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Showing NP-Card for .+-.-malic acid (NP0303950)

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Record Information
Version2.0
Created at2022-09-10 18:42:31 UTC
Updated at2022-09-10 18:42:31 UTC
NP-MRD IDNP0303950
Secondary Accession NumbersNone
Natural Product Identification
Common Name.+-.-malic acid
DescriptionD-Malic acid, also known as D-malate, belongs to the class of organic compounds known as beta hydroxy acids and derivatives. Beta hydroxy acids and derivatives are compounds containing a carboxylic acid substituted with a hydroxyl group on the C3 carbon atom. D-Malic acid is an extremely weak basic (essentially neutral) compound (based on its pKa). D-Malic acid exists in all living organisms, ranging from bacteria to humans. .+-.-malic acid is found in Arabidopsis thaliana, Homalomena occulta, Pogostemon cablin, Salmonella enterica, Trypanosoma brucei and Vaccinium macrocarpon. .+-.-malic acid was first documented in 1960 (PMID: 13842473). An optically active form of malic acid having (R)-configuration.
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0303950 (.+-.-malic acid)


  Mrv1652309042000372D          

  9  8  0  0  1  0            999 V2000
    1.9520    1.9520    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    1.1270    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1914    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    1.9520    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809    1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664   -0.1105    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  4  6  2  0  0  0  0
  2  7  1  0  0  0  0
  7  8  1  0  0  0  0
  7  9  2  0  0  0  0
M  END
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3D MOL for NP0303950 (.+-.-malic acid)

     RDKit          3D

 15 14  0  0  0  0  0  0  0  0999 V2000
    2.0867    1.0318   -0.6588 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9342    0.0006    0.0135 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0096   -0.7773    0.4191 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5810   -0.4578    0.4218 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4477    0.5145   -0.1121 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.3840    0.5756   -1.4869 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8084    0.1987    0.3765 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1144    0.0906    1.5726 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8036    0.0132   -0.5978 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4957   -1.3550   -0.2521 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3493   -1.4699    0.0490 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5344   -0.5079    1.5257 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2085    1.5403    0.2719 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9057   -0.1862   -1.8508 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3186    0.7887   -0.9579 H   0  0  0  0  0  0  0  0  0  0  0  0
  6  5  1  0
  5  4  1  0
  4  2  1  0
  2  3  1  0
  2  1  2  0
  5  7  1  0
  7  9  1  0
  7  8  2  0
  6 14  1  0
  5 13  1  1
  4 11  1  0
  4 12  1  0
  3 10  1  0
  9 15  1  0
M  END
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3D SDF for NP0303950 (.+-.-malic acid)


  Mrv1652309042000372D          

  9  8  0  0  1  0            999 V2000
    1.9520    1.9520    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    1.1270    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1914    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    1.9520    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809    1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664   -0.1105    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  4  6  2  0  0  0  0
  2  7  1  0  0  0  0
  7  8  1  0  0  0  0
  7  9  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0303950

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C4H6O5/c5-2(4(8)9)1-3(6)7/h2,5H,1H2,(H,6,7)(H,8,9)/t2-/m1/s1

> <INCHI_KEY>
BJEPYKJPYRNKOW-UWTATZPHSA-N

> <FORMULA>
C4H6O5

> <MOLECULAR_WEIGHT>
134.0874

> <EXACT_MASS>
134.021523302

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
15

> <JCHEM_AVERAGE_POLARIZABILITY>
10.926494198525464

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R)-2-hydroxybutanedioic acid

> <ALOGPS_LOGP>
-0.87

> <JCHEM_LOGP>
-1.1136414279999998

> <ALOGPS_LOGS>
0.21

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
5.127730317344291

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.1983571934669475

> <JCHEM_PKA_STRONGEST_BASIC>
-3.913035238851454

> <JCHEM_POLAR_SURFACE_AREA>
94.83000000000001

> <JCHEM_REFRACTIVITY>
24.8752

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.18e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
.+-.-malic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0303950 (.+-.-malic acid)

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PDB for NP0303950 (.+-.-malic acid)
HEADER    PROTEIN                                 04-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-20         0                                  
HETATM    1  O   UNK     0       3.644   3.644   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       3.644   2.104   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.976   2.104   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      -0.357   1.334   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0       0.976   3.644   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       4.977   1.334   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       6.311   2.104   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       4.977  -0.206   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    7                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4                                                            
CONECT    7    2    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7                                                            
MASTER        0    0    0    0    0    0    0    0    9    0   16    0
END

