Showing NP-Card for cis-Aconitic acid (NP0000811)

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Record Information
Version2.0
Created at2005-11-16 15:48:42 UTC
Updated at2021-08-19 23:58:29 UTC
NP-MRD IDNP0000811
Secondary Accession NumbersNone
Natural Product Identification
Common Namecis-Aconitic acid
DescriptionCis-Aconitic acid is an intermediate in the tricarboxylic acid cycle produced by the dehydration of citric acid. The enzyme aconitase (aconitate hydratase; EC 4.2.1.3) Catalyses the stereo-specific isomerization of citrate to isocitrate via cis-aconitate in the tricarboxylic acid cycle.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0000811 (cis-Aconitic acid)

cis-Aconitic acid.mol
  Mrv1652309032023512D          

 12 11  0  0  0  0            999 V2000
    1.4289   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  1  7  2  0  0  0  0
  1  8  1  0  0  0  0
  4  9  2  0  0  0  0
  4 10  1  0  0  0  0
  6 11  2  0  0  0  0
  6 12  1  0  0  0  0
M  END
Download

3D MOL for NP0000811 (cis-Aconitic acid)

HMDB0000072
     RDKit          3D
cis-Aconitic acid
 18 17  0  0  0  0  0  0  0  0999 V2000
   -2.7888   -1.5143   -1.7892 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1240   -0.5858   -1.1948 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6224    0.6546   -1.3609 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9605   -0.9479   -0.4416 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1584   -0.1745    0.2255 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0013   -0.8291    0.9339 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2877   -0.3142    0.4506 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3324   -0.7860    0.9680 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4224    0.6514   -0.5321 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3162    1.2307    0.3189 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1773    1.9348   -0.1757 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6361    1.9623    1.0839 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5941    0.8826   -1.5185 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7158   -2.0569   -0.4325 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9438   -0.5671    2.0316 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9579   -1.9222    0.8901 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4068    0.4152   -1.5331 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4691    1.9662    2.0758 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  7  9  1  0
  5 10  1  0
 10 11  2  0
 10 12  1  0
  3 13  1  0
  4 14  1  0
  6 15  1  0
  6 16  1  0
  9 17  1  0
 12 18  1  0
M  END
Download

3D SDF for NP0000811 (cis-Aconitic acid)

cis-Aconitic acid.mol
  Mrv1652309032023512D          

 12 11  0  0  0  0            999 V2000
    1.4289   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  1  7  2  0  0  0  0
  1  8  1  0  0  0  0
  4  9  2  0  0  0  0
  4 10  1  0  0  0  0
  6 11  2  0  0  0  0
  6 12  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0000811

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC(=O)C\C(=C\C(O)=O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C6H6O6/c7-4(8)1-3(6(11)12)2-5(9)10/h1H,2H2,(H,7,8)(H,9,10)(H,11,12)/b3-1-

> <INCHI_KEY>
GTZCVFVGUGFEME-IWQZZHSRSA-N

> <FORMULA>
C6H6O6

> <MOLECULAR_WEIGHT>
174.1082

> <EXACT_MASS>
174.016437924

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
18

> <JCHEM_AVERAGE_POLARIZABILITY>
14.15997033984106

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1Z)-prop-1-ene-1,2,3-tricarboxylic acid

> <ALOGPS_LOGP>
-0.41

> <JCHEM_LOGP>
-0.521036942

> <ALOGPS_LOGS>
-1.41

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-3

> <JCHEM_PKA>
3.727127446992898

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.106091815369544

> <JCHEM_POLAR_SURFACE_AREA>
111.89999999999999

> <JCHEM_REFRACTIVITY>
35.2305

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.72e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
cis-aconitic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0000811 (cis-Aconitic acid)

HMDB0000072
     RDKit          3D
cis-Aconitic acid
 18 17  0  0  0  0  0  0  0  0999 V2000
   -2.7888   -1.5143   -1.7892 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1240   -0.5858   -1.1948 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6224    0.6546   -1.3609 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9605   -0.9479   -0.4416 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1584   -0.1745    0.2255 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0013   -0.8291    0.9339 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2877   -0.3142    0.4506 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3324   -0.7860    0.9680 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4224    0.6514   -0.5321 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3162    1.2307    0.3189 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1773    1.9348   -0.1757 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6361    1.9623    1.0839 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5941    0.8826   -1.5185 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7158   -2.0569   -0.4325 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9438   -0.5671    2.0316 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9579   -1.9222    0.8901 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4068    0.4152   -1.5331 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4691    1.9662    2.0758 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  7  9  1  0
  5 10  1  0
 10 11  2  0
 10 12  1  0
  3 13  1  0
  4 14  1  0
  6 15  1  0
  6 16  1  0
  9 17  1  0
 12 18  1  0
M  END
Download

PDB for NP0000811 (cis-Aconitic acid)

HEADER    PROTEIN                                 03-SEP-20   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: cis-Aconitic acid.mol                             
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-SEP-20         0                                  
HETATM    1  C   UNK     0       2.667  -0.770   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.334  -1.540   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000  -0.770   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.770   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -1.334  -1.540   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -2.667  -0.770   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       2.667   0.770   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       4.001  -1.540   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      -1.334   1.540   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       1.334   1.540   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0      -2.667   0.770   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      -4.001  -1.540   0.000  0.00  0.00           O+0
CONECT    1    2    7    8                                                  
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3    9   10                                                  
CONECT    5    3    6                                                       
CONECT    6    5   11   12                                                  
CONECT    7    1                                                            
CONECT    8    1                                                            
CONECT    9    4                                                            
CONECT   10    4                                                            
CONECT   11    6                                                            
CONECT   12    6                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   22    0
END
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3D PDB for NP0000811 (cis-Aconitic acid)

