NP-MRD: Showing NP-Card for 1-methyl-pseudouridine (NP0023937)

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Record Information

Version

2.0

Created at

2021-01-06 08:57:32 UTC

Updated at

2021-07-15 17:43:06 UTC

NP-MRD ID

NP0023937

Secondary Accession Numbers

None

Natural Product Identification

Common Name

1-methyl-pseudouridine

Provided By

NPAtlas

Description

1-Methylpseudouridine is also known as m(1)F. 1-methyl-pseudouridine is found in Streptomyces lincolnensis. 1-methyl-pseudouridine was first documented in 1976 (PMID: 993120). Based on a literature review a small amount of articles have been published on 1-Methylpseudouridine (PMID: 22274953) (PMID: 7061499) (PMID: 32090264).

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306242121043D          

 32 33  0  0  0  0            999 V2000
    3.7755    1.8287    0.6844 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0097    0.7191    0.1809 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6437    0.7337    0.2392 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9760   -0.3064   -0.3178 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4865   -0.4374   -0.4967 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.1284    0.7769   -0.1582 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4531    0.3771   -0.0902 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.3984    1.4191    0.4661 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.3243    2.5720   -0.2755 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3462   -0.7764    0.9382 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.4237   -1.6559    0.8188 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0580   -1.3994    0.5352 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.3789   -2.5750   -0.2388 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7227   -1.3335   -0.9158 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1291   -2.3201   -1.4448 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0576   -1.3131   -0.9454 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.6945   -0.2904   -0.4009 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9536   -0.2887   -0.4479 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7464    1.8809    0.0844 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3031    2.8249    0.5089 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0881    1.6744    1.7272 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0877    1.5140    0.6907 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7415   -0.6762   -1.5163 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7875   -0.0254   -1.0616 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2881    1.5144    1.5432 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4231    0.9982    0.2815 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9134    3.2999    0.2878 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2890   -0.3304    1.9361 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1866   -2.4597    0.3147 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3511   -1.6551    1.3121 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7614   -2.1673   -1.0922 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5516   -2.1224   -1.3936 H   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  2  0  0  0  0
  4  5  1  0  0  0  0
  5  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
  7 10  1  0  0  0  0
 10 11  1  0  0  0  0
 10 12  1  0  0  0  0
 12 13  1  0  0  0  0
  4 14  1  0  0  0  0
 14 15  2  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
 17  2  1  0  0  0  0
 12  5  1  0  0  0  0
  1 19  1  0  0  0  0
  1 20  1  0  0  0  0
  1 21  1  0  0  0  0
  3 22  1  0  0  0  0
  5 23  1  6  0  0  0
  7 24  1  6  0  0  0
  8 25  1  0  0  0  0
  8 26  1  0  0  0  0
  9 27  1  0  0  0  0
 10 28  1  1  0  0  0
 11 29  1  0  0  0  0
 12 30  1  1  0  0  0
 13 31  1  0  0  0  0
 16 32  1  0  0  0  0
M  END

     RDKit          3D

 32 33  0  0  0  0  0  0  0  0999 V2000
    3.7755    1.8287    0.6844 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0097    0.7191    0.1809 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6437    0.7337    0.2392 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9760   -0.3064   -0.3178 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4865   -0.4374   -0.4967 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.1284    0.7769   -0.1582 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4531    0.3771   -0.0902 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.3984    1.4191    0.4661 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3243    2.5720   -0.2755 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3462   -0.7764    0.9382 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.4237   -1.6559    0.8188 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0580   -1.3994    0.5352 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.3789   -2.5750   -0.2388 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7227   -1.3335   -0.9158 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1291   -2.3201   -1.4448 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0576   -1.3131   -0.9454 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.6945   -0.2904   -0.4009 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9536   -0.2887   -0.4479 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7464    1.8809    0.0844 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3031    2.8249    0.5089 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0881    1.6744    1.7272 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0877    1.5140    0.6907 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7415   -0.6762   -1.5163 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7875   -0.0254   -1.0616 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2881    1.5144    1.5432 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4231    0.9982    0.2815 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9134    3.2999    0.2878 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2890   -0.3304    1.9361 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1866   -2.4597    0.3147 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3511   -1.6551    1.3121 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7614   -2.1673   -1.0922 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5516   -2.1224   -1.3936 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  7 10  1  0
 10 11  1  0
 10 12  1  0
 12 13  1  0
  4 14  1  0
 14 15  2  0
 14 16  1  0
 16 17  1  0
 17 18  2  0
 17  2  1  0
 12  5  1  0
  1 19  1  0
  1 20  1  0
  1 21  1  0
  3 22  1  0
  5 23  1  6
  7 24  1  6
  8 25  1  0
  8 26  1  0
  9 27  1  0
 10 28  1  1
 11 29  1  0
 12 30  1  1
 13 31  1  0
 16 32  1  0
M  END


