NP-MRD: Showing NP-Card for Ibotenic acid (NP0004872)

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Record Information

Version

2.0

Created at

2020-12-09 02:16:36 UTC

Updated at

2021-08-19 23:59:36 UTC

NP-MRD ID

NP0004872

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Ibotenic acid

Provided By

NPAtlas

Description

Ibotenic acid, also known as ibotenate or acid, ibotenic, belongs to the class of organic compounds known as alpha amino acids. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon). Ibotenic acid is found in Amanita muscaria and Amanita parcivolvata. Ibotenic acid was first documented in 2021 (PMID: 34348611). Based on a literature review a significant number of articles have been published on Ibotenic acid (PMID: 34499937) (PMID: 34104335) (PMID: 34080326) (PMID: 33932777) (PMID: 33901435) (PMID: 33716095).

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306242121113D          

 17 17  0  0  0  0            999 V2000
   -1.4667   -1.6197   -0.1057 N   0  0  1  0  0  0  0  0  0  0  0  0
   -1.2166   -0.2507    0.2718 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.0347    0.6798   -0.5502 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8215    0.2447   -1.4425 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9821    2.0561   -0.3874 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2410    0.0772    0.1388 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2488   -0.7534    0.5878 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4504   -0.1351    0.3001 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6167   -0.5546    0.5426 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1145    1.0218   -0.2998 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8147    1.1178   -0.3799 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5872   -2.0500   -0.5046 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7982   -2.1979    0.6800 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4633   -0.1282    1.3466 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1142    2.5080   -0.6464 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1630   -1.7250    1.0829 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8354    1.7092   -0.6343 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  3  5  1  0  0  0  0
  2  6  1  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
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11  6  1  0  0  0  0
  1 12  1  0  0  0  0
  1 13  1  0  0  0  0
  2 14  1  1  0  0  0
  5 15  1  0  0  0  0
  7 16  1  0  0  0  0
 10 17  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0004872

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]OC(=O)[C@@]([H])(N([H])[H])C1=C([H])C(=O)N([H])O1

> <INCHI_IDENTIFIER>
InChI=1S/C5H6N2O4/c6-4(5(9)10)2-1-3(8)7-11-2/h1,4H,6H2,(H,7,8)(H,9,10)/t4-/m0/s1

> <INCHI_KEY>
IRJCBFDCFXCWGO-UHFFFAOYSA-N

> <FORMULA>
C5H6N2O4

> <MOLECULAR_WEIGHT>
158.113

> <EXACT_MASS>
158.032756681

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
17

> <JCHEM_AVERAGE_POLARIZABILITY>
13.253135029577622

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-2-amino-2-(3-oxo-2,3-dihydro-1,2-oxazol-5-yl)acetic acid

> <ALOGPS_LOGP>
-2.73

> <JCHEM_LOGP>
-3.89285467019753

> <ALOGPS_LOGS>
-0.19

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
5.412347260771049

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.5552531538254861

> <JCHEM_PKA_STRONGEST_BASIC>
8.768014773258923

> <JCHEM_POLAR_SURFACE_AREA>
101.65000000000002

> <JCHEM_REFRACTIVITY>
33.927099999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.02e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
amanita muscaria