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3D PDB for NP0303950 (.+-.-malic acid)
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SMILES for NP0303950 (.+-.-malic acid)
O[C@H](CC(O)=O)C(O)=O
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INCHI for NP0303950 (.+-.-malic acid)
InChI=1S/C4H6O5/c5-2(4(8)9)1-3(6)7/h2,5H,1H2,(H,6,7)(H,8,9)/t2-/m1/s1
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View in JSmol
Synonyms
ValueSource
(+)-D-Malic acidChEBI
(R)-2-Hydroxybutanedioic acidChEBI
2-HYDROXY-succinIC ACIDChEBI
D-MalateKegg
(+)-D-MalateGenerator
(R)-2-HydroxybutanedioateGenerator
2-HYDROXY-succinateGenerator
(R)-MalateHMDB
(R)-Hydroxybutanedioic acidHMDB
D-(+)-Malic acidHMDB
D-Hydroxybutanedioic acidHMDB
Hydroxy-(R)-butanedioic acidHMDB
R-Malic acidHMDB
D-Malic acidChEBI
Chemical FormulaC4H6O5
Average Mass134.0874 Da
Monoisotopic Mass134.02152 Da
IUPAC Name(2R)-2-hydroxybutanedioic acid
Traditional Name.+-.-malic acid
CAS Registry NumberNot Available
SMILES
O[C@H](CC(O)=O)C(O)=O
InChI Identifier
InChI=1S/C4H6O5/c5-2(4(8)9)1-3(6)7/h2,5H,1H2,(H,6,7)(H,8,9)/t2-/m1/s1
InChI KeyBJEPYKJPYRNKOW-UWTATZPHSA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Arabidopsis thalianaLOTUS Database
Homalomena occultaLOTUS Database
Pogostemon cablinLOTUS Database
Salmonella entericaLOTUS Database
Trypanosoma bruceiLOTUS Database
Vaccinium macrocarponLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as beta hydroxy acids and derivatives. Beta hydroxy acids and derivatives are compounds containing a carboxylic acid substituted with a hydroxyl group on the C3 carbon atom.
KingdomOrganic compounds  
Super ClassOrganic acids and derivatives  
ClassHydroxy acids and derivatives  
Sub ClassBeta hydroxy acids and derivatives  
Direct ParentBeta hydroxy acids and derivatives  
Alternative Parents
Substituents
  • Short-chain hydroxy acid
    • 

  • Beta-hydroxy acid
    • 

  • Fatty acid
    • 

  • Dicarboxylic acid or derivatives
    • 

  • Alpha-hydroxy acid
    • 

  • Secondary alcohol
    • 

  • Carboxylic acid
    • 

  • Carboxylic acid derivative
    • 

  • Organic oxygen compound
    • 

  • Organic oxide
    • 

  • Hydrocarbon derivative
    • 

  • Organooxygen compound
    • 

  • Carbonyl group
    • 

  • Alcohol
    • 

  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic 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
logP-0.87ALOGPS
logP-1.1ChemAxon
logS0.21ALOGPS
pKa (Strongest Acidic)3.2ChemAxon
pKa (Strongest Basic)-3.9ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area94.83 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity24.88 m³·mol⁻¹ChemAxon
Polarizability10.93 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0031518  
DrugBank IDDB03499  
Phenol Explorer Compound IDNot Available
FoodDB IDFDB008115  
KNApSAcK IDNot Available
Chemspider ID83793  
KEGG Compound IDC00497  
BioCyc IDCPD-660  
BiGG IDNot Available
Wikipedia LinkMalic_acid  
METLIN IDNot Available
PubChem Compound92824  
PDB IDDMR  
ChEBI ID30796  
Good Scents IDNot Available
References
General References
  1. VISHWAKARMA P, LOTSPEICH WD: Excretion of D-malic acid in the chicken. Am J Physiol. 1960 Apr;198:824-8. doi: 10.1152/ajplegacy.1960.198.4.824. [PubMed:13842473  ] 
  2. LOTUS database [Link]