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Showing NP-Card for R-(-)-Citramalic acid (NP0002736)

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Record Information
Version1.0
Created at2020-11-23 19:39:09 UTC
Updated at2021-08-12 19:52:00 UTC
NP-MRD IDNP0002736
Secondary Accession NumbersNone
Natural Product Identification
Common NameR-(-)-Citramalic acid
Provided ByBMRBBMRB logo
Description(R)-Citramalate is also known as D-citramalic acid. R-(-)-Citramalic acid is found in Arabidopsis thaliana, Hylocereus undatus, Lotus corniculatus and Lotus uliginosus. It was first documented in 2008 (PMID: 17984079). Based on a literature review a significant number of articles have been published on (R)-Citramalate (PMID: 30830363) (PMID: 29231156) (PMID: 28744578) (PMID: 25240212) (PMID: 24113828) (PMID: 22033339).
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0002736 (R-(-)-Citramalic acid)


     RDKit          2D

 18 17  0  0  0  0  0  0  0  0999 V2000
    1.9206    0.7454    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4651    0.3826    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1023    1.8380    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9903    0.0197    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4458   -0.3431    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8593   -1.7850    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4878    0.7359    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8279   -1.0729    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1160   -2.2386    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2698   -1.4864    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7378    2.2342    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6248   -0.5790    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3760    1.1082    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0463    3.0037    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8076   -1.4691    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3532    1.4752    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9432    0.3731    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6327   -2.9419    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  1
  2  4  1  0
  4  5  1  0
  5  6  2  0
  5  7  1  0
  2  8  1  0
  8  9  2  0
  8 10  1  0
  1 11  1  1
  1 12  1  0
  1 13  1  0
  3 14  1  0
  4 15  1  6
  4 16  1  0
  7 17  1  0
 10 18  1  0
M  END
Download

3D MOL for NP0002736 (R-(-)-Citramalic acid)

NP0002736
     RDKit          3D

 18 17  0  0  0  0  0  0  0  0999 V2000
   -1.2455   -1.4475    0.1718 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4940   -0.1089    0.1594 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7463    0.5755    1.3617 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9588   -0.4217    0.1018 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8331    0.7472    0.0829 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3419    1.8995    0.1146 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2103    0.6329    0.0304 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9951    0.6539   -0.9809 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8757    0.2294   -2.1471 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6156    1.8713   -0.7770 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0230   -1.9031   -0.8289 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3298   -1.2637    0.2774 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8398   -2.0750    0.9912 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7183    0.5202    1.5585 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1701   -1.0838   -0.7662 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2044   -1.0416    1.0055 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6021   -0.2166   -0.3994 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4375    2.4319    0.0444 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  1
  2  4  1  0
  4  5  1  0
  5  6  2  0
  5  7  1  0
  2  8  1  0
  8  9  2  0
  8 10  1  0
  1 11  1  0
  1 12  1  0
  1 13  1  0
  3 14  1  0
  4 15  1  0
  4 16  1  0
  7 17  1  0
 10 18  1  0
M  END
Download

3D SDF for NP0002736 (R-(-)-Citramalic acid)


     RDKit          2D

 18 17  0  0  0  0  0  0  0  0999 V2000
    1.9206    0.7454    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4651    0.3826    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1023    1.8380    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9903    0.0197    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4458   -0.3431    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8593   -1.7850    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4878    0.7359    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8279   -1.0729    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1160   -2.2386    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2698   -1.4864    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7378    2.2342    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6248   -0.5790    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3760    1.1082    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0463    3.0037    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8076   -1.4691    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3532    1.4752    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9432    0.3731    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6327   -2.9419    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  1
  2  4  1  0
  4  5  1  0
  5  6  2  0
  5  7  1  0
  2  8  1  0
  8  9  2  0
  8 10  1  0
  1 11  1  1
  1 12  1  0
  1 13  1  0
  3 14  1  0
  4 15  1  6
  4 16  1  0
  7 17  1  0
 10 18  1  0
M  END
> <DATABASE_ID>
NP0002736

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H8O5/c1-5(10,4(8)9)2-3(6)7/h10H,2H2,1H3,(H,6,7)(H,8,9)/t5-/m1/s1

> <INCHI_KEY>
XFTRTWQBIOMVPK-RXMQYKEDSA-N

> <FORMULA>
C5H8O5

> <MOLECULAR_WEIGHT>
148.114

> <EXACT_MASS>
148.037173366

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
18

> <JCHEM_AVERAGE_POLARIZABILITY>
12.717410457646801

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R)-2-hydroxy-2-methylbutanedioic acid

> <ALOGPS_LOGP>
-0.91

> <JCHEM_LOGP>
-0.6808755420000001

> <ALOGPS_LOGS>
0.30

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
5.3015290068332295

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.3477157472119226

> <JCHEM_PKA_STRONGEST_BASIC>
-3.967730895376275

> <JCHEM_POLAR_SURFACE_AREA>
94.83

> <JCHEM_REFRACTIVITY>
29.5885

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.97e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
D-citramalic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0002736 (R-(-)-Citramalic acid)

NP0002736
     RDKit          3D

 18 17  0  0  0  0  0  0  0  0999 V2000
   -1.2455   -1.4475    0.1718 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4940   -0.1089    0.1594 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7463    0.5755    1.3617 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9588   -0.4217    0.1018 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8331    0.7472    0.0829 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3419    1.8995    0.1146 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2103    0.6329    0.0304 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9951    0.6539   -0.9809 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8757    0.2294   -2.1471 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6156    1.8713   -0.7770 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0230   -1.9031   -0.8289 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3298   -1.2637    0.2774 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8398   -2.0750    0.9912 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7183    0.5202    1.5585 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1701   -1.0838   -0.7662 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2044   -1.0416    1.0055 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6021   -0.2166   -0.3994 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4375    2.4319    0.0444 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  1
  2  4  1  0
  4  5  1  0
  5  6  2  0
  5  7  1  0
  2  8  1  0
  8  9  2  0
  8 10  1  0
  1 11  1  0
  1 12  1  0
  1 13  1  0
  3 14  1  0
  4 15  1  0
  4 16  1  0
  7 17  1  0
 10 18  1  0
M  END
Download

PDB for NP0002736 (R-(-)-Citramalic acid)

HEADER    PROTEIN                                 08-MAR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   08-MAR-20         0                                  
HETATM    1  C   UNK     0       3.080   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.540   1.540   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.206   2.310   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.540  -1.540   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       0.206   3.850   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0      -1.127   1.540   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       2.874  -2.310   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       0.206  -2.310   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
CONECT    1    5                                                            
CONECT    2    3    5                                                       
CONECT    3    2    6    7                                                  
CONECT    4    5    8    9                                                  
CONECT    5    1    2    4   10                                             
CONECT    6    3                                                            
CONECT    7    3                                                            
CONECT    8    4                                                            
CONECT    9    4                                                            
CONECT   10    5                                                            
MASTER        0    0    0    0    0    0    0    0   10    0   18    0
END
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3D PDB for NP0002736 (R-(-)-Citramalic acid)

COMPND    NP0002736
HETATM    1  C1  UNL     1      -1.245  -1.448   0.172  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.494  -0.109   0.159  1.00  0.00           C  
HETATM    3  O1  UNL     1      -0.746   0.576   1.362  1.00  0.00           O  
HETATM    4  C3  UNL     1       0.959  -0.422   0.102  1.00  0.00           C  
HETATM    5  C4  UNL     1       1.833   0.747   0.083  1.00  0.00           C  
HETATM    6  O2  UNL     1       1.342   1.900   0.115  1.00  0.00           O  
HETATM    7  O3  UNL     1       3.210   0.633   0.030  1.00  0.00           O  
HETATM    8  C5  UNL     1      -0.995   0.654  -0.981  1.00  0.00           C  
HETATM    9  O4  UNL     1      -0.876   0.229  -2.147  1.00  0.00           O  
HETATM   10  O5  UNL     1      -1.616   1.871  -0.777  1.00  0.00           O  
HETATM   11  H1  UNL     1      -1.023  -1.903  -0.829  1.00  0.00           H  
HETATM   12  H2  UNL     1      -2.330  -1.264   0.277  1.00  0.00           H  
HETATM   13  H3  UNL     1      -0.840  -2.075   0.991  1.00  0.00           H  
HETATM   14  H4  UNL     1      -1.718   0.520   1.558  1.00  0.00           H  
HETATM   15  H5  UNL     1       1.170  -1.084  -0.766  1.00  0.00           H  
HETATM   16  H6  UNL     1       1.204  -1.042   1.006  1.00  0.00           H  
HETATM   17  H7  UNL     1       3.602  -0.217  -0.399  1.00  0.00           H  
HETATM   18  H8  UNL     1      -1.437   2.432   0.044  1.00  0.00           H  
CONECT    1    2   11   12   13
CONECT    2    3    4    8
CONECT    3   14
CONECT    4    5   15   16
CONECT    5    6    6    7
CONECT    7   17
CONECT    8    9    9   10
CONECT   10   18
END
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SMILES for NP0002736 (R-(-)-Citramalic acid)

C[C@@](O)(CC(O)=O)C(O)=O
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INCHI for NP0002736 (R-(-)-Citramalic acid)

InChI=1S/C5H8O5/c1-5(10,4(8)9)2-3(6)7/h10H,2H2,1H3,(H,6,7)(H,8,9)/t5-/m1/s1
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View in JSmol
Synonyms
ValueSource
(2R)-2-Hydroxy-2-methylbutanedioateChEBI
(2R)-2-Hydroxy-2-methylsuccinic acidChEBI
(3R)-alpha-Hydroxypyrotartaric acidChEBI
(3R)-Citramalic acidChEBI
(R)-2-Methylmalic acidChEBI
D-(-)-2-Methylmalic acidChEBI
D-alpha-Hydroxypyrotartaric acidChEBI
(R)-Citramalic acidKegg
(R)-alpha-Hydroxypyrotartaric acidKegg
D-CitramalateKegg
D-Citramalic acidKegg
(2R)-2-Hydroxy-2-methylbutanedioic acidGenerator
(2R)-2-Hydroxy-2-methylsuccinateGenerator
(3R)-a-HydroxypyrotartarateGenerator
(3R)-a-Hydroxypyrotartaric acidGenerator
(3R)-alpha-HydroxypyrotartarateGenerator
(3R)-Α-hydroxypyrotartarateGenerator
(3R)-Α-hydroxypyrotartaric acidGenerator
(3R)-CitramalateGenerator
(R)-2-MethylmalateGenerator
D-(-)-2-MethylmalateGenerator
D-a-HydroxypyrotartarateGenerator
D-a-Hydroxypyrotartaric acidGenerator
D-alpha-HydroxypyrotartarateGenerator
D-Α-hydroxypyrotartarateGenerator
D-Α-hydroxypyrotartaric acidGenerator
(R)-a-HydroxypyrotartarateGenerator
(R)-a-Hydroxypyrotartaric acidGenerator
(R)-alpha-HydroxypyrotartarateGenerator
(R)-Α-hydroxypyrotartarateGenerator
(R)-Α-hydroxypyrotartaric acidGenerator
Chemical FormulaC5H8O5
Average Mass148.1140 Da
Monoisotopic Mass148.03717 Da
IUPAC Name(2R)-2-hydroxy-2-methylbutanedioic acid
Traditional NameD-citramalic acid
CAS Registry NumberNot Available
SMILES
C[C@@](O)(CC(O)=O)C(O)=O
InChI Identifier
InChI=1S/C5H8O5/c1-5(10,4(8)9)2-3(6)7/h10H,2H2,1H3,(H,6,7)(H,8,9)/t5-/m1/s1
InChI KeyXFTRTWQBIOMVPK-RXMQYKEDSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Arabidopsis thalianaLOTUS Database
Hylocereus undatusLOTUS Database
Lotus corniculatusLOTUS Database
Lotus uliginosusLOTUS Database
Chemical Taxonomy
DescriptionThis compound belongs to the class of organic compounds known as hydroxy fatty acids. These are fatty acids in which the chain bears a hydroxyl group.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassFatty Acyls
Sub ClassFatty acids and conjugates
Direct ParentHydroxy fatty acids
Alternative Parents
Substituents
  • Branched fatty acid
  • Methyl-branched fatty acid
  • Short-chain hydroxy acid
  • Hydroxy fatty acid
  • Alpha-hydroxy acid
  • Dicarboxylic acid or derivatives
  • Hydroxy acid
  • Tertiary alcohol
  • Carboxylic acid
  • Carboxylic acid derivative
  • Alcohol
  • Hydrocarbon derivative
  • Carbonyl group
  • Organic oxide
  • Organic oxygen compound
  • Organooxygen compound
  • 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-0.91ALOGPS
logP-0.68ChemAxon
logS0.3ALOGPS
pKa (Strongest Acidic)3.35ChemAxon
pKa (Strongest Basic)-4ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area94.83 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity29.59 m³·mol⁻¹ChemAxon
Polarizability12.72 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
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Chemspider ID388822
KEGG Compound IDC02612
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ChEBI ID15586
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References
General References
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  2. Putri SP, Nakayama Y, Shen C, Noguchi S, Nitta K, Bamba T, Pontrelli S, Liao J, Fukusaki E: Identifying metabolic elements that contribute to productivity of 1-propanol bioproduction using metabolomic analysis. Metabolomics. 2018 Jul 4;14(7):96. doi: 10.1007/s11306-018-1386-0. [PubMed:30830363 ]
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  4. Wu X, Eiteman MA: Synthesis of citramalic acid from glycerol by metabolically engineered Escherichia coli. J Ind Microbiol Biotechnol. 2017 Oct;44(10):1483-1490. doi: 10.1007/s10295-017-1971-7. Epub 2017 Jul 25. [PubMed:28744578 ]
  5. Chen CY, Chen ML, Chen HB, Wang H, Cramer SP, Zhou ZH: alpha-Hydroxy coordination of mononuclear vanadyl citrate, malate and S-citramalate with N-heterocycle ligand, implying a new protonation pathway of iron-vanadium cofactor in nitrogenase. J Inorg Biochem. 2014 Dec;141:114-120. doi: 10.1016/j.jinorgbio.2014.08.003. Epub 2014 Aug 11. [PubMed:25240212 ]
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  7. Frantom PA: Structural and functional characterization of alpha-isopropylmalate synthase and citramalate synthase, members of the LeuA dimer superfamily. Arch Biochem Biophys. 2012 Mar 15;519(2):202-9. doi: 10.1016/j.abb.2011.10.009. Epub 2011 Oct 19. [PubMed:22033339 ]
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