-9. [PubMed:37875653  ] 
  2. Naqvi KF, Staker BL, Dobson RC, Serbzhinskiy D, Sankaran B, Myler PJ, Hudson AO: Cloning, expression, purification, crystallization and X-ray diffraction analysis of dihydrodipicolinate synthase from the human pathogenic bacterium Bartonella henselae strain Houston-1 at 2.1 A resolution. Acta Crystallogr F Struct Biol Commun. 2016 Jan;72(Pt 1):2-9. doi:  10.1107/S2053230X15023213. Epub 2016 Jan 1. [PubMed:26750477  ]