NP-MRD: Showing NP-Card for Dolichol phosphate (NP0087500)

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Record Information

Version

1.0

Created at

2022-05-11 16:51:23 UTC

Updated at

2022-05-11 16:51:23 UTC

NP-MRD ID

NP0087500

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Dolichol phosphate

Description

Dolichol phosphate, also known as dolichol-p, belongs to the class of organic compounds known as sesquiterpenoids. These are terpenes with three consecutive isoprene units. Dolichol phosphate is possibly neutral. Dolichol phosphate is the most prevalent polyisoprenyl-glycosyl carrier found in mammals. Dolichol phosphate exists in all eukaryotes, ranging from yeast to humans. The final step in dolichol phosphate synthesis is catalyzed by dolichol kinase (DK1), an enzyme that transfers a phosphate from choline-phosphate cytidine triphosphate (CTP) to dolichol. After the polyisoprene pyrophosphate chain has reached its final length, both phosphate residues are released by mono- or pyrophosphatases. The chain length of eukaryotic dolichol molecules differs from 14 to 17 isoprene units in unicellular organisms like yeast whereas mammalian cells produce dolichol with 18-21 isoprene units. Symptoms include secondary microencephaly, dry, thin, parchmentlike skin, hyperkeratosis, minimal hair growth and muscular hypotonia. Once synthesized, dolichol phosphate can react with cytosolic GDP-mannose in the endoplasmic reticulum membrane to form dolichyl phosphate D-mannose. It was first documented in 2007 (PMID: 17273964). A new inherited metabolic disorder, Dolichol kinase (DK1) deficiency has recently been discovered.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 49 48  0  0  0  0  0  0  0  0999 V2000
    7.1505    1.3148   -0.8692 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9277    0.7449   -0.2748 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0210   -0.4509    0.6300 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7431    1.2325   -0.5601 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4504    0.7801   -0.0481 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6507    0.0662   -1.1040 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3933   -0.3121   -0.3691 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6783    0.8266    0.2348 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9672   -1.5370   -0.2277 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2810   -1.6848    0.5944 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4771   -1.5077   -0.2957 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7568   -1.2641    0.4811 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.2490   -2.2806    1.3575 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5453   -0.2059   -0.1300 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7680   -0.4502   -0.9476 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0263    0.8474   -1.4937 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1785    1.7072   -0.6796 P   0  0  1  0  0  5  0  0  0  0  0  0
   -6.6114    1.0227    0.6077 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4766    3.2495   -0.2545 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.5023    2.0672   -1.6060 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.2640    2.3777   -0.4795 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.0631    1.3645   -1.9631 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.0627    0.7364   -0.6027 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0667   -0.6481    1.1199 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7629   -0.2806    1.4568 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3031   -1.3750    0.0351 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7376    2.1002   -1.2670 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4296    0.2609    0.9019 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8583    1.7628    0.1108 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1940   -0.8530   -1.3764 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4330    0.6761   -1.9628 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2630    1.3334    1.0526 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5164    1.6045   -0.5464 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2806    0.5840    0.7253 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4598   -2.3617   -0.6586 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3160   -2.7710    0.9923 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3428   -1.0870    1.4827 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5650   -2.3660   -0.9473 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3097   -0.6317   -0.9863 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1854   -0.5521    1.3886 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8114   -1.8271    2.2176 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8458   -3.1016    0.8999 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3966   -2.8061    1.8541 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8879    0.4908   -0.7707 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8893    0.5218    0.6726 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6370   -0.8254   -0.4484 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5535   -1.0981   -1.8247 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2675    3.1678    0.7063 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.2356    1.4380   -1.5709 H   0  0  0  0  0  0  0  0  0  0  0  0
 13 12  1  0
 12 14  1  0
 14 15  1  0
 15 16  1  0
 17 16  1  6
 17 19  1  0
 17 20  1  0
 17 18  2  0
 12 11  1  0
 11 10  1  0
 10  9  1  0
  9  7  2  0
  7  8  1  0
  7  6  1  0
  6  5  1  0
  5  4  1  0
  4  2  2  3
  2  1  1  0
  2  3  1  0
 13 41  1  0
 13 42  1  0
 13 43  1  0
 12 40  1  1
 14 44  1  0
 14 45  1  0
 15 46  1  0
 15 47  1  0
 19 48  1  0
 20 49  1  0
 11 38  1  0
 11 39  1  0
 10 36  1  0
 10 37  1  0
  9 35  1  0
  8 32  1  0
  8 33  1  0
  8 34  1  0
  6 30  1  0
  6 31  1  0
  5 28  1  0
  5 29  1  0
  4 27  1  0
  1 21  1  0
  1 22  1  0
  1 23  1  0
  3 24  1  0
  3 25  1  0
  3 26  1  0
M  END


  Mrv1652309121723102D          

 20 19  0  0  0  0            999 V2000
    4.4395   -0.3017    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    3.6168   -0.3017    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2659   -0.3017    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4361    0.5211    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4361   -1.1278    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9037    0.1063    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1907   -0.2983    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4775    0.1165    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7646   -0.2949    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4742    0.9392    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0514    0.1200    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7611   -0.2949    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4775    0.1200    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1907   -0.2949    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4844    0.9427    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9620    0.1200    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6752   -0.2949    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3915    0.1200    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1081   -0.2949    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3950    0.9427    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  0  0  0
  1  5  2  0  0  0  0
  2  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 10  1  0  0  0  0
  9 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
 13 15  1  0  0  0  0
 14 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
 18 19  1  0  0  0  0
 18 20  1  0  0  0  0
M  STY  1   1 SRU
M  SCN  1   1 HT 
M  SAL   1  5  11  12  13  14  15
M  SDI   1  4   -2.5848   -0.4697   -2.5848    0.3360
M  SDI   1  4    0.3189    0.3360    0.3189   -0.4697
M  SBL   1  2  10  15
M  SMT   1 n
M  END
> <DATABASE_ID>
NP0087500

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(CCOP(O)(O)=O)CC\C=C(/C)CCC=C(C)C

> <INCHI_IDENTIFIER>
InChI=1S/C15H29O4P/c1-13(2)7-5-8-14(3)9-6-10-15(4)11-12-19-20(16,17)18/h7,9,15H,5-6,8,10-12H2,1-4H3,(H2,16,17,18)/b14-9+

> <INCHI_KEY>
DZHSRPJGCZHWOM-NTEUORMPSA-N

> <FORMULA>
(C5H8)nC10H21O4P

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <ALOGPS_LOGP>
3.40

> <ALOGPS_LOGS>
-3.80

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
4.85e-02 g/l

$$$$

HEADER    PROTEIN                                 12-SEP-17   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   12-SEP-17         0                                  
HETATM    1  P   UNK     0       8.287  -0.563   0.000  0.00  0.00           P+0
HETATM    2  O   UNK     0       6.751  -0.563   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0       9.830  -0.563   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0       8.281   0.973   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0       8.281  -2.105   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       5.420   0.198   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.089  -0.557   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.758   0.217   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.427  -0.550   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.752   1.753   0.000  0.00  0.00           C+0
HETATM   11  C     n     1      -0.096   0.224   0.000  0.00  0.00           C+0
HETATM   12  C     n     1      -1.421  -0.550   0.000  0.00  0.00           C+0
HETATM   13  C     n     1      -2.758   0.224   0.000  0.00  0.00           C+0
HETATM   14  C     n     1      -4.089  -0.550   0.000  0.00  0.00           C+0
HETATM   15  C     n     1      -2.771   1.760   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -5.529   0.224   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -6.860  -0.550   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -8.197   0.224   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -9.535  -0.550   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -8.204   1.760   0.000  0.00  0.00           C+0
CONECT    1    2    3    4    5                                             
CONECT    2    1    6                                                       
CONECT    3    1                                                            
CONECT    4    1                                                            
CONECT    5    1                                                            
CONECT    6    2    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   10                                                  
CONECT    9    8   11                                                       
CONECT   10    8                                                            
CONECT   11    9   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14   15                                                  
CONECT   14   13   16                                                       
CONECT   15   13                                                            
CONECT   16   14   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18                                                            
MASTER        0    0    0    0    0    0    0    0   20    0   38    0
END

View in JSmol

Synonyms

Value	Source
Dolichol phosphoric acid	Generator
Dolichol monophosphate	HMDB
Dolichol-p	HMDB
Dolichol-phosphate	HMDB
Dolichol-PO4	HMDB
Dolichyl-phosphate	HMDB
Dolychol phosphate	HMDB

Chemical Formula

(C₅H₈)nC₁₀H₂₁O₄P

Average Mass

Not Available

Monoisotopic Mass

Not Available

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

CC(CCOP(O)(O)=O)CC\C=C(/C)CCC=C(C)C

InChI Identifier

InChI=1S/C15H29O4P/c1-13(2)7-5-8-14(3)9-6-10-15(4)11-12-19-20(16,17)18/h7,9,15H,5-6,8,10-12H2,1-4H3,(H2,16,17,18)/b14-9+

InChI Key

DZHSRPJGCZHWOM-NTEUORMPSA-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 sesquiterpenoids. These are terpenes with three consecutive isoprene units.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Sesquiterpenoids

Direct Parent

Sesquiterpenoids

Alternative Parents

Substituents

Farsesane sesquiterpenoid
Sesquiterpenoid
Monoalkyl phosphate
Alkyl phosphate
Phosphoric acid ester
Organic phosphoric acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic 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	3.4	ALOGPS
logS	-3.8	ALOGPS
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon

External Links

HMDB ID

HMDB0006353

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB023901

KNApSAcK ID

Not Available

Chemspider ID

4444045

KEGG Compound ID

C00110

BioCyc ID

Not Available

BiGG ID

1809214

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5280322

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Kranz C, Jungeblut C, Denecke J, Erlekotte A, Sohlbach C, Debus V, Kehl HG, Harms E, Reith A, Reichel S, Grobe H, Hammersen G, Schwarzer U, Marquardt T: A defect in dolichol phosphate biosynthesis causes a new inherited disorder with death in early infancy. Am J Hum Genet. 2007 Mar;80(3):433-40. doi: 10.1086/512130. Epub 2007 Jan 31. [PubMed:17273964 ]

Showing NP-Card for Dolichol phosphate (NP0087500)

MOL for NP0087500 (Dolichol phosphate)

3D MOL for NP0087500 (Dolichol phosphate)

3D SDF for NP0087500 (Dolichol phosphate)

3D-SDF for NP0087500 (Dolichol phosphate)

PDB for NP0087500 (Dolichol phosphate)

3D PDB for NP0087500 (Dolichol phosphate)

SMILES for NP0087500 (Dolichol phosphate)

INCHI for NP0087500 (Dolichol phosphate)

Structure for NP0087500 (Dolichol phosphate)

3D Structure for NP0087500 (Dolichol phosphate)