NP-MRD: Showing NP-Card for Butyl (5R,6R,7S,8S)-5,6,7,8-tetrahydro-6,7,8-trihydroxy-5-(hydroxymethyl)imidazo[1,2-a]pyridine-2-carboxylate (NP0332002)

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Record Information

Version

2.0

Created at

2023-10-18 12:00:30 UTC

Updated at

2025-02-11 15:45:16 UTC

NP-MRD ID

NP0332002

Natural Product DOI

https://doi.org/10.57994/1124

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Butyl (5R,6R,7S,8S)-5,6,7,8-tetrahydro-6,7,8-trihydroxy-5-(hydroxymethyl)imidazo[1,2-a]pyridine-2-carboxylate

Description

Butyl (5R,6R,7S,8S)-5,6,7,8-tetrahydro-6,7,8-trihydroxy-5-(hydroxymethyl)imidazo[1,2-a]pyridine-2-carboxylate belongs to the class of organic compounds known as alpha amino acids and derivatives. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon), or a derivative thereof. Butyl (5R,6R,7S,8S)-5,6,7,8-tetrahydro-6,7,8-trihydroxy-5-(hydroxymethyl)imidazo[1,2-a]pyridine-2-carboxylate was first documented in 2023 (PMID: 37794774). Based on a literature review very few articles have been published on Butyl (5R,6R,7S,8S)-5,6,7,8-tetrahydro-6,7,8-trihydroxy-5-(hydroxymethyl)imidazo[1,2-a]pyridine-2-carboxylate.

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 10182312002D          

 21 22  0  0  1  0            999 V2000
    0.2658    0.3881    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6783    1.1025    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.2658    1.8170    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.5592    1.8170    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6783    2.5315    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.2658    3.2459    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5033    2.5315    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.9158    3.2459    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7408    3.2459    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9158    1.8170    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.5033    1.1025    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0553    0.4894    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8090    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5235    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2380    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9524    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6669    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3814    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0958    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5235   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7228    1.6455    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  6  0  0  0
  3  2  1  0  0  0  0
  3  4  1  1  0  0  0
  3  5  1  0  0  0  0
  5  6  1  6  0  0  0
  5  7  1  0  0  0  0
  7  8  1  1  0  0  0
  8  9  1  0  0  0  0
  7 10  1  0  0  0  0
 10 11  1  0  0  0  0
  2 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 14 20  2  0  0  0  0
 13 21  2  0  0  0  0
 10 21  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0332002

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CCCCOC(=O)C1=CN2[C@H](CO)[C@@H](O)[C@H](O)[C@@H](O)C2=N1

> <INCHI_IDENTIFIER>
InChI=1S/C13H20N2O6/c1-2-3-4-21-13(20)7-5-15-8(6-16)9(17)10(18)11(19)12(15)14-7/h5,8-11,16-19H,2-4,6H2,1H3/t8-,9-,10+,11-/m1/s1

> <INCHI_KEY>
YVGKEFMUEYKSPR-CHWFTXMASA-N

> <FORMULA>
C13H20N2O6

> <MOLECULAR_WEIGHT>
300.311

> <EXACT_MASS>
300.132136372

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
41

> <JCHEM_AVERAGE_POLARIZABILITY>
31.089956489189156

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
butyl (5R,6R,7S,8S)-6,7,8-trihydroxy-5-(hydroxymethyl)-5H,6H,7H,8H-imidazo[1,2-a]pyridine-2-carboxylate

> <JCHEM_LOGP>
-0.9530786339999995

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.404140324080347

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.258960811549896

> <JCHEM_PKA_STRONGEST_BASIC>
2.4163435138920106

> <JCHEM_POLAR_SURFACE_AREA>
125.03999999999999

> <JCHEM_REFRACTIVITY>
71.2431

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
butyl (5R,6R,7S,8S)-6,7,8-trihydroxy-5-(hydroxymethyl)-5H,6H,7H,8H-imidazo[1,2-a]pyridine-2-carboxylate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 18-OCT-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   18-OCT-23         0                                  
HETATM    1  O   UNK     0       0.496   0.724   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       1.266   2.058   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.496   3.392   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      -1.044   3.392   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       1.266   4.725   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       0.496   6.059   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       2.806   4.725   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       3.576   6.059   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       5.116   6.059   0.000  0.00  0.00           O+0
HETATM   10  N   UNK     0       3.576   3.392   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0       2.806   2.058   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0       3.837   0.914   0.000  0.00  0.00           N+0
HETATM   13  C   UNK     0       5.243   1.540   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       6.577   0.770   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       7.911   1.540   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       9.245   0.770   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      10.578   1.540   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      11.912   0.770   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      13.246   1.540   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       6.577  -0.770   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       5.083   3.072   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   11                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8   10                                                  
CONECT    8    7    9                                                       
CONECT    9    8                                                            
CONECT   10    7   11   21                                                  
CONECT   11   10    2   12                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14   21                                                  
CONECT   14   13   15   20                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18                                                            
CONECT   20   14                                                            
CONECT   21   13   10                                                       
MASTER        0    0    0    0    0    0    0    0   21    0   44    0
END

View in JSmol

Synonyms

Value	Source
Butyl (5R,6R,7S,8S)-5,6,7,8-tetrahydro-6,7,8-trihydroxy-5-(hydroxymethyl)imidazo[1,2-a]pyridine-2-carboxylic acid	Generator

