NP-MRD: Showing NP-Card for 5,6-Dihydrouridine (NP0086597)

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Record Information

Version

2.0

Created at

2022-05-11 16:25:33 UTC

Updated at

2022-05-11 16:25:34 UTC

NP-MRD ID

NP0086597

Secondary Accession Numbers

None

Natural Product Identification

Common Name

5,6-Dihydrouridine

Description

5,6-Dihydrouridine belongs to the class of organic compounds known as glycosylamines. Glycosylamines are compounds consisting of an amine with a beta-N-glycosidic bond to a carbohydrate, thus forming a cyclic hemiaminal ether bond (alpha-amino ether). 5,6-Dihydrouridine was first documented in 2002 (PMID: 12003496). 5,6-Dihydrouridine is an extremely weak basic (essentially neutral) compound (based on its pKa) (PMID: 19139092) (PMID: 19488969) (PMID: 21628433) (PMID: 22123979).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 31 32  0  0  0  0  0  0  0  0999 V2000
   -5.2485    0.3870    0.0805 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0469    0.0212    0.1261 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1493    0.0006   -1.0560 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8110    0.5959   -0.7015 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2250    0.0284    0.4713 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.1733   -0.1493    0.6493 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.9265    1.0083    0.5426 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2301    0.5529    0.6202 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.1697    1.4847   -0.1111 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0568    2.7475    0.5116 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2889   -0.7884   -0.0667 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.5680   -1.7486    0.8971 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8188   -0.9931   -0.4603 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.4465   -2.3113   -0.3728 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1020   -0.3838    1.5284 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6441   -0.7554    2.6429 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5221   -0.3933    1.3711 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0866   -0.9806   -1.5408 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6179    0.6879   -1.8129 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1525    0.4635   -1.5793 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9726    1.7008   -0.6101 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4173   -0.6042    1.6291 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5697    0.4886    1.6655 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9288    1.5719   -1.1865 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2170    1.1675    0.0542 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9492    3.4615   -0.1791 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9552   -0.8089   -0.9271 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2468   -2.3700    0.5333 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6210   -0.5240   -1.4255 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1149   -2.8550    0.0870 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1202   -0.7024    2.1714 H   0  0  0  0  0  0  0  0  0  0  0  0
 10  9  1  0
  9  8  1  0
  8  7  1  0
  7  6  1  0
  6 13  1  0
 13 14  1  0
 13 11  1  0
 11 12  1  0
  6  5  1  0
  5  4  1  0
  4  3  1  0
  3  2  1  0
  2  1  2  0
  2 17  1  0
 17 15  1  0
 15 16  2  0
 11  8  1  0
 15  5  1  0
 10 26  1  0
  9 24  1  0
  9 25  1  0
  8 23  1  1
  6 22  1  1
 13 29  1  6
 14 30  1  0
 11 27  1  6
 12 28  1  0
  4 20  1  0
  4 21  1  0
  3 18  1  0
  3 19  1  0
 17 31  1  0
M  END


  Mrv0541 02231218332D          

 17 18  0  0  1  0            999 V2000
   18.1059   -6.9732    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.9863   -6.7182    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.5410   -8.4252    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   19.1563   -8.3390    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.4384   -3.1883    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.0095   -5.6633    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.4384   -5.6633    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   16.7240   -4.4257    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   17.4384   -6.4883    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   16.7710   -6.9732    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   17.0259   -7.7577    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   17.8509   -7.7577    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   18.1528   -5.2509    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.1528   -4.4257    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.3359   -8.4252    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.7240   -5.2509    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.4384   -4.0133    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  9  1  0  0  0  0
  1 12  1  0  0  0  0
 10  2  1  1  0  0  0
 11  3  1  1  0  0  0
  4 15  1  0  0  0  0
  5 17  2  0  0  0  0
  6 16  2  0  0  0  0
  9  7  1  6  0  0  0
  7 13  1  0  0  0  0
  7 16  1  0  0  0  0
  8 16  1  0  0  0  0
  8 17  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 15  1  6  0  0  0
 13 14  1  0  0  0  0
 14 17  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0086597

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1CCC(=O)NC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C9H14N2O6/c12-3-4-6(14)7(15)8(17-4)11-2-1-5(13)10-9(11)16/h4,6-8,12,14-15H,1-3H2,(H,10,13,16)/t4-,6-,7-,8-/m1/s1

> <INCHI_KEY>
ZPTBLXKRQACLCR-XVFCMESISA-N

> <FORMULA>
C9H14N2O6

> <MOLECULAR_WEIGHT>
246.2173

> <EXACT_MASS>
246.08518619

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_AVERAGE_POLARIZABILITY>
22.979371465591967

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,3-diazinane-2,4-dione

> <ALOGPS_LOGP>
-2.10

> <JCHEM_LOGP>
-2.773158873

> <ALOGPS_LOGS>
-0.03

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.679741618594914

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.585075095621693

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9802898593286598

> <JCHEM_POLAR_SURFACE_AREA>
119.33

> <JCHEM_REFRACTIVITY>
52.3418

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.31e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
dihydrouridine