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-JUN-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-JUN-21         0                                  
HETATM    1  N   UNK     0      -1.467  -1.620  -0.106  0.00  0.00           N+0
HETATM    2  C   UNK     0      -1.217  -0.251   0.272  0.00  0.00           C+0
HETATM    3  C   UNK     0      -2.035   0.680  -0.550  0.00  0.00           C+0
HETATM    4  O   UNK     0      -2.821   0.245  -1.442  0.00  0.00           O+0
HETATM    5  O   UNK     0      -1.982   2.056  -0.387  0.00  0.00           O+0
HETATM    6  C   UNK     0       0.241   0.077   0.139  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.249  -0.753   0.588  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.450  -0.135   0.300  0.00  0.00           C+0
HETATM    9  O   UNK     0       3.617  -0.555   0.543  0.00  0.00           O+0
HETATM   10  N   UNK     0       2.115   1.022  -0.300  0.00  0.00           N+0
HETATM   11  O   UNK     0       0.815   1.118  -0.380  0.00  0.00           O+0
HETATM   12  H   UNK     0      -0.587  -2.050  -0.505  0.00  0.00           H+0
HETATM   13  H   UNK     0      -1.798  -2.198   0.680  0.00  0.00           H+0
HETATM   14  H   UNK     0      -1.463  -0.128   1.347  0.00  0.00           H+0
HETATM   15  H   UNK     0      -1.114   2.508  -0.646  0.00  0.00           H+0
HETATM   16  H   UNK     0       1.163  -1.725   1.083  0.00  0.00           H+0
HETATM   17  H   UNK     0       2.835   1.709  -0.634  0.00  0.00           H+0
CONECT    1    2   12   13                                                  
CONECT    2    1    3    6   14                                             
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3   15                                                       
CONECT    6    2    7   11                                                  
CONECT    7    6    8   16                                                  
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11   17                                                  
CONECT   11   10    6                                                       
CONECT   12    1                                                            
CONECT   13    1                                                            
CONECT   14    2                                                            
CONECT   15    5                                                            
CONECT   16    7                                                            
CONECT   17   10                                                            
MASTER        0    0    0    0    0    0    0    0   17    0   34    0
END

View in JSmol View NMR Assignments

Synonyms

Value	Source
Ibotenate	Generator
Acid, ibotenic	HMDB
(+/-)-ibotenic acid	HMDB
(+/-)-ibotenate	HMDB
2-Amino-2-(3-hydroxy-1,2-oxazol-5-yl)acetate	HMDB

Chemical Formula

C₅H₆N₂O₄

Average Mass

158.1130 Da

Monoisotopic Mass

158.03276 Da

IUPAC Name

(2S)-2-amino-2-(3-oxo-2,3-dihydro-1,2-oxazol-5-yl)acetic acid

Traditional Name

amanita muscaria

CAS Registry Number

Not Available

SMILES

NC(C(O)=O)C1=CC(O)=NO1

InChI Identifier

InChI=1S/C5H6N2O4/c6-4(5(9)10)2-1-3(8)7-11-2/h1,4H,6H2,(H,7,8)(H,9,10)

InChI Key

IRJCBFDCFXCWGO-UHFFFAOYSA-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
Amanita muscaria	NPAtlas	14321964
Amanita parcivolvata	LOTUS Database	35616633

Species Where Detected

Species Name	Source	Reference
Amanita cothurnata	KNApSAcK Database	22123792
Amanita gemmata	KNApSAcK Database	22123792
Amanita pantherina	KNApSAcK Database	22123792
Amanita smithiana	KNApSAcK Database	22123792
Amanita spp.	KNApSAcK Database	22123792
Amanita strobiliformis	KNApSAcK Database	22123792

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as alpha amino acids. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon).

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Alpha amino acids

Alternative Parents

Substituents

Alpha-amino acid
Aralkylamine
Azole
Isoxazole
Heteroaromatic compound
Amino acid
Carboxylic acid
Monocarboxylic acid or derivatives
Organoheterocyclic compound
Azacycle
Oxacycle
Primary amine
Organooxygen compound
Organonitrogen compound
Amine
Primary aliphatic amine
Organopnictogen compound
Organic nitrogen compound
Organic oxide
Organic oxygen compound
Carbonyl group
Hydrocarbon derivative
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

non-proteinogenic alpha-amino acid (CHEBI:5854 )
Mushroom toxins (C10600 )

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	458.80 °C. @ 760.00 mm Hg (est)	The Good Scents Company Information System
Water Solubility	377600 mg/L @ 25 °C (est)	The Good Scents Company Information System
LogP	-1.070 (est)	The Good Scents Company Information System

