NP-MRD: Showing NP-Card for 2-keto-3-deoxy-L-rhamnonate (NP0334310)

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Record Information

Version

2.0

Created at

2024-09-09 23:06:26 UTC

Updated at

2024-09-09 23:06:26 UTC

NP-MRD ID

NP0334310

Secondary Accession Numbers

None

Natural Product Identification

Common Name

2-keto-3-deoxy-L-rhamnonate

Description

2-Keto-3-deoxy-l-rhamnonate, also known as kdr or 2-dehydro-3,6-dideoxy-L-mannonate, belongs to medium-chain keto acids and derivatives class of compounds. Those are keto acids with a 6 to 12 carbon atoms long side chain. 2-Keto-3-deoxy-l-rhamnonate is soluble (in water) and a weakly acidic compound (based on its pKa). 2-Keto-3-deoxy-l-rhamnonate can be found in a number of food items such as red beetroot, evergreen huckleberry, winter squash, and pepper (c. Pubescens), which makes 2-keto-3-deoxy-l-rhamnonate a potential biomarker for the consumption of these food products.

Structure

MOL SDF PDB SMILES InChI


  Mrv1533007131514082D          

 13 12  0  0  1  0            999 V2000
    1.7605    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.1895    1.8414    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.6184    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474    1.8414    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    5.3329    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    2.2539    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    1.0164    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  4  3  1  0  0  0  0
  5  2  1  0  0  0  0
  6  5  1  0  0  0  0
  3  7  1  6  0  0  0
  4  8  1  1  0  0  0
  9  5  2  0  0  0  0
 10  6  1  0  0  0  0
 11  6  2  0  0  0  0
  3 12  1  6  0  0  0
  4 13  1  1  0  0  0
M  CHG  1  10  -1
M  END
> <DATABASE_ID>
NP0334310

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@@](C)(O)[C@]([H])(O)CC(=O)C([O-])=O

> <INCHI_IDENTIFIER>
InChI=1S/C6H10O5/c1-3(7)4(8)2-5(9)6(10)11/h3-4,7-8H,2H2,1H3,(H,10,11)/p-1/t3-,4+/m0/s1

> <INCHI_KEY>
FRIWJYNKZPJVRL-IUYQGCFVSA-M

> <FORMULA>
C6H9O5

> <MOLECULAR_WEIGHT>
161.134

> <EXACT_MASS>
161.04554697

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
20

> <JCHEM_AVERAGE_POLARIZABILITY>
14.181948737963035

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
-1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(4R,5S)-4,5-dihydroxy-2-oxohexanoate

> <ALOGPS_LOGP>
-1.22

> <JCHEM_LOGP>
-0.7281212736666668

> <ALOGPS_LOGS>
0.35

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
13.893889380196693

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.0645523555521614

> <JCHEM_PKA_STRONGEST_BASIC>
-3.017945905375046

> <JCHEM_POLAR_SURFACE_AREA>
97.66

> <JCHEM_REFRACTIVITY>
45.6097

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.03e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-dehydro-3-deoxy-L-rhamnonate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 13-JUL-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   13-JUL-15         0                                  
HETATM    1  C   UNK     0       3.286   3.437   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       7.287   2.667   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.620   2.667   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.954   3.437   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       8.621   3.437   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       9.955   2.667   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       4.620   1.127   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       5.954   4.977   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       8.621   4.977   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      11.288   3.437   0.000  0.00  0.00           O-1
HETATM   11  O   UNK     0       9.955   1.127   0.000  0.00  0.00           O+0
HETATM   12  H   UNK     0       4.620   4.207   0.000  0.00  0.00           H+0
HETATM   13  H   UNK     0       5.954   1.897   0.000  0.00  0.00           H+0
CONECT    1    3                                                            
CONECT    2    4    5                                                       
CONECT    3    1    4    7   12                                             
CONECT    4    2    3    8   13                                             
CONECT    5    2    6    9                                                  
CONECT    6    5   10   11                                                  
CONECT    7    3                                                            
CONECT    8    4                                                            
CONECT    9    5                                                            
CONECT   10    6                                                            
CONECT   11    6                                                            
CONECT   12    3                                                            
CONECT   13    4                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   24    0
END

View in JSmol

Synonyms

Value	Source
2-Dehydro-3-deoxy-L-rhamnonate anion	ChEBI
2-Dehydro-3-deoxy-L-rhamnonate(1-)	ChEBI
2-Dehydro-3-deoxy-L-rhamnonic acid anion	Generator
2-Dehydro-3-deoxy-L-rhamnonic acid(1-)	Generator
2-Keto-3-deoxy-L-rhamnonic acid	Generator
2-dehydro-3-Deoxy-L-rhamnonic acid	Generator

Chemical Formula

C₆H₉O₅

Average Mass

161.1340 Da

Monoisotopic Mass

161.04555 Da

IUPAC Name

(4R,5S)-4,5-dihydroxy-2-oxohexanoate

Traditional Name

2-dehydro-3-deoxy-L-rhamnonate

CAS Registry Number

Not Available

SMILES

[H][C@@](C)(O)[C@]([H])(O)CC(=O)C([O-])=O

InChI Identifier

InChI=1S/C6H10O5/c1-3(7)4(8)2-5(9)6(10)11/h3-4,7-8H,2H2,1H3,(H,10,11)/p-1/t3-,4+/m0/s1

InChI Key

FRIWJYNKZPJVRL-IUYQGCFVSA-M

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as medium-chain keto acids and derivatives. These are keto acids with a 6 to 12 carbon atoms long side chain.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Keto acids and derivatives

Sub Class

Medium-chain keto acids and derivatives

Direct Parent

Medium-chain keto acids and derivatives

Alternative Parents

Substituents

Medium-chain keto acid
Alpha-keto acid
Beta-hydroxy ketone
1,2-diol
Ketone
Secondary alcohol
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Hydrocarbon derivative
Alcohol
Carbonyl group
Organic oxide
Organic oxygen compound
Organooxygen compound
Organic anion
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

carbohydrate acid anion (CHEBI:58371 )

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
logP	-1.2	ALOGPS
logP	-0.73	ChemAxon
logS	0.35	ALOGPS
pKa (Strongest Acidic)	3.06	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	97.66 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	45.61 m³·mol⁻¹	ChemAxon
Polarizability	14.18 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB030341

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

49852300

PDB ID

Not Available

ChEBI ID

58371

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for 2-keto-3-deoxy-L-rhamnonate (NP0334310)

MOL for NP0334310 (2-keto-3-deoxy-L-rhamnonate)

3D MOL for NP0334310 (2-keto-3-deoxy-L-rhamnonate)

3D SDF for NP0334310 (2-keto-3-deoxy-L-rhamnonate)

3D-SDF for NP0334310 (2-keto-3-deoxy-L-rhamnonate)

PDB for NP0334310 (2-keto-3-deoxy-L-rhamnonate)

3D PDB for NP0334310 (2-keto-3-deoxy-L-rhamnonate)

SMILES for NP0334310 (2-keto-3-deoxy-L-rhamnonate)

INCHI for NP0334310 (2-keto-3-deoxy-L-rhamnonate)

Structure for NP0334310 (2-keto-3-deoxy-L-rhamnonate)

3D Structure for NP0334310 (2-keto-3-deoxy-L-rhamnonate)