NP-MRD: Showing NP-Card for n-[(2s,3r,4r,5s,6r)-2,4,5-trihydroxy-6-[(phosphonooxy)methyl]oxan-3-yl]ethanimidic acid (NP0321111)

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Record Information

Version

2.0

Created at

2022-09-11 23:08:27 UTC

Updated at

2022-09-11 23:08:28 UTC

NP-MRD ID

NP0321111

Secondary Accession Numbers

None

Natural Product Identification

Common Name

n-[(2s,3r,4r,5s,6r)-2,4,5-trihydroxy-6-[(phosphonooxy)methyl]oxan-3-yl]ethanimidic acid

Description

N-Acetylglucosamine 6-phosphate, also known as GLCNAC6P, belongs to the class of organic compounds known as acylaminosugars. These are organic compounds containing a sugar linked to a chain through N-acyl group. N-Acetylglucosamine 6-phosphate is a monosaccharide derivative of glucose, a main component of the peptidoglycan cell wall in bacteria. N-Acetylglucosamine 6-phosphate is an extremely weak basic (essentially neutral) compound (based on its pKa). GlcNAc is also of note in neurotransmission, where it is thought to be an atypical neurotransmitter functioning in nocioceptive (pain) pathways. N-Acetylglucosamine 6-phosphate exists in all living organisms, ranging from bacteria to humans. Outside of the human body, N-Acetylglucosamine 6-phosphate has been detected, but not quantified in, several different foods, such as apricots, enokitakes, peppers, spinachs, and small-leaf lindens. This could make N-acetylglucosamine 6-phosphate a potential biomarker for the consumption of these foods. N-Acetylglucosamine 6-phosphate has been identified in the human placenta (PMID: 32033212 ).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 35 35  0  0  0  0  0  0  0  0999 V2000
    5.4624   -0.0759    0.5571 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1164   -0.5079    0.1391 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9643   -1.4530   -0.6656 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9742    0.1463    0.6472 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6247   -0.2186    0.2859 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.8078   -0.6880    1.4542 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.6201    0.3153    2.4042 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4003   -1.1748    0.9713 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1586   -0.1535    0.3798 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.5295   -0.6857    0.0554 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2580    0.3361   -0.5256 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8258   -0.1515   -0.9345 P   0  0  0  0  0  5  0  0  0  0  0  0
   -5.8271    0.2547    0.1372 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8636   -1.8257   -1.1311 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2443    0.6446   -2.3608 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4218    0.3138   -0.8508 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.1576    1.1465   -1.6498 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8727    0.9253   -0.3602 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.6078    1.5036   -1.3797 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2167   -0.1793   -0.2491 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8136   -0.5958    1.4755 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4255    1.0094    0.8000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1309    0.9363    1.3211 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6945   -1.0666   -0.4285 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3262   -1.5585    1.9271 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1484    0.1355    2.9821 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2361    0.6720    1.0896 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9911   -1.0672    0.9850 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4063   -1.5646   -0.6125 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6951   -2.2273   -0.7758 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1483    1.6128   -2.2095 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1478   -0.6079   -1.4349 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0810    2.1047   -1.4523 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5969    1.6466    0.4367 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2860    2.0981   -1.0279 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 14  1  0
 12 15  1  0
 12 13  2  0
  9 16  1  0
 16 17  1  0
 16 18  1  0
 18 19  1  0
 18  5  1  0
  1 20  1  0
  1 21  1  0
  1 22  1  0
  4 23  1  0
  5 24  1  6
  6 25  1  1
  7 26  1  0
  9 27  1  1
 10 28  1  0
 10 29  1  0
 14 30  1  0
 15 31  1  0
 16 32  1  6
 17 33  1  0
 18 34  1  1
 19 35  1  0
M  END

Untitled Document-8
  Mrv0541 02231219352D          

 19 19  0  0  0  0            999 V2000
   -0.3572    0.4678    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.3572   -0.3572    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.3572   -0.7697    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.0717   -0.3572    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.0717    0.4678    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.3572    0.8803    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0717    0.8803    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3572   -1.5947    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0717   -0.7697    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7862   -0.7697    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7862    0.8803    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5006   -0.3572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2151   -0.7697    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5006    0.4678    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7862    0.4678    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5006    0.8803    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0881    1.5947    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2151    1.2928    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9131    0.1658    0.0000 O   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  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  1  1  0  0  0  0
  1  7  1  1  0  0  0
  3  8  1  1  0  0  0
  2  9  1  6  0  0  0
  4 10  1  6  0  0  0
  5 11  1  6  0  0  0
 10 12  1  0  0  0  0
 12 13  1  0  0  0  0
 12 14  2  0  0  0  0
  7 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  2  0  0  0  0
 16 18  1  0  0  0  0
 16 19  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0321111

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(=O)N[C@H]1[C@@H](O)O[C@H](COP(O)(O)=O)[C@@H](O)[C@@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C8H16NO9P/c1-3(10)9-5-7(12)6(11)4(18-8(5)13)2-17-19(14,15)16/h4-8,11-13H,2H2,1H3,(H,9,10)(H2,14,15,16)/t4-,5-,6-,7-,8+/m1/s1

> <INCHI_KEY>
BRGMHAYQAZFZDJ-PVFLNQBWSA-N

> <FORMULA>
C8H16NO9P

> <MOLECULAR_WEIGHT>
301.1877

> <EXACT_MASS>
301.056267627

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_AVERAGE_POLARIZABILITY>
25.689768584275207

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{[(2R,3S,4R,5R,6S)-5-acetamido-3,4,6-trihydroxyoxan-2-yl]methoxy}phosphonic acid

> <ALOGPS_LOGP>
-2.02

> <JCHEM_LOGP>
-3.3441404429999997

> <ALOGPS_LOGS>
-1.23

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.248988545780628

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.2274470828963118

> <JCHEM_PKA_STRONGEST_BASIC>
-0.7858520307052878

> <JCHEM_POLAR_SURFACE_AREA>
165.78

> <JCHEM_REFRACTIVITY>
57.8976

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.76e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[(2R,3S,4R,5R,6S)-5-acetamido-3,4,6-trihydroxyoxan-2-yl]methoxyphosphonic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: Untitled Document-8                               
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  C   UNK     0      -0.667   0.873   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.667  -0.667   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.667  -1.437   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.001  -0.667   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.001   0.873   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       0.667   1.643   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      -2.001   1.643   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       0.667  -2.977   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      -2.001  -1.437   0.000  0.00  0.00           O+0
HETATM   10  N   UNK     0       3.334  -1.437   0.000  0.00  0.00           N+0
HETATM   11  O   UNK     0       3.334   1.643   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       4.668  -0.667   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       6.002  -1.437   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       4.668   0.873   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0      -3.334   0.873   0.000  0.00  0.00           O+0
HETATM   16  P   UNK     0      -4.668   1.643   0.000  0.00  0.00           P+0
HETATM   17  O   UNK     0      -3.898   2.977   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0      -6.002   2.413   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      -5.438   0.309   0.000  0.00  0.00           O+0
CONECT    1    2    6    7                                                  
CONECT    2    1    3    9                                                  
CONECT    3    2    4    8                                                  
CONECT    4    3    5   10                                                  
CONECT    5    4    6   11                                                  
CONECT    6    5    1                                                       
CONECT    7    1   15                                                       
CONECT    8    3                                                            
CONECT    9    2                                                            
CONECT   10    4   12                                                       
CONECT   11    5                                                            
CONECT   12   10   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12                                                            
CONECT   15    7   16                                                       
CONECT   16   15   17   18   19                                             
CONECT   17   16                                                            
CONECT   18   16                                                            
CONECT   19   16                                                            
MASTER        0    0    0    0    0    0    0    0   19    0   38    0
END

View in JSmol

Synonyms

Value	Source
GlcNAc6P	HMDB, MeSH
N-Acetylglucosamine 6-phosphoric acid	Generator
2-Acetamido-2-deoxy-D-glucose 6-phosphate	HMDB
GlcNAc-6-P	HMDB
N-Acetyl-D-glucosamine 6-phosphate	HMDB
N-Acetylglucosamine 6-phosphate	HMDB

Chemical Formula

C₈H₁₆NO₉P

Average Mass

301.1877 Da

Monoisotopic Mass

301.05627 Da

IUPAC Name

{[(2R,3S,4R,5R,6S)-5-acetamido-3,4,6-trihydroxyoxan-2-yl]methoxy}phosphonic acid

Traditional Name

[(2R,3S,4R,5R,6S)-5-acetamido-3,4,6-trihydroxyoxan-2-yl]methoxyphosphonic acid

CAS Registry Number

Not Available

SMILES

CC(=O)N[C@H]1[C@@H](O)O[C@H](COP(O)(O)=O)[C@@H](O)[C@@H]1O

InChI Identifier

InChI=1S/C8H16NO9P/c1-3(10)9-5-7(12)6(11)4(18-8(5)13)2-17-19(14,15)16/h4-8,11-13H,2H2,1H3,(H,9,10)(H2,14,15,16)/t4-,5-,6-,7-,8+/m1/s1

InChI Key

BRGMHAYQAZFZDJ-PVFLNQBWSA-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, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as acylaminosugars. These are organic compounds containing a sugar linked to a chain through N-acyl group.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Acylaminosugars

Alternative Parents

Substituents

Acylaminosugar
Hexose phosphate
N-acyl-alpha-hexosamine
Monosaccharide phosphate
Monoalkyl phosphate
Monosaccharide
Organic phosphoric acid derivative
Alkyl phosphate
Oxane
Phosphoric acid ester
Acetamide
1,2-diol
Carboxamide group
Hemiacetal
Secondary carboxylic acid amide
Secondary alcohol
Oxacycle
Carboxylic acid derivative
Organoheterocyclic compound
Polyol
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Alcohol
Organic nitrogen compound
Organonitrogen compound
Carbonyl group
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

amino sugar (CHEBI:49359 )

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	ALOGPS
logP	-3.3	ChemAxon
logS	-1.2	ALOGPS
pKa (Strongest Acidic)	1.23	ChemAxon
pKa (Strongest Basic)	-0.79	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	165.78 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	57.9 m³·mol⁻¹	ChemAxon
Polarizability	25.69 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

HMDB0002817

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB031017

KNApSAcK ID

Not Available

Chemspider ID

388358

KEGG Compound ID

Not Available

BioCyc ID

N-ACETYL-D-GLUCOSAMINE-6-P

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

3429

PubChem Compound

439219

PDB ID

16G

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for n-[(2s,3r,4r,5s,6r)-2,4,5-trihydroxy-6-[(phosphonooxy)methyl]oxan-3-yl]ethanimidic acid (NP0321111)

MOL for NP0321111 (n-[(2s,3r,4r,5s,6r)-2,4,5-trihydroxy-6-[(phosphonooxy)methyl]oxan-3-yl]ethanimidic acid)

3D MOL for NP0321111 (n-[(2s,3r,4r,5s,6r)-2,4,5-trihydroxy-6-[(phosphonooxy)methyl]oxan-3-yl]ethanimidic acid)

3D SDF for NP0321111 (n-[(2s,3r,4r,5s,6r)-2,4,5-trihydroxy-6-[(phosphonooxy)methyl]oxan-3-yl]ethanimidic acid)

3D-SDF for NP0321111 (n-[(2s,3r,4r,5s,6r)-2,4,5-trihydroxy-6-[(phosphonooxy)methyl]oxan-3-yl]ethanimidic acid)

PDB for NP0321111 (n-[(2s,3r,4r,5s,6r)-2,4,5-trihydroxy-6-[(phosphonooxy)methyl]oxan-3-yl]ethanimidic acid)

3D PDB for NP0321111 (n-[(2s,3r,4r,5s,6r)-2,4,5-trihydroxy-6-[(phosphonooxy)methyl]oxan-3-yl]ethanimidic acid)

SMILES for NP0321111 (n-[(2s,3r,4r,5s,6r)-2,4,5-trihydroxy-6-[(phosphonooxy)methyl]oxan-3-yl]ethanimidic acid)

INCHI for NP0321111 (n-[(2s,3r,4r,5s,6r)-2,4,5-trihydroxy-6-[(phosphonooxy)methyl]oxan-3-yl]ethanimidic acid)

Structure for NP0321111 (n-[(2s,3r,4r,5s,6r)-2,4,5-trihydroxy-6-[(phosphonooxy)methyl]oxan-3-yl]ethanimidic acid)

3D Structure for NP0321111 (n-[(2s,3r,4r,5s,6r)-2,4,5-trihydroxy-6-[(phosphonooxy)methyl]oxan-3-yl]ethanimidic acid)