NP-MRD: Showing NP-Card for d-xylaric acid (NP0323216)

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Record Information

Version

2.0

Created at

2022-09-12 02:30:00 UTC

Updated at

2022-09-12 02:30:00 UTC

NP-MRD ID

NP0323216

Secondary Accession Numbers

None

Natural Product Identification

Common Name

d-xylaric acid

Description

(2R,3s,4S)-2,3,4-trihydroxypentanedioic acid is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv0541 05041403082D          

 15 14  0  0  0  0            999 V2000
    3.9039    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  1  0  0  0  0  0  0  0  0  0
    4.6184    1.8414    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    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
    3.9039    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
    1.7605    1.8414    0.0000 O   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
    6.0474    1.8414    0.0000 O   0  0  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
    3.9039    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
    4.6184    1.0164    0.0000 H   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  2  1  0  0  0  0
  5  3  1  0  0  0  0
  1  6  1  6  0  0  0
  2  7  1  6  0  0  0
  3  8  1  6  0  0  0
  9  4  2  0  0  0  0
 10  4  1  0  0  0  0
 11  5  2  0  0  0  0
 12  5  1  0  0  0  0
  1 13  1  6  0  0  0
  2 14  1  6  0  0  0
  3 15  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0323216

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H8O7/c6-1(2(7)4(9)10)3(8)5(11)12/h1-3,6-8H,(H,9,10)(H,11,12)/t1-,2-,3+

> <INCHI_KEY>
NPTTZSYLTYJCPR-FFEAPLRNSA-N

> <FORMULA>
C5H8O7

> <MOLECULAR_WEIGHT>
180.1128

> <EXACT_MASS>
180.02700261

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_AVERAGE_POLARIZABILITY>
14.356438206676884

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3s,4S)-2,3,4-trihydroxypentanedioic acid

> <ALOGPS_LOGP>
-1.41

> <JCHEM_LOGP>
-2.4591348306666667

> <ALOGPS_LOGS>
-0.32

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.518885023851425

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.786220846412511

> <JCHEM_PKA_STRONGEST_BASIC>
-3.8007073200227532

> <JCHEM_POLAR_SURFACE_AREA>
135.29

> <JCHEM_REFRACTIVITY>
32.1759

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.69e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3s,4S)-2,3,4-trihydroxypentanedioic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 04-MAY-14   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-MAY-14         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   13  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   14  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   15  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
CONECT    1    2    3    6   13                                             
CONECT    2    1    4    7   14                                             
CONECT    3    1    5    8   15                                             
CONECT    4    2    9   10                                                  
CONECT    5    3   11   12                                                  
CONECT    6    1                                                            
CONECT    7    2                                                            
CONECT    8    3                                                            
CONECT    9    4                                                            
CONECT   10    4                                                            
CONECT   11    5                                                            
CONECT   12    5                                                            
CONECT   13    1                                                            
CONECT   14    2                                                            
CONECT   15    3                                                            
MASTER        0    0    0    0    0    0    0    0   15    0   28    0
END

View in JSmol

Synonyms

Value	Source
(2R,3S,4S)-2,3,4-Trihydroxypentanedioate	Generator

Chemical Formula

C₅H₈O₇

Average Mass

180.1128 Da

Monoisotopic Mass

180.02700 Da

IUPAC Name

(2R,3s,4S)-2,3,4-trihydroxypentanedioic acid

Traditional Name

(2R,3s,4S)-2,3,4-trihydroxypentanedioic acid

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C5H8O7/c6-1(2(7)4(9)10)3(8)5(11)12/h1-3,6-8H,(H,9,10)(H,11,12)/t1-,2-,3+

InChI Key

NPTTZSYLTYJCPR-FFEAPLRNSA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Not Available

Chemical Taxonomy

Description

This compound belongs to the class of organic compounds known as beta hydroxy acids and derivatives. These are compounds containing a carboxylic acid substituted with a hydroxyl group on the C3 carbon atom.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Hydroxy acids and derivatives

Sub Class

Beta hydroxy acids and derivatives

Direct Parent

Beta hydroxy acids and derivatives

Alternative Parents

Substituents

Short-chain hydroxy acid
Beta-hydroxy acid
Fatty acid
Monosaccharide
Dicarboxylic acid or derivatives
Alpha-hydroxy acid
Secondary alcohol
Polyol
Carboxylic acid
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Alcohol
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

Not Available

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	-1.4	ALOGPS
logP	-2.5	ChemAxon
logS	-0.32	ALOGPS
pKa (Strongest Acidic)	2.79	ChemAxon
pKa (Strongest Basic)	-3.8	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	135.29 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	32.18 m³·mol⁻¹	ChemAxon
Polarizability	14.36 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

Not Available

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

Not Available

PDB ID

DXL

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for d-xylaric acid (NP0323216)

MOL for NP0323216 (d-xylaric acid)

3D MOL for NP0323216 (d-xylaric acid)

3D SDF for NP0323216 (d-xylaric acid)

3D-SDF for NP0323216 (d-xylaric acid)

PDB for NP0323216 (d-xylaric acid)

3D PDB for NP0323216 (d-xylaric acid)

SMILES for NP0323216 (d-xylaric acid)

INCHI for NP0323216 (d-xylaric acid)

Structure for NP0323216 (d-xylaric acid)

3D Structure for NP0323216 (d-xylaric acid)