> <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  O   UNK     0      33.798 -13.017   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      29.841 -12.541   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      30.877 -15.727   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      35.758 -15.566   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0      32.552  -5.951   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0      29.884 -10.571   0.000  0.00  0.00           O+0
HETATM    7  N   UNK     0      32.552 -10.571   0.000  0.00  0.00           N+0
HETATM    8  N   UNK     0      31.218  -8.261   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0      32.552 -12.111   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      31.306 -13.017   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      31.782 -14.481   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      33.322 -14.481   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      33.885  -9.802   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      33.885  -8.261   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      34.227 -15.727   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      31.218  -9.802   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      32.552  -7.491   0.000  0.00  0.00           C+0
CONECT    1    9   12                                                       
CONECT    2   10                                                            
CONECT    3   11                                                            
CONECT    4   15                                                            
CONECT    5   17                                                            
CONECT    6   16                                                            
CONECT    7    9   13   16                                                  
CONECT    8   16   17                                                       
CONECT    9    1    7   10                                                  
CONECT   10    2    9   11                                                  
CONECT   11    3   10   12                                                  
CONECT   12    1   11   15                                                  
CONECT   13    7   14                                                       
CONECT   14   13   17                                                       
CONECT   15    4   12                                                       
CONECT   16    6    7    8                                                  
CONECT   17    5    8   14                                                  
MASTER        0    0    0    0    0    0    0    0   17    0   36    0
END

View in JSmol

Synonyms

Value	Source
1-beta-D-Ribofuranosylhydrouracil	ChEBI
3,4-Dihydrouridine	ChEBI
D	ChEBI
1-b-D-Ribofuranosylhydrouracil	Generator
1-Β-D-ribofuranosylhydrouracil	Generator
Dihydro-1-b-D-ribofuranosyl-2,4(1H,3H)-pyrimidinedione	HMDB
Dihydro-1-beta-delta-ribofuranosyl-2,4(1H,3H)-pyrimidinedione	HMDB
Dihydrouridine	HMDB
5,6-Dihydrouridine	MeSH

Chemical Formula

C₉H₁₄N₂O₆

Average Mass

246.2173 Da

Monoisotopic Mass

246.08519 Da

IUPAC Name

1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,3-diazinane-2,4-dione

Traditional Name

dihydrouridine

CAS Registry Number

Not Available

SMILES

OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1CCC(=O)NC1=O

InChI Identifier

InChI=1S/C9H14N2O6/c12-3-4-6(14)7(15)8(17-4)11-2-1-5(13)10-9(11)16/h4,6-8,12,14-15H,1-3H2,(H,10,13,16)/t4-,6-,7-,8-/m1/s1

InChI Key

ZPTBLXKRQACLCR-XVFCMESISA-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 glycosylamines. Glycosylamines are compounds consisting of an amine with a beta-N-glycosidic bond to a carbohydrate, thus forming a cyclic hemiaminal ether bond (alpha-amino ether).

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Glycosylamines

Alternative Parents

Substituents

N-glycosyl compound
Pentose monosaccharide
Pyrimidone
Hydropyrimidine
1,2,5,6-tetrahydropyrimidine
Monosaccharide
Pyrimidine
Tetrahydrofuran
Secondary alcohol
Carbonic acid derivative
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Oxacycle
Azacycle
Organoheterocyclic compound
Hydrocarbon derivative
Organonitrogen compound
Organopnictogen compound
Carbonyl group
Alcohol
Primary alcohol
Organic nitrogen compound
Organic oxide
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

uridines (CHEBI:23774 )

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	-2.1	ALOGPS
logP	-2.8	ChemAxon
logS	-0.03	ALOGPS
pKa (Strongest Acidic)	11.59	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	119.33 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	52.34 m³·mol⁻¹	ChemAxon
Polarizability	22.98 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

HMDB0000497

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB022076

KNApSAcK ID

Not Available

Chemspider ID

85115

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Dihydrouridine

METLIN ID

5483

PubChem Compound

94312

PDB ID

Not Available

ChEBI ID

23774

Good Scents ID

Not Available

References

General References

Xing F, Martzen MR, Phizicky EM: A conserved family of Saccharomyces cerevisiae synthases effects dihydrouridine modification of tRNA. RNA. 2002 Mar;8(3):370-81. doi: 10.1017/s1355838202029825. [PubMed:12003496 ]
Rider LW, Ottosen MB, Gattis SG, Palfey BA: Mechanism of dihydrouridine synthase 2 from yeast and the importance of modifications for efficient tRNA reduction. J Biol Chem. 2009 Apr 17;284(16):10324-33. doi: 10.1074/jbc.M806137200. Epub 2009 Jan 12. [PubMed:19139092 ]
Nawrot B, Sochacka E: Preparation of short interfering RNA containing the modified nucleosides 2-thiouridine, pseudouridine, or dihydrouridine. Curr Protoc Nucleic Acid Chem. 2009 Jun;Chapter 16:Unit 16.2. doi: 10.1002/0471142700.nc1602s37. [PubMed:19488969 ]
Kaur J, Raj M, Cooperman BS: Fluorescent labeling of tRNA dihydrouridine residues: Mechanism and distribution. RNA. 2011 Jul;17(7):1393-400. doi: 10.1261/rna.2670811. Epub 2011 May 31. [PubMed:21628433 ]
Yu F, Tanaka Y, Yamashita K, Suzuki T, Nakamura A, Hirano N, Suzuki T, Yao M, Tanaka I: Molecular basis of dihydrouridine formation on tRNA. Proc Natl Acad Sci U S A. 2011 Dec 6;108(49):19593-8. doi: 10.1073/pnas.1112352108. Epub 2011 Nov 28. [PubMed:22123979 ]

Showing NP-Card for 5,6-Dihydrouridine (NP0086597)

MOL for NP0086597 (5,6-Dihydrouridine)

3D MOL for NP0086597 (5,6-Dihydrouridine)

3D SDF for NP0086597 (5,6-Dihydrouridine)

3D-SDF for NP0086597 (5,6-Dihydrouridine)

PDB for NP0086597 (5,6-Dihydrouridine)

3D PDB for NP0086597 (5,6-Dihydrouridine)

SMILES for NP0086597 (5,6-Dihydrouridine)

INCHI for NP0086597 (5,6-Dihydrouridine)

Structure for NP0086597 (5,6-Dihydrouridine)

3D Structure for NP0086597 (5,6-Dihydrouridine)