Chemical Formula

C₁₃H₂₀N₂O₆

Average Mass

300.3110 Da

Monoisotopic Mass

300.13214 Da

IUPAC Name

butyl (5R,6R,7S,8S)-6,7,8-trihydroxy-5-(hydroxymethyl)-5H,6H,7H,8H-imidazo[1,2-a]pyridine-2-carboxylate

Traditional Name

butyl (5R,6R,7S,8S)-6,7,8-trihydroxy-5-(hydroxymethyl)-5H,6H,7H,8H-imidazo[1,2-a]pyridine-2-carboxylate

CAS Registry Number

Not Available

SMILES

CCCCOC(=O)C1=CN2[C@H](CO)[C@@H](O)[C@H](O)[C@@H](O)C2=N1

InChI Identifier

InChI=1S/C13H20N2O6/c1-2-3-4-21-13(20)7-5-15-8(6-16)9(17)10(18)11(19)12(15)14-7/h5,8-11,16-19H,2-4,6H2,1H3/t8-,9-,10+,11-/m1/s1

InChI Key

YVGKEFMUEYKSPR-CHWFTXMASA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View

Predicted Spectra

Not Available

Chemical Shift Submissions

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹H NMR Spectrum (1D, 600, C2D6OS, simulated)	zhanglihua200061@163.com	Tianjin University of Traditional Chinese Medicine	zhanglihua	2024-05-09	View Spectrum

Species

Species of Origin

Species Name	Source	Reference
Paraconiothyrium sp. YK-03		Not Available

Chemical Taxonomy

Description

This compound belongs to the class of organic compounds known as alpha amino acids and derivatives. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon), or a derivative thereof.

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 and derivatives

Alternative Parents

Substituents

Alpha-amino acid or derivatives
Imidazopyridine
Imidazole-4-carbonyl group
Piperidine
N-substituted imidazole
Heteroaromatic compound
Vinylogous amide
Alpha,beta-unsaturated carboxylic ester
Enoate ester
Azole
Secondary alcohol
Carboxylic acid ester
Azacycle
Organoheterocyclic compound
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Carboximidamide
Monocarboxylic acid or derivatives
Amidine
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Alcohol
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic 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	-0.95	ChemAxon
pKa (Strongest Acidic)	12.26	ChemAxon
pKa (Strongest Basic)	2.42	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	125.04 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	71.24 m³·mol⁻¹	ChemAxon
Polarizability	31.09 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

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Gao WK, Song XY, Li SW, Xue BX, Wu HH, Zhang LH, Pei YH: A rare tetrahydroimidazopyridine from the marine-derived fungus Paraconiothyrium sp. YK-03. Nat Prod Res. 2023 Oct 5:1-7. doi: 10.1080/14786419.2023.2262720. [PubMed:37794774 ]
DOI: 10.1080/14786419.2023.2262720

Showing NP-Card for Butyl (5R,6R,7S,8S)-5,6,7,8-tetrahydro-6,7,8-trihydroxy-5-(hydroxymethyl)imidazo[1,2-a]pyridine-2-carboxylate (NP0332002)

MOL for NP0332002 (Butyl (5R,6R,7S,8S)-5,6,7,8-tetrahydro-6,7,8-trihydroxy-5-(hydroxymethyl)imidazo[1,2-a]pyridine-2-carboxylate)

3D MOL for NP0332002 (Butyl (5R,6R,7S,8S)-5,6,7,8-tetrahydro-6,7,8-trihydroxy-5-(hydroxymethyl)imidazo[1,2-a]pyridine-2-carboxylate)

3D SDF for NP0332002 (Butyl (5R,6R,7S,8S)-5,6,7,8-tetrahydro-6,7,8-trihydroxy-5-(hydroxymethyl)imidazo[1,2-a]pyridine-2-carboxylate)

3D-SDF for NP0332002 (Butyl (5R,6R,7S,8S)-5,6,7,8-tetrahydro-6,7,8-trihydroxy-5-(hydroxymethyl)imidazo[1,2-a]pyridine-2-carboxylate)

PDB for NP0332002 (Butyl (5R,6R,7S,8S)-5,6,7,8-tetrahydro-6,7,8-trihydroxy-5-(hydroxymethyl)imidazo[1,2-a]pyridine-2-carboxylate)

3D PDB for NP0332002 (Butyl (5R,6R,7S,8S)-5,6,7,8-tetrahydro-6,7,8-trihydroxy-5-(hydroxymethyl)imidazo[1,2-a]pyridine-2-carboxylate)

SMILES for NP0332002 (Butyl (5R,6R,7S,8S)-5,6,7,8-tetrahydro-6,7,8-trihydroxy-5-(hydroxymethyl)imidazo[1,2-a]pyridine-2-carboxylate)

INCHI for NP0332002 (Butyl (5R,6R,7S,8S)-5,6,7,8-tetrahydro-6,7,8-trihydroxy-5-(hydroxymethyl)imidazo[1,2-a]pyridine-2-carboxylate)

Structure for NP0332002 (Butyl (5R,6R,7S,8S)-5,6,7,8-tetrahydro-6,7,8-trihydroxy-5-(hydroxymethyl)imidazo[1,2-a]pyridine-2-carboxylate)

3D Structure for NP0332002 (Butyl (5R,6R,7S,8S)-5,6,7,8-tetrahydro-6,7,8-trihydroxy-5-(hydroxymethyl)imidazo[1,2-a]pyridine-2-carboxylate)