NP-MRD: Showing NP-Card for N-Acetyl-D-glucosaminyldiphosphodolichol (NP0086788)

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Record Information

Version

2.0

Created at

2022-05-11 16:31:01 UTC

Updated at

2022-05-11 16:31:01 UTC

NP-MRD ID

NP0086788

Secondary Accession Numbers

None

Natural Product Identification

Common Name

N-Acetyl-D-glucosaminyldiphosphodolichol

Description

N-Acetyl-D-glucosaminyldiphosphodolichol belongs to the class of organic compounds known as n-acyl-alpha-hexosamines. These are carbohydrate derivatives containing a hexose moiety in which the oxygen atom is replaced by an n-acyl group. N-Acetyl-D-glucosaminyldiphosphodolichol is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv0541 02231219082D          

 38 38  0  0  1  0            999 V2000
   15.6768  -11.7933    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   15.6768  -12.6183    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.3912  -13.0309    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   17.1057  -12.6183    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   17.1057  -11.7933    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   16.3912  -11.3808    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   14.9623  -11.3808    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.9623  -10.5558    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.3912  -10.5558    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.8202  -13.0309    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   17.8202  -11.3808    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.3912  -14.5572    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.1057  -14.9697    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   17.1057  -15.7947    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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   17.1057  -14.1447    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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   19.2492  -14.5572    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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   19.9637  -14.9697    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   21.3927  -14.9697    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   21.3927  -15.7947    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   22.8216  -14.9697    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.5361  -14.5572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.2506  -14.9697    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.2506  -15.7947    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.9651  -14.5572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   25.6795  -14.9697    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   26.3941  -14.5572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   27.1086  -14.9697    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.5347  -12.6183    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   27.8230  -14.5572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
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  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
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 17 20  2  0  0  0  0
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 10 34  1  0  0  0  0
 34 35  2  0  0  0  0
 34 36  1  0  0  0  0
 33 37  1  0  0  0  0
 33 38  1  0  0  0  0
M  END

     RDKit          3D

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M  END


  Mrv0541 02231219082D          

 38 38  0  0  1  0            999 V2000
   15.6768  -11.7933    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   15.6768  -12.6183    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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   27.1086  -14.9697    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.5347  -12.6183    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.5347  -11.9996    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   19.2492  -13.0309    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   27.1086  -15.7947    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   27.8230  -14.5572    0.0000 C   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  6  0  0  0
  7  8  1  0  0  0  0
  6  9  1  1  0  0  0
  4 10  1  1  0  0  0
  5 11  1  6  0  0  0
  3 12  1  6  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 13 15  1  0  0  0  0
 13 16  2  0  0  0  0
 15 17  1  0  0  0  0
 17 18  1  0  0  0  0
 17 19  1  0  0  0  0
 17 20  2  0  0  0  0
 19 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 23 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 27 28  2  0  0  0  0
 28 29  1  0  0  0  0
 28 30  1  0  0  0  0
 30 31  1  0  0  0  0
 31 32  1  0  0  0  0
 32 33  2  0  0  0  0
 10 34  1  0  0  0  0
 34 35  2  0  0  0  0
 34 36  1  0  0  0  0
 33 37  1  0  0  0  0
 33 38  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0086788

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC[C@H]1O[C@@H](OP(O)(=O)OP(O)(=O)OCCC(C)CC\C=C(/C)CCC=C(C)C)[C@H](NC(=O)C)[C@@H](O)[C@@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C23H43NO12P2/c1-15(2)8-6-9-16(3)10-7-11-17(4)12-13-33-37(29,30)36-38(31,32)35-23-20(24-18(5)26)22(28)21(27)19(14-25)34-23/h8,10,17,19-23,25,27-28H,6-7,9,11-14H2,1-5H3,(H,24,26)(H,29,30)(H,31,32)/b16-10+/t17?,19-,20-,21-,22-,23+/m1/s1

> <INCHI_KEY>
OZGJPDIBINDRGZ-GKXPKBPWSA-N

> <FORMULA>
C23H43NO12P2

> <MOLECULAR_WEIGHT>
587.5345

> <EXACT_MASS>
587.226048869

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_AVERAGE_POLARIZABILITY>
58.81843540701715

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{[(2S,3R,4R,5S,6R)-3-acetamido-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}({[hydroxy({[(6E)-3,7,11-trimethyldodeca-6,10-dien-1-yl]oxy})phosphoryl]oxy})phosphinic acid