COMPND    HMDB0000072
HETATM    1  O1  UNL     1      -2.789  -1.514  -1.789  1.00  0.00           O  
HETATM    2  C1  UNL     1      -2.124  -0.586  -1.195  1.00  0.00           C  
HETATM    3  O2  UNL     1      -2.622   0.655  -1.361  1.00  0.00           O  
HETATM    4  C2  UNL     1      -0.961  -0.948  -0.442  1.00  0.00           C  
HETATM    5  C3  UNL     1      -0.158  -0.174   0.225  1.00  0.00           C  
HETATM    6  C4  UNL     1       1.001  -0.829   0.934  1.00  0.00           C  
HETATM    7  C5  UNL     1       2.288  -0.314   0.451  1.00  0.00           C  
HETATM    8  O3  UNL     1       3.332  -0.786   0.968  1.00  0.00           O  
HETATM    9  O4  UNL     1       2.422   0.651  -0.532  1.00  0.00           O  
HETATM   10  C6  UNL     1      -0.316   1.231   0.319  1.00  0.00           C  
HETATM   11  O5  UNL     1      -1.177   1.935  -0.176  1.00  0.00           O  
HETATM   12  O6  UNL     1       0.636   1.962   1.084  1.00  0.00           O  
HETATM   13  H1  UNL     1      -3.594   0.883  -1.518  1.00  0.00           H  
HETATM   14  H2  UNL     1      -0.716  -2.057  -0.432  1.00  0.00           H  
HETATM   15  H3  UNL     1       0.944  -0.567   2.032  1.00  0.00           H  
HETATM   16  H4  UNL     1       0.958  -1.922   0.890  1.00  0.00           H  
HETATM   17  H5  UNL     1       2.407   0.415  -1.533  1.00  0.00           H  
HETATM   18  H6  UNL     1       0.469   1.966   2.076  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3   13
CONECT    4    5    5   14
CONECT    5    6   10
CONECT    6    7   15   16
CONECT    7    8    8    9
CONECT    9   17
CONECT   10   11   11   12
CONECT   12   18
END
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SMILES for NP0000811 (cis-Aconitic acid)

OC(=O)C\C(=C\C(O)=O)C(O)=O
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INCHI for NP0000811 (cis-Aconitic acid)

InChI=1S/C6H6O6/c7-4(8)1-3(6(11)12)2-5(9)10/h1H,2H2,(H,7,8)(H,9,10)(H,11,12)/b3-1-
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View in JSmol
Synonyms
Chemical FormulaC6H6O6
Average Mass174.1082 Da
Monoisotopic Mass174.01644 Da
IUPAC Name(1Z)-prop-1-ene-1,2,3-tricarboxylic acid
Traditional Namecis-aconitic acid
CAS Registry Number585-84-2
SMILES
OC(=O)C\C(=C\C(O)=O)C(O)=O
InChI Identifier
InChI=1S/C6H6O6/c7-4(8)1-3(6(11)12)2-5(9)10/h1H,2H2,(H,7,8)(H,9,10)(H,11,12)/b3-1-
InChI KeyGTZCVFVGUGFEME-IWQZZHSRSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species Where Detected
Species NameSourceReference
Homo sapiens (Urine)KNApSAcK Database
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.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassTricarboxylic acids and derivatives
Direct ParentTricarboxylic acids and derivatives
Alternative Parents
Substituents
  • Tricarboxylic acid or derivatives
  • Carboxylic acid
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Carbonyl group
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point125 °CNot Available
Boiling Point542.00 to 543.00 °C. @ 760.00 mm HgThe Good Scents Company Information System
Water Solubility400 mg/mLNot Available
LogP-0.140The Good Scents Company Information System
Predicted Properties
PropertyValueSource
Water Solubility6.72 g/LALOGPS
logP-0.41ALOGPS
logP-0.52ChemAxon
logS-1.4ALOGPS
pKa (Strongest Acidic)2.11ChemAxon
Physiological Charge-3ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area111.9 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity35.23 m³·mol⁻¹ChemAxon
Polarizability14.16 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0000072
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB030729
KNApSAcK IDC00001177
Chemspider ID558863
KEGG Compound IDC00417
BioCyc IDCIS-ACONITATE
BiGG IDNot Available
Wikipedia LinkCitric acid cycle
METLIN ID5130
PubChem Compound643757
PDB IDNot Available
ChEBI ID32805
Good Scents IDrw1057191
References
General References
  1. Swart PJ, Kuipers EM, Smit C, Van Der Strate BW, Harmsen MC, Meijer DK: Lactoferrin. Antiviral activity of lactoferrin. Adv Exp Med Biol. 1998;443:205-13. [PubMed:9781360 ]
  2. Stromme JH, Borud O, Moe PJ: Fatal lactic acidosis in a newborn attributable to a congenital defect of pyruvate dehydrogenase. Pediatr Res. 1976 Jan;10(1):62-6. [PubMed:813176 ]
  3. Swart PJ, Kuipers ME, Smit C, Pauwels R, deBethune MP, de Clercq E, Meijer DK, Huisman JG: Antiviral effects of milk proteins: acylation results in polyanionic compounds with potent activity against human immunodeficiency virus types 1 and 2 in vitro. AIDS Res Hum Retroviruses. 1996 Jun 10;12(9):769-75. [PubMed:8738428 ]
  4. Matsuishi T, Urabe F, Percy AK, Komori H, Yamashita Y, Schultz RS, Ohtani Y, Kuriya N, Kato H: Abnormal carbohydrate metabolism in cerebrospinal fluid in Rett syndrome. J Child Neurol. 1994 Jan;9(1):26-30. [PubMed:8151077 ]