NP-MRD: Showing NP-Card for Indolepyruvate (NP0001305)

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Record Information

Version

1.0

Created at

2013-05-17 01:24:10 UTC

Updated at

2021-08-19 23:59:00 UTC

NP-MRD ID

NP0001305

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Indolepyruvate

Description

The thiamin diphosphate (ThDP)-dependent enzyme indolepyruvate decarboxylase (IPDC) is involved in the biosynthetic pathway of the phytohormone 3-indoleacetic acid and catalyzes the nonoxidative decarboxylation of 3-indolepyruvate to 3-indoleacetaldehyde and carbon dioxide. (PMID:15835904 )¬† In addition, the enzyme was compared with the phenylpyruvate decarboxylase from Azospirillum brasilense and the indolepyruvate decarboxylase from Enterobacter cloacae. (PMID:21501384 ) Indole-3-pyruvate is a microbial metabolite, urinary indole-3-pyruvate is produced by Clostridium sporogenes (PMID:29168502 ) And Trypanasoma brucei (PMID:27856732 ).

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI


  Mrv1652307222018322D          

 15 16  0  0  0  0            999 V2000
   -1.6433    0.2558    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8982   -0.5288    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3462   -1.1418    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5392   -0.9704    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4239    1.1418    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8363    0.4273    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2843   -0.1857    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4693    0.1498    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3830    0.9702    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1838   -0.2626    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8982    0.1498    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8982    0.9748    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6127   -0.2626    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6127   -1.0876    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3271    0.1499    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  5  6  1  0  0  0  0
  5  9  1  0  0  0  0
  8 10  1  0  0  0  0
  4  7  1  0  0  0  0
  6  1  1  0  0  0  0
 13 14  2  0  0  0  0
 13 15  1  0  0  0  0
 10 11  1  0  0  0  0
 11 13  1  0  0  0  0
 11 12  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0001305

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC(=O)C(=O)CC1=CNC2=C1C=CC=C2

> <INCHI_IDENTIFIER>
InChI=1S/C11H9NO3/c13-10(11(14)15)5-7-6-12-9-4-2-1-3-8(7)9/h1-4,6,12H,5H2,(H,14,15)

> <INCHI_KEY>
RSTKLPZEZYGQPY-UHFFFAOYSA-N

> <FORMULA>
C11H9NO3

> <MOLECULAR_WEIGHT>
203.1941

> <EXACT_MASS>
203.058243159

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
24

> <JCHEM_AVERAGE_POLARIZABILITY>
19.72292001680295

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
3-(1H-indol-3-yl)-2-oxopropanoic acid

> <ALOGPS_LOGP>
1.71

> <JCHEM_LOGP>
1.9989757659999996

> <ALOGPS_LOGS>
-2.93

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
15.040628284598952

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.4941090875988134

> <JCHEM_PKA_STRONGEST_BASIC>
-9.759146672079298

> <JCHEM_POLAR_SURFACE_AREA>
70.16

> <JCHEM_REFRACTIVITY>
53.79810000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.37e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-(indol-3-yl)pyruvic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 22-JUL-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   22-JUL-20         0                                  
HETATM    1  C   UNK     0      -3.067   0.477   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -3.543  -0.987   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -2.513  -2.131   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -1.007  -1.811   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0      -0.791   2.131   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0      -1.561   0.798   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -0.531  -0.347   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.876   0.280   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.715   1.811   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.210  -0.490   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       3.543   0.280   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       3.543   1.820   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       4.877  -0.490   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       4.877  -2.030   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       6.211   0.280   0.000  0.00  0.00           O+0
CONECT    1    2    6                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    7                                                       
CONECT    5    6    9                                                       
CONECT    6    7    5    1                                                  
CONECT    7    6    8    4                                                  
CONECT    8    7    9   10                                                  
CONECT    9    8    5                                                       
CONECT   10    8   11                                                       
CONECT   11   10   13   12                                                  
CONECT   12   11                                                            
CONECT   13   14   15   11                                                  
CONECT   14   13                                                            
CONECT   15   13                                                            
MASTER        0    0    0    0    0    0    0    0   15    0   32    0
END

View in JSmol View NMR Assignments

Synonyms

Value	Source
Indole-3-pyruvic acid	ChEBI
Indolepyruvic acid	ChEBI
(indol-3-yl)Pyruvate	Kegg
Indole-3-pyruvate	Kegg
3-(indol-3-yl)Pyruvate	Kegg
(indol-3-yl)Pyruvic acid	Generator
3-(indol-3-yl)Pyruvic acid	Generator
indol-3-yl Pyruvic acid	HMDB
1H-Indole-3-pyruvic acid	HMDB
3-(1H-indol-3-yl)-2-Oxopropanoic acid	HMDB
3-(1H-indol-3-yl)-2-Oxopropionic acid	HMDB
3-(3-Indolyl)-2-oxopropanoic acid	HMDB
3-(3-Indolyl)-2-oxopropionic acid	HMDB
3-(3-Indolyl)pyruvic acid	HMDB
3-Indole-2-oxopropanoate	HMDB
3-Indole-2-oxopropionate	HMDB
3-Indolylpyroracemic acid	HMDB
3-Indolylpyruvic acid	HMDB
IPA	HMDB
Indolyl-3-pyruvate	HMDB
alpha-oxo-1H-Indole-3-propanoic acid	HMDB
alpha-oxo-1H-Indole-3-propionic acid	HMDB
beta-Indolepyruvic acid	HMDB
beta-Indolylpyruvic acid	HMDB
Α-oxo-1H-indole-3-propanoic acid	HMDB
Α-oxo-1H-indole-3-propionic acid	HMDB
Β-indolepyruvic acid	HMDB
Β-indolylpyruvic acid	HMDB
Indolepyruvate	HMDB, Generator

Chemical Formula

C₁₁H₉NO₃

Average Mass

203.1941 Da

Monoisotopic Mass

203.05824 Da

IUPAC Name

3-(1H-indol-3-yl)-2-oxopropanoic acid

Traditional Name

3-(indol-3-yl)pyruvic acid

CAS Registry Number

35656-49-6

SMILES

OC(=O)C(=O)CC1=CNC2=CC=CC=C12

InChI Identifier

InChI=1S/C11H9NO3/c13-10(11(14)15)5-7-6-12-9-4-2-1-3-8(7)9/h1-4,6,12H,5H2,(H,14,15)

InChI Key

RSTKLPZEZYGQPY-UHFFFAOYSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
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, 25 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	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, 50 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	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, 101 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	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, 151 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	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, 201 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
1D NMR	¹³C NMR Spectrum (1D, 226 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
Solanum lycopersicum	KNApSAcK Database	22123792
Trypanosoma brucei	LOTUS Database	35616633

Species Where Detected

Species Name	Source	Reference
Aspergillus nidulans	KNApSAcK Database	22123792
Aspergillus terreus	KNApSAcK Database	22123792

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as indolyl carboxylic acids and derivatives. Indolyl carboxylic acids and derivatives are compounds containing a carboxylic acid chain (of at least 2 carbon atoms) linked to an indole ring.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Indoles and derivatives

Sub Class

Indolyl carboxylic acids and derivatives

Direct Parent

Indolyl carboxylic acids and derivatives

Alternative Parents

Substituents

Indolyl carboxylic acid derivative
3-alkylindole
Indole
Alpha-keto acid
Keto acid
Substituted pyrrole
Benzenoid
Alpha-hydroxy ketone
Pyrrole
Heteroaromatic compound
Ketone
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Azacycle
Organic nitrogen compound
Organooxygen compound
Organonitrogen compound
Organic oxide
Organopnictogen compound
Organic oxygen compound
Carbonyl group
Hydrocarbon derivative
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

2-oxo monocarboxylic acid (CHEBI:29750 )
indol-3-yl carboxylic acid (CHEBI:29750 )

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	37160 mg/L @ 25 °C (est)	The Good Scents Company Information System
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
Water Solubility	0.24 g/L	ALOGPS
logP	1.71	ALOGPS
logP	2	ChemAxon
logS	-2.9	ALOGPS
pKa (Strongest Acidic)	3.49	ChemAxon
pKa (Strongest Basic)	-9.8	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	70.16 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	53.8 m³·mol⁻¹	ChemAxon
Polarizability	19.72 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

HMDB0060484

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

PDB ID

ChEBI ID

Good Scents ID

References

General References

Magrane M: UniProt Knowledgebase: a hub of integrated protein data. Database (Oxford). 2011 Mar 29;2011:bar009. doi: 10.1093/database/bar009. Print 2011. [PubMed:21447597 ]
Schutz A, Golbik R, Konig S, Hubner G, Tittmann K: Intermediates and transition states in thiamin diphosphate-dependent decarboxylases. A kinetic and NMR study on wild-type indolepyruvate decarboxylase and variants using indolepyruvate, benzoylformate, and pyruvate as substrates. Biochemistry. 2005 Apr 26;44(16):6164-79. [PubMed:15835904 ]
Kneen MM, Stan R, Yep A, Tyler RP, Saehuan C, McLeish MJ: Characterization of a thiamin diphosphate-dependent phenylpyruvate decarboxylase from Saccharomyces cerevisiae. FEBS J. 2011 Jun;278(11):1842-53. doi: 10.1111/j.1742-4658.2011.08103.x. Epub 2011 Apr 18. [PubMed:21501384 ]
Dodd D, Spitzer MH, Van Treuren W, Merrill BD, Hryckowian AJ, Higginbottom SK, Le A, Cowan TM, Nolan GP, Fischbach MA, Sonnenburg JL: A gut bacterial pathway metabolizes aromatic amino acids into nine circulating metabolites. Nature. 2017 Nov 30;551(7682):648-652. doi: 10.1038/nature24661. Epub 2017 Nov 22. [PubMed:29168502 ]
McGettrick AF, Corcoran SE, Barry PJ, McFarland J, Cres C, Curtis AM, Franklin E, Corr SC, Mok KH, Cummins EP, Taylor CT, O'Neill LA, Nolan DP: Trypanosoma brucei metabolite indolepyruvate decreases HIF-1alpha and glycolysis in macrophages as a mechanism of innate immune evasion. Proc Natl Acad Sci U S A. 2016 Nov 29;113(48):E7778-E7787. doi: 10.1073/pnas.1608221113. Epub 2016 Nov 15. [PubMed:27856732 ]

Showing NP-Card for Indolepyruvate (NP0001305)

MOL for NP0001305 (Indolepyruvate)

3D MOL for NP0001305 (Indolepyruvate)

3D SDF for NP0001305 (Indolepyruvate)

3D-SDF for NP0001305 (Indolepyruvate)

PDB for NP0001305 (Indolepyruvate)

3D PDB for NP0001305 (Indolepyruvate)

SMILES for NP0001305 (Indolepyruvate)

INCHI for NP0001305 (Indolepyruvate)

Structure for NP0001305 (Indolepyruvate)

3D Structure for NP0001305 (Indolepyruvate)