> <ALOGPS_LOGP>
1.30

> <JCHEM_LOGP>
1.5423684616666653

> <ALOGPS_LOGS>
-2.77

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.171830961728888

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.7457526571666602

> <JCHEM_PKA_STRONGEST_BASIC>
-0.7842632652706848

> <JCHEM_POLAR_SURFACE_AREA>
201.30999999999997

> <JCHEM_REFRACTIVITY>
139.2802

> <JCHEM_ROTATABLE_BOND_COUNT>
16

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.00e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[(2S,3R,4R,5S,6R)-3-acetamido-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy({hydroxy[(6E)-3,7,11-trimethyldodeca-6,10-dien-1-yl]oxyphosphoryl}oxy)phosphinic 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  C   UNK     0      29.263 -22.014   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0      29.263 -23.554   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0      30.597 -24.324   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      31.931 -23.554   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      31.931 -22.014   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      30.597 -21.244   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      27.930 -21.244   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      27.930 -19.704   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      30.597 -19.704   0.000  0.00  0.00           O+0
HETATM   10  N   UNK     0      33.264 -24.324   0.000  0.00  0.00           N+0
HETATM   11  O   UNK     0      33.264 -21.244   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      30.597 -27.173   0.000  0.00  0.00           O+0
HETATM   13  P   UNK     0      31.931 -27.943   0.000  0.00  0.00           P+0
HETATM   14  O   UNK     0      31.931 -29.483   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0      33.264 -27.173   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0      31.931 -26.403   0.000  0.00  0.00           O+0
HETATM   17  P   UNK     0      34.598 -27.943   0.000  0.00  0.00           P+0
HETATM   18  O   UNK     0      34.598 -29.483   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      35.932 -27.173   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0      34.598 -26.403   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0      37.266 -27.943   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      38.599 -27.173   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      39.933 -27.943   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      39.933 -29.483   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      41.267 -27.173   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      42.600 -27.943   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      43.934 -27.173   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      45.268 -27.943   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      45.268 -29.483   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      46.602 -27.173   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      47.935 -27.943   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      49.269 -27.173   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      50.603 -27.943   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      34.598 -23.554   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0      34.598 -22.399   0.000  0.00  0.00           O+0
HETATM   36  C   UNK     0      35.932 -24.324   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0      50.603 -29.483   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0      51.936 -27.173   0.000  0.00  0.00           C+0
CONECT    1    2    6    7                                                  
CONECT    2    1    3                                                       
CONECT    3    2    4   12                                                  
CONECT    4    3    5   10                                                  
CONECT    5    4    6   11                                                  
CONECT    6    5    1    9                                                  
CONECT    7    1    8                                                       
CONECT    8    7                                                            
CONECT    9    6                                                            
CONECT   10    4   34                                                       
CONECT   11    5                                                            
CONECT   12    3   13                                                       
CONECT   13   12   14   15   16                                             
CONECT   14   13                                                            
CONECT   15   13   17                                                       
CONECT   16   13                                                            
CONECT   17   15   18   19   20                                             
CONECT   18   17                                                            
CONECT   19   17   21                                                       
CONECT   20   17                                                            
CONECT   21   19   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   28                                                       
CONECT   28   27   29   30                                                  
CONECT   29   28                                                            
CONECT   30   28   31                                                       
CONECT   31   30   32                                                       
CONECT   32   31   33                                                       
CONECT   33   32   37   38                                                  
CONECT   34   10   35   36                                                  
CONECT   35   34                                                            
CONECT   36   34                                                            
CONECT   37   33                                                            
CONECT   38   33                                                            
MASTER        0    0    0    0    0    0    0    0   38    0   76    0
END

View in JSmol

Synonyms

Value	Source
N-Acetyl-D-glucosaminyl-diphosphodolichol	HMDB
N-[(2S,3R,4R,5S,6R)-4,5-Dihydroxy-2-{[hydroxy({[hydroxy({[(6E)-3,7,11-trimethyldodeca-6,10-dien-1-yl]oxy})phosphoryl]oxy})phosphoryl]oxy}-6-(hydroxymethyl)oxan-3-yl]ethanimidate	HMDB

Chemical Formula

C₂₃H₄₃NO₁₂P₂

Average Mass

587.5345 Da

Monoisotopic Mass

587.22605 Da

IUPAC Name

{[(2S,3R,4R,5S,6R)-3-acetamido-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}({[hydroxy({[(6E)-3,7,11-trimethyldodeca-6,10-dien-1-yl]oxy})phosphoryl]oxy})phosphinic acid

Traditional Name

[(2S,3R,4R,5S,6R)-3-acetamido-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy({hydroxy[(6E)-3,7,11-trimethyldodeca-6,10-dien-1-yl]oxyphosphoryl}oxy)phosphinic acid

CAS Registry Number

Not Available

SMILES

OC[C@H]1O[C@@H](OP(O)(=O)OP(O)(=O)OCCC(C)CC\C=C(/C)CCC=C(C)C)[C@H](NC(=O)C)[C@@H](O)[C@@H]1O

InChI Identifier

InChI=1S/C23H43NO12P2/c1-15(2)8-6-9-16(3)10-7-11-17(4)12-13-33-37(29,30)36-38(31,32)35-23-20(24-18(5)26)22(28)21(27)19(14-25)34-23/h8,10,17,19-23,25,27-28H,6-7,9,11-14H2,1-5H3,(H,24,26)(H,29,30)(H,31,32)/b16-10+/t17?,19-,20-,21-,22-,23+/m1/s1

InChI Key

OZGJPDIBINDRGZ-GKXPKBPWSA-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 n-acyl-alpha-hexosamines. These are carbohydrate derivatives containing a hexose moiety in which the oxygen atom is replaced by an n-acyl group.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

N-acyl-alpha-hexosamines

Alternative Parents

Substituents

N-acyl-alpha-hexosamine
Farsesane sesquiterpenoid
Sesquiterpenoid
Hexose monosaccharide
Monosaccharide phosphate
Organic pyrophosphate
Monoalkyl phosphate
Monosaccharide
Organic phosphoric acid derivative
Alkyl phosphate
Phosphoric acid ester
Oxane
Acetamide
Carboxamide group
Secondary carboxylic acid amide
Secondary alcohol
Carboxylic acid derivative
Oxacycle
Organoheterocyclic compound
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Alcohol
Organic nitrogen compound
Carbonyl group
Primary alcohol
Organonitrogen compound
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic 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	1.3	ALOGPS
logP	1.54	ChemAxon
logS	-2.8	ALOGPS
pKa (Strongest Acidic)	1.75	ChemAxon
pKa (Strongest Basic)	-0.78	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	201.31 Å²	ChemAxon
Rotatable Bond Count	16	ChemAxon
Refractivity	139.28 m³·mol⁻¹	ChemAxon
Polarizability	58.82 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon