NP-MRD: Showing NP-Card for Homocitric acid (NP0087060)

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Record Information

Version

2.0

Created at

2022-05-11 16:38:49 UTC

Updated at

2022-05-11 16:38:49 UTC

NP-MRD ID

NP0087060

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Homocitric acid

Description

Homocitric acid, also known as homocitrate, belongs to the class of organic compounds known as tricarboxylic acids and derivatives. These are carboxylic acids containing exactly three carboxyl groups. The (R)-enantiomer of homocitric acid. Homocitric acid is an extremely weak basic (essentially neutral) compound (based on its pKa). Homocitric acid was first documented in 1994 (PMID: 7850997). Homocitric acid exists in all living species, ranging from bacteria to humans.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652310231917012D          

 14 13  0  0  0  0            999 V2000
 9993.1424 9992.7759    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9992.4284 9993.1882    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9991.7139 9992.7759    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9990.9992 9993.1882    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9990.2846 9992.7759    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9990.9992 9994.0128    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9993.8577 9993.1882    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9994.5730 9992.7759    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9995.2863 9993.1882    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9994.5730 9991.9517    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9993.1424 9991.9517    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9993.8577 9991.5381    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9992.4284 9991.5381    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9993.8577 9992.3634    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  7  1  0  0  0  0
  1 11  1  0  0  0  0
  1 14  1  6  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
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 10  2  0  0  0  0
 11 12  1  0  0  0  0
 11 13  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0087060

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C7H10O7/c8-4(9)1-2-7(14,6(12)13)3-5(10)11/h14H,1-3H2,(H,8,9)(H,10,11)(H,12,13)/t7-/m1/s1

> <INCHI_KEY>
XKJVEVRQMLKSMO-SSDOTTSWSA-N

> <FORMULA>
C7H10O7

> <MOLECULAR_WEIGHT>
206.1501

> <EXACT_MASS>
206.042652674

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
24

> <JCHEM_AVERAGE_POLARIZABILITY>
17.44345390081851

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R)-2-hydroxybutane-1,2,4-tricarboxylic acid

> <ALOGPS_LOGP>
-1.50

> <JCHEM_LOGP>
-1.0340262470000003

> <ALOGPS_LOGS>
-0.03

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-3

> <JCHEM_PKA>
3.9251914717112886

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.086703991163821

> <JCHEM_PKA_STRONGEST_BASIC>
-4.0751445556736625

> <JCHEM_POLAR_SURFACE_AREA>
132.13

> <JCHEM_REFRACTIVITY>
40.37890000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.91e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(R)-homocitric acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 23-OCT-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-OCT-19         0                                  
HETATM    1  C   UNK     0    8653.8668653.182   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0    8652.5338653.951   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0    8651.1998653.182   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0    8649.8658653.951   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0    8648.5318653.182   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0    8649.8658655.491   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0    8655.2018653.951   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0    8656.5368653.182   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0    8657.8688653.951   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0    8656.5368651.643   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0    8653.8668651.643   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0    8655.2018650.871   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0    8652.5338650.871   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0    8655.2018652.412   0.000  0.00  0.00           O+0
CONECT    1    2    7   11   14                                             
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4                                                            
CONECT    7    1    8                                                       
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8                                                            
CONECT   11    1   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11                                                            
CONECT   14    1                                                            
MASTER        0    0    0    0    0    0    0    0   14    0   26    0
END

View in JSmol

Synonyms

Value	Source
(R)-2-Hydroxy-1,2,4-butanetricarboxylic acid	ChEBI
(R)-2-Hydroxybutane-1,2,4-tricarboxylic acid	ChEBI
(R)-Homocitric acid	ChEBI
3-Hydroxy-3-carboxyadipic acid	ChEBI
Homocitrate	ChEBI
(R)-2-Hydroxy-1,2,4-butanetricarboxylate	Generator
(R)-2-Hydroxybutane-1,2,4-tricarboxylate	Generator
(R)-Homocitrate	Generator
3-Hydroxy-3-carboxyadipate	Generator
2-Hydroxybutane-1,2,4-tricarboxylate	HMDB
(2R)-2-Hydroxy-1,2,4-butanetricarboxylate	HMDB
(2R)-2-Hydroxy-1,2,4-butanetricarboxylic acid	HMDB
(±)-homocitrate	HMDB
(±)-homocitric acid	HMDB
2-Hydroxy-1,2,4-butanetricarboxylate	HMDB
2-Hydroxy-1,2,4-butanetricarboxylic acid	HMDB
Homocitric acid	HMDB

Chemical Formula

C₇H₁₀O₇

Average Mass

206.1501 Da

Monoisotopic Mass

206.04265 Da

IUPAC Name

(2R)-2-hydroxybutane-1,2,4-tricarboxylic acid

Traditional Name

(R)-homocitric acid

CAS Registry Number

Not Available

SMILES

OC(=O)CC[C@@](O)(CC(O)=O)C(O)=O

InChI Identifier

InChI=1S/C7H10O7/c8-4(9)1-2-7(14,6(12)13)3-5(10)11/h14H,1-3H2,(H,8,9)(H,10,11)(H,12,13)/t7-/m1/s1

InChI Key

XKJVEVRQMLKSMO-SSDOTTSWSA-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, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Anas platyrhynchos	FooDB	FooDB
Anatidae	FooDB	FooDB
Anser anser	FooDB	FooDB
Bison bison	FooDB	FooDB
Bos taurus	FooDB	FooDB
Bos taurus X Bison bison	FooDB	FooDB
Bubalus bubalis	FooDB	FooDB
Capra aegagrus hircus	FooDB	FooDB
Cervidae	FooDB	FooDB
Cervus canadensis	FooDB	FooDB
Columba	FooDB	FooDB
Columbidae	FooDB	FooDB
Dromaius novaehollandiae	FooDB	FooDB
Equus caballus	FooDB	FooDB
Gallus gallus	FooDB	FooDB
Lagopus muta	FooDB	FooDB
Leporidae	FooDB	FooDB
Lepus timidus	FooDB	FooDB
Melanitta fusca	FooDB	FooDB
Meleagris gallopavo	FooDB	FooDB
Numida meleagris	FooDB	FooDB
Odocoileus	FooDB	FooDB
Oryctolagus	FooDB	FooDB
Ovis aries	FooDB	FooDB
Phasianidae	FooDB	FooDB
Phasianus colchicus	FooDB	FooDB
Struthio camelus	FooDB	FooDB
Sus scrofa	FooDB	FooDB
Sus scrofa domestica	FooDB	FooDB

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as tricarboxylic acids and derivatives. These are carboxylic acids containing exactly three carboxyl groups.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Tricarboxylic acids and derivatives

Direct Parent

Tricarboxylic acids and derivatives

Alternative Parents

Substituents

Tricarboxylic acid or derivatives
Hydroxy acid
Alpha-hydroxy acid
Tertiary alcohol
Carboxylic acid
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Alcohol
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

homocitric acid (CHEBI:52222 )

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	-1.5	ALOGPS
logP	-1	ChemAxon
logS	-0.03	ALOGPS
pKa (Strongest Acidic)	3.09	ChemAxon
pKa (Strongest Basic)	-4.1	ChemAxon
Physiological Charge	-3	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	132.13 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	40.38 m³·mol⁻¹	ChemAxon
Polarizability	17.44 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

HMDB0003518

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB023186

KNApSAcK ID

Not Available

Chemspider ID

388564

KEGG Compound ID

C01251

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Homocitric acid

METLIN ID

6943

PubChem Compound

439459

PDB ID

Not Available

ChEBI ID

52222

Good Scents ID

Not Available

References

General References

van Rooyen JP, Mienie LJ, Erasmus E, de Wet WJ, Duran M, Wadman SK: Urinary excretion of homocitric acid and methylhomocitric acid in propionic acidaemia: minor metabolic products of the citrate synthase aldol condensation reaction. Clin Chim Acta. 1994 Oct 14;230(1):91-9. doi: 10.1016/0009-8981(94)90092-2. [PubMed:7850997 ]

Showing NP-Card for Homocitric acid (NP0087060)

MOL for NP0087060 (Homocitric acid)

3D MOL for NP0087060 (Homocitric acid)

3D SDF for NP0087060 (Homocitric acid)

3D-SDF for NP0087060 (Homocitric acid)

PDB for NP0087060 (Homocitric acid)

3D PDB for NP0087060 (Homocitric acid)

SMILES for NP0087060 (Homocitric acid)

INCHI for NP0087060 (Homocitric acid)

Structure for NP0087060 (Homocitric acid)

3D Structure for NP0087060 (Homocitric acid)