NP-MRD: Showing NP-Card for Methyl (5R,6R,7S,8S)-5,6,7,8-tetrahydro-6,7,8-trihydroxy-5-(hydroxymethyl)imidazo[1,2-a]pyridine-2 carboxylate (NP0332004)

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Record Information

Version

2.0

Created at

2023-10-18 12:00:48 UTC

Updated at

2024-09-03 04:17:40 UTC

NP-MRD ID

NP0332004

Natural Product DOI

https://doi.org/10.57994/1127

Secondary Accession Numbers

None

Natural Product Identification

Common Name

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

Description

Methyl (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 (5R)-5alpha-(Hydroxymethyl)-6beta,7alpha,8beta-trihydroxy-5,6,7,8-tetrahydroimidazo[1,2-a]pyridine-2-carboxylic acid methyl ester.

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 10182312002D          

 18 19  0  0  1  0            999 V2000
    3.2789    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2789    1.2375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.9934    0.8250    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.7079    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934    0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.7079   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2789   -0.4125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.2789   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5645   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5645    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.5645    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7798    1.0799    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2949    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4699    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0574    1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7676    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0574   -0.3020    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7798   -0.2549    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
 14 17  2  0  0  0  0
 13 18  2  0  0  0  0
 10 18  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0332004

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C10H14N2O6/c1-18-10(17)4-2-12-5(3-13)6(14)7(15)8(16)9(12)11-4/h2,5-8,13-16H,3H2,1H3/t5-,6-,7+,8-/m1/s1

> <INCHI_KEY>
LJYCTHOGEIUQFM-OOJXKGFFSA-N

> <FORMULA>
C10H14N2O6

> <MOLECULAR_WEIGHT>
258.23

> <EXACT_MASS>
258.085186179

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
32

> <JCHEM_AVERAGE_POLARIZABILITY>
24.725118647912296

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <JCHEM_LOGP>
-2.2769776486666666

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.404169512127666

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.259005880033664

> <JCHEM_PKA_STRONGEST_BASIC>
2.4171598118071156

> <JCHEM_POLAR_SURFACE_AREA>
125.03999999999999

> <JCHEM_REFRACTIVITY>
57.3695

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
methyl (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       6.121   3.850   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       6.121   2.310   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       7.454   1.540   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       8.788   2.310   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       7.454   0.000   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       8.788  -0.770   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       6.121  -0.770   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       6.121  -2.310   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       4.787  -3.080   0.000  0.00  0.00           O+0
HETATM   10  N   UNK     0       4.787   0.000   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0       4.787   1.540   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0       3.322   2.016   0.000  0.00  0.00           N+0
HETATM   13  C   UNK     0       2.417   0.770   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       0.877   0.770   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       0.107   2.104   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      -1.433   2.104   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       0.107  -0.564   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       3.322  -0.476   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   18                                                  
CONECT   11   10    2   12                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14   18                                                  
CONECT   14   13   15   17                                                  
CONECT   15   14   16                                                       
CONECT   16   15                                                            
CONECT   17   14                                                            
CONECT   18   13   10                                                       
MASTER        0    0    0    0    0    0    0    0   18    0   38    0
END

View in JSmol

Synonyms

Value	Source
(5R)-5a-(Hydroxymethyl)-6b,7a,8b-trihydroxy-5,6,7,8-tetrahydroimidazo[1,2-a]pyridine-2-carboxylate methyl ester	Generator
(5R)-5a-(Hydroxymethyl)-6b,7a,8b-trihydroxy-5,6,7,8-tetrahydroimidazo[1,2-a]pyridine-2-carboxylic acid methyl ester	Generator
(5R)-5alpha-(Hydroxymethyl)-6beta,7alpha,8beta-trihydroxy-5,6,7,8-tetrahydroimidazo[1,2-a]pyridine-2-carboxylate methyl ester	Generator
(5R)-5Α-(hydroxymethyl)-6β,7α,8β-trihydroxy-5,6,7,8-tetrahydroimidazo[1,2-a]pyridine-2-carboxylate methyl ester	Generator
(5R)-5Α-(hydroxymethyl)-6β,7α,8β-trihydroxy-5,6,7,8-tetrahydroimidazo[1,2-a]pyridine-2-carboxylic acid methyl ester	Generator

Chemical Formula

C₁₀H₁₄N₂O₆

Average Mass

258.2300 Da

Monoisotopic Mass

258.08519 Da

IUPAC Name

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

Traditional Name

methyl (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

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

InChI Identifier

InChI=1S/C10H14N2O6/c1-18-10(17)4-2-12-5(3-13)6(14)7(15)8(16)9(12)11-4/h2,5-8,13-16H,3H2,1H3/t5-,6-,7+,8-/m1/s1

InChI Key

LJYCTHOGEIUQFM-OOJXKGFFSA-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, 400, 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
sp. YK-03		Not Available

Chemical Taxonomy

Classification

Not classified

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	-2.3	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	3	ChemAxon
Refractivity	57.37 m³·mol⁻¹	ChemAxon
Polarizability	24.73 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

9509342

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

11334396

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 ]

Showing NP-Card for Methyl (5R,6R,7S,8S)-5,6,7,8-tetrahydro-6,7,8-trihydroxy-5-(hydroxymethyl)imidazo[1,2-a]pyridine-2 carboxylate (NP0332004)

MOL for NP0332004 (Methyl (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 NP0332004 (Methyl (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 NP0332004 (Methyl (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 NP0332004 (Methyl (5R,6R,7S,8S)-5,6,7,8-tetrahydro-6,7,8-trihydroxy-5-(hydroxymethyl)imidazo[1,2-a]pyridine-2 carboxylate)

PDB for NP0332004 (Methyl (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 NP0332004 (Methyl (5R,6R,7S,8S)-5,6,7,8-tetrahydro-6,7,8-trihydroxy-5-(hydroxymethyl)imidazo[1,2-a]pyridine-2 carboxylate)

SMILES for NP0332004 (Methyl (5R,6R,7S,8S)-5,6,7,8-tetrahydro-6,7,8-trihydroxy-5-(hydroxymethyl)imidazo[1,2-a]pyridine-2 carboxylate)

INCHI for NP0332004 (Methyl (5R,6R,7S,8S)-5,6,7,8-tetrahydro-6,7,8-trihydroxy-5-(hydroxymethyl)imidazo[1,2-a]pyridine-2 carboxylate)

Structure for NP0332004 (Methyl (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 NP0332004 (Methyl (5R,6R,7S,8S)-5,6,7,8-tetrahydro-6,7,8-trihydroxy-5-(hydroxymethyl)imidazo[1,2-a]pyridine-2 carboxylate)