Predicted Properties

Property	Value	Source
logP	-2.7	ALOGPS
logP	-3.9	ChemAxon
logS	-0.19	ALOGPS
pKa (Strongest Acidic)	1.56	ChemAxon
pKa (Strongest Basic)	8.77	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	101.65 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	33.93 m³·mol⁻¹	ChemAxon
Polarizability	13.25 Å³	ChemAxon
Number of Rings	1	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

NPAtlas ID

NPA024729

HMDB ID

HMDB0253330

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00002345

Chemspider ID

1196

KEGG Compound ID

C10600

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Ibotenic acid

METLIN ID

Not Available

PubChem Compound

1233

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

rw1700111

References

General References

Pimentel GA, Crestani AM, Florindo LH: Do spatial and recognition memories have a lateralized processing by the dorsal hippocampus CA3? Behav Brain Res. 2022 Jan 7;416:113566. doi: 10.1016/j.bbr.2021.113566. Epub 2021 Sep 6. [PubMed:34499937 ]
Mohi-Ud-Din R, Mir RH, Wani TU, Shah AJ, Banday N, Pottoo FH: Berberine in the Treatment of Neurodegenerative Diseases and Nanotechnology Enabled Targeted Delivery. Comb Chem High Throughput Screen. 2021 Aug 4. pii: CCHTS-EPUB-117035. doi: 10.2174/1386207324666210804122539. [PubMed:34348611 ]
Sriji SN, Akhtar N, Mallick HN: Mediodorsal thalamus lesion increases paradoxical sleep in rats. Sleep Sci. 2021 Jan-Mar;14(1):33-38. doi: 10.5935/1984-0063.20190155. [PubMed:34104335 ]
Bambauer TP, Wagmann L, Weber AA, Meyer MR: Further development of a liquid chromatography-high-resolution mass spectrometry/mass spectrometry-based strategy for analyzing eight biomarkers in human urine indicating toxic mushroom or Ricinus communis ingestions. Drug Test Anal. 2021 Sep;13(9):1603-1613. doi: 10.1002/dta.3106. Epub 2021 Jun 10. [PubMed:34080326 ]
Sasaki T, Saito H, Hiradate Y, Hara K, Tanemura K: Behavioural effects in mice orally exposed to domoic acid or ibotenic acid are influenced by developmental stages and sex differences. Biochem Biophys Res Commun. 2021 Jun 18;558:175-182. doi: 10.1016/j.bbrc.2021.04.080. Epub 2021 Apr 28. [PubMed:33932777 ]
Lee YA, Kim YJ, Lee JS, Lee S, Goto Y: Imbalance between dopamine and serotonin caused by neonatal habenula lesion. Behav Brain Res. 2021 Jul 9;409:113316. doi: 10.1016/j.bbr.2021.113316. Epub 2021 Apr 24. [PubMed:33901435 ]
Fink AM, Burke LA, Sharma K: Lesioning of the pedunculopontine nucleus reduces rapid eye movement sleep, but does not alter cardiorespiratory activities during sleep, under hypoxic conditions in rats. Respir Physiol Neurobiol. 2021 Jun;288:103653. doi: 10.1016/j.resp.2021.103653. Epub 2021 Mar 11. [PubMed:33716095 ]

Showing NP-Card for Ibotenic acid (NP0004872)

MOL for NP0004872 (Ibotenic acid)

3D MOL for NP0004872 (Ibotenic acid)

3D SDF for NP0004872 (Ibotenic acid)

3D-SDF for NP0004872 (Ibotenic acid)

PDB for NP0004872 (Ibotenic acid)

3D PDB for NP0004872 (Ibotenic acid)

SMILES for NP0004872 (Ibotenic acid)

INCHI for NP0004872 (Ibotenic acid)

Structure for NP0004872 (Ibotenic acid)

3D Structure for NP0004872 (Ibotenic acid)