NP-MRD: Showing NP-Card for Imidazoleacetic acid riboside (NP0086948)

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Record Information

Version

1.0

Created at

2022-05-11 16:35:27 UTC

Updated at

2022-05-11 16:35:27 UTC

NP-MRD ID

NP0086948

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Imidazoleacetic acid riboside

Description

Imidazoleacetic acid riboside, also known as 1-ribosylimidazole-4-acetic acid or IAA-R, belongs to the class of organic compounds known as imidazole ribonucleosides and ribonucleotides. These are organic compounds in which the C-1 of a ribosyl moiety is N-linked to an imidazole ring. Nucleotides have a phosphate group linked to the C5 carbon of the ribose (or deoxyribose) moiety. This class does not contain benzimidazole nucleosides and nucleotides. It was first documented in 1995 (PMID: 7616240). Imidazoleacetic acid riboside is a very strong basic compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 32 33  0  0  0  0  0  0  0  0999 V2000
    4.7080    0.2635    1.6810 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7330    0.0502    0.4357 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2373    1.0456   -0.4065 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2490   -1.2053   -0.1617 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7709   -1.3106   -0.1171 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8574   -0.3038    0.1793 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6253   -0.8042    0.1016 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6025   -0.1454    0.3486 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.7023   -0.7702   -0.3003 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7030    0.0731    0.2085 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.0782   -0.3039   -0.1568 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3672   -0.3317   -1.5033 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2261    1.4085   -0.2813 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.7235    2.4628    0.4798 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7112    1.2789   -0.0779 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.3792    2.0949    1.0057 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7275   -2.1095   -0.2427 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0343   -2.3959   -0.3683 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.7083    1.9161   -0.5072 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6282   -2.0621    0.4796 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6034   -1.4233   -1.1703 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1226    0.7143    0.4284 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9125   -0.2050    1.4397 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5917   -0.0031    1.3121 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2719   -1.3210    0.2677 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7681    0.3737    0.4231 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1531   -0.9434   -1.6117 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4312    1.5427   -1.3401 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3259    2.0965    1.1846 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1562    1.5482   -0.9964 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1724    1.5859    1.6587 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0738   -2.8163   -0.4016 H   0  0  0  0  0  0  0  0  0  0  0  0
 12 11  1  0
 11 10  1  0
 10  9  1  0
  9  8  1  0
  8 15  1  0
 15 16  1  0
 15 13  1  0
 13 14  1  0
  8  7  1  0
  7 17  1  0
 17 18  2  0
 18  5  1  0
  5  4  1  0
  4  2  1  0
  2  3  1  0
  2  1  2  0
  5  6  2  0
 13 10  1  0
  6  7  1  0
 12 27  1  0
 11 25  1  0
 11 26  1  0
 10 24  1  1
  8 23  1  1
 15 30  1  6
 16 31  1  0
 13 28  1  6
 14 29  1  0
 17 32  1  0
  4 20  1  0
  4 21  1  0
  3 19  1  0
  6 22  1  0
M  END


  Mrv0541 02231219292D          

 18 19  0  0  1  0            999 V2000
   27.2188  -16.5705    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   25.0993  -16.3155    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   25.6539  -18.0225    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   28.2693  -17.9363    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   27.5982  -11.9025    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   26.2928  -12.4836    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   26.5514  -15.2606    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   26.1389  -13.9910    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   25.8839  -16.5705    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   26.1389  -17.3551    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   26.5514  -16.0856    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   26.9639  -17.3551    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   27.4488  -18.0225    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   27.2188  -14.7756    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   25.8839  -14.7756    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   26.9639  -13.9910    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   27.4488  -13.3235    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   27.1133  -12.5699    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1 11  1  0  0  0  0
  1 12  1  0  0  0  0
  9  2  1  1  0  0  0
 10  3  1  1  0  0  0
  4 13  1  0  0  0  0
  5 18  1  0  0  0  0
  6 18  2  0  0  0  0
 11  7  1  6  0  0  0
  7 14  1  0  0  0  0
  7 15  1  0  0  0  0
  8 15  2  0  0  0  0
  8 16  1  0  0  0  0
  9 10  1  0  0  0  0
  9 11  1  0  0  0  0
 10 12  1  0  0  0  0
 12 13  1  6  0  0  0
 14 16  2  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0086948

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C=NC(CC(O)=O)=C1

> <INCHI_IDENTIFIER>
InChI=1S/C10H14N2O6/c13-3-6-8(16)9(17)10(18-6)12-2-5(11-4-12)1-7(14)15/h2,4,6,8-10,13,16-17H,1,3H2,(H,14,15)/t6-,8-,9-,10-/m1/s1

> <INCHI_KEY>
AHPWEWASPTZMEK-PEBGCTIMSA-N

> <FORMULA>
C10H14N2O6

> <MOLECULAR_WEIGHT>
258.228

> <EXACT_MASS>
258.08518619

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_AVERAGE_POLARIZABILITY>
24.334607202972002

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-{1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1H-imidazol-4-yl}acetic acid

> <ALOGPS_LOGP>
-1.45

> <JCHEM_LOGP>
-2.9660430869288064

> <ALOGPS_LOGS>
-0.98

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
12.456212028133127

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.3958212012333453

> <JCHEM_PKA_STRONGEST_BASIC>
6.163633876430828

> <JCHEM_POLAR_SURFACE_AREA>
125.04

> <JCHEM_REFRACTIVITY>
56.544700000000006

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.70e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
ribosylimidazole acetic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  O   UNK     0      50.808 -30.932   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      46.852 -30.456   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      47.887 -33.642   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      52.769 -33.481   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0      51.517 -22.218   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0      49.080 -23.303   0.000  0.00  0.00           O+0
HETATM    7  N   UNK     0      49.563 -28.486   0.000  0.00  0.00           N+0
HETATM    8  N   UNK     0      48.793 -26.117   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0      48.317 -30.932   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      48.793 -32.396   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      49.563 -30.026   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      50.333 -32.396   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      51.238 -33.642   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      50.808 -27.581   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      48.317 -27.581   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      50.333 -26.117   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      51.238 -24.871   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      50.611 -23.464   0.000  0.00  0.00           C+0
CONECT    1   11   12                                                       
CONECT    2    9                                                            
CONECT    3   10                                                            
CONECT    4   13                                                            
CONECT    5   18                                                            
CONECT    6   18                                                            
CONECT    7   11   14   15                                                  
CONECT    8   15   16                                                       
CONECT    9    2   10   11                                                  
CONECT   10    3    9   12                                                  
CONECT   11    1    7    9                                                  
CONECT   12    1   10   13                                                  
CONECT   13    4   12                                                       
CONECT   14    7   16                                                       
CONECT   15    7    8                                                       
CONECT   16    8   14   17                                                  
CONECT   17   16   18                                                       
CONECT   18    5    6   17                                                  
MASTER        0    0    0    0    0    0    0    0   18    0   38    0
END

View in JSmol

Synonyms

Value	Source
Imidazoleacetate riboside	Generator
1-b-D-Ribofuranosyl-imidazole-4-acetic acid	HMDB
1-beta-delta-Ribofuranosyl-imidazole-4-acetic acid	HMDB
1-Ribosylimidazole-4-acetic acid	HMDB
Ribosylimidazole acetic acid	HMDB
Ribosylimidazoleacetate	HMDB
IAA-R	HMDB
Ribosylimidazole-4-acetic acid	HMDB
(1-Ribosylimidazole)-4-acetic acid	HMDB
Imidazoleacetic acid riboside	MeSH

Chemical Formula

C₁₀H₁₄N₂O₆

Average Mass

258.2280 Da

Monoisotopic Mass

258.08519 Da

IUPAC Name

2-{1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1H-imidazol-4-yl}acetic acid

Traditional Name

ribosylimidazole acetic acid

CAS Registry Number

Not Available

SMILES

OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C=NC(CC(O)=O)=C1

InChI Identifier

InChI=1S/C10H14N2O6/c13-3-6-8(16)9(17)10(18-6)12-2-5(11-4-12)1-7(14)15/h2,4,6,8-10,13,16-17H,1,3H2,(H,14,15)/t6-,8-,9-,10-/m1/s1

InChI Key

AHPWEWASPTZMEK-PEBGCTIMSA-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 imidazole ribonucleosides and ribonucleotides. These are organic compounds in which the C-1 of a ribosyl moiety is N-linked to an imidazole ring. Nucleotides have a phosphate group linked to the C5 carbon of the ribose (or deoxyribose) moiety. This class does not contain benzimidazole nucleosides and nucleotides.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Imidazole ribonucleosides and ribonucleotides

Sub Class

Not Available

Direct Parent

Imidazole ribonucleosides and ribonucleotides

Alternative Parents

Substituents

Imidazole ribonucleoside
Glycosyl compound
N-glycosyl compound
Pentose monosaccharide
Imidazolyl carboxylic acid derivative
Monosaccharide
N-substituted imidazole
Azole
Imidazole
Heteroaromatic compound
Tetrahydrofuran
Secondary alcohol
Carboxylic acid derivative
Carboxylic acid
Oxacycle
Monocarboxylic acid or derivatives
Azacycle
Organoheterocyclic compound
Organic nitrogen compound
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Organic oxygen compound
Carbonyl group
Alcohol
Organonitrogen compound
Organooxygen compound
Primary alcohol
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

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	-1.4	ALOGPS
logP	-3	ChemAxon
logS	-0.98	ALOGPS
pKa (Strongest Acidic)	3.4	ChemAxon
pKa (Strongest Basic)	6.16	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	125.04 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	56.54 m³·mol⁻¹	ChemAxon
Polarizability	24.33 Å³	ChemAxon
Number of Rings	2	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

HMDB0002331

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB022964

KNApSAcK ID

Not Available

Chemspider ID

389469

KEGG Compound ID

C05131

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

6626

PubChem Compound

440569

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Thomas B, Prell GD: Imidazoleacetic acid, a gamma-aminobutyric acid receptor agonist, can be formed in rat brain by oxidation of histamine. J Neurochem. 1995 Aug;65(2):818-26. doi: 10.1046/j.1471-4159.1995.65020818.x. [PubMed:7616240 ]

Showing NP-Card for Imidazoleacetic acid riboside (NP0086948)

MOL for NP0086948 (Imidazoleacetic acid riboside)

3D MOL for NP0086948 (Imidazoleacetic acid riboside)

3D SDF for NP0086948 (Imidazoleacetic acid riboside)

3D-SDF for NP0086948 (Imidazoleacetic acid riboside)

PDB for NP0086948 (Imidazoleacetic acid riboside)

3D PDB for NP0086948 (Imidazoleacetic acid riboside)

SMILES for NP0086948 (Imidazoleacetic acid riboside)

INCHI for NP0086948 (Imidazoleacetic acid riboside)

Structure for NP0086948 (Imidazoleacetic acid riboside)

3D Structure for NP0086948 (Imidazoleacetic acid riboside)