  Mrv1652306242121043D          

 32 33  0  0  0  0            999 V2000
    3.7755    1.8287    0.6844 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0097    0.7191    0.1809 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6437    0.7337    0.2392 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9760   -0.3064   -0.3178 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4865   -0.4374   -0.4967 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.1284    0.7769   -0.1582 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4531    0.3771   -0.0902 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.3984    1.4191    0.4661 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.3243    2.5720   -0.2755 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3462   -0.7764    0.9382 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.4237   -1.6559    0.8188 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0580   -1.3994    0.5352 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.3789   -2.5750   -0.2388 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7227   -1.3335   -0.9158 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1291   -2.3201   -1.4448 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0576   -1.3131   -0.9454 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.6945   -0.2904   -0.4009 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9536   -0.2887   -0.4479 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7464    1.8809    0.0844 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3031    2.8249    0.5089 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0881    1.6744    1.7272 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0877    1.5140    0.6907 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7415   -0.6762   -1.5163 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7875   -0.0254   -1.0616 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2881    1.5144    1.5432 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4231    0.9982    0.2815 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9134    3.2999    0.2878 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2890   -0.3304    1.9361 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1866   -2.4597    0.3147 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3511   -1.6551    1.3121 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7614   -2.1673   -1.0922 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5516   -2.1224   -1.3936 H   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  2  0  0  0  0
  4  5  1  0  0  0  0
  5  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
  7 10  1  0  0  0  0
 10 11  1  0  0  0  0
 10 12  1  0  0  0  0
 12 13  1  0  0  0  0
  4 14  1  0  0  0  0
 14 15  2  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
 17  2  1  0  0  0  0
 12  5  1  0  0  0  0
  1 19  1  0  0  0  0
  1 20  1  0  0  0  0
  1 21  1  0  0  0  0
  3 22  1  0  0  0  0
  5 23  1  6  0  0  0
  7 24  1  6  0  0  0
  8 25  1  0  0  0  0
  8 26  1  0  0  0  0
  9 27  1  0  0  0  0
 10 28  1  1  0  0  0
 11 29  1  0  0  0  0
 12 30  1  1  0  0  0
 13 31  1  0  0  0  0
 16 32  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0023937

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]OC([H])([H])[C@@]1([H])O[C@@]([H])(C2=C([H])N(C(=O)N([H])C2=O)C([H])([H])[H])[C@]([H])(O[H])[C@]1([H])O[H]

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

> <INCHI_KEY>
UVBYMVOUBXYSFV-XUTVFYLZSA-N

> <FORMULA>
C10H14N2O6

> <MOLECULAR_WEIGHT>
258.23

> <EXACT_MASS>
258.085186179

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
32

> <JCHEM_AVERAGE_POLARIZABILITY>
24.123957190264584

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-1.76

> <JCHEM_LOGP>
-2.876471797333333

> <ALOGPS_LOGS>
-0.27

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.781959979909338

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.639977112593556

> <JCHEM_PKA_STRONGEST_BASIC>
-2.979200101316839

> <JCHEM_POLAR_SURFACE_AREA>
119.33000000000001

> <JCHEM_REFRACTIVITY>
57.3377

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.40e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-[(2S,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1-methyl-3H-pyrimidine-2,4-dione

> <JCHEM_VEBER_RULE>
0

$$$$

     RDKit          3D

 32 33  0  0  0  0  0  0  0  0999 V2000
    3.7755    1.8287    0.6844 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0097    0.7191    0.1809 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6437    0.7337    0.2392 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9760   -0.3064   -0.3178 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4865   -0.4374   -0.4967 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.1284    0.7769   -0.1582 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4531    0.3771   -0.0902 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.3984    1.4191    0.4661 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3243    2.5720   -0.2755 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3462   -0.7764    0.9382 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.4237   -1.6559    0.8188 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0580   -1.3994    0.5352 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.3789   -2.5750   -0.2388 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7227   -1.3335   -0.9158 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1291   -2.3201   -1.4448 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0576   -1.3131   -0.9454 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.6945   -0.2904   -0.4009 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9536   -0.2887   -0.4479 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7464    1.8809    0.0844 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3031    2.8249    0.5089 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0881    1.6744    1.7272 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0877    1.5140    0.6907 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7415   -0.6762   -1.5163 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7875   -0.0254   -1.0616 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2881    1.5144    1.5432 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4231    0.9982    0.2815 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9134    3.2999    0.2878 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2890   -0.3304    1.9361 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1866   -2.4597    0.3147 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3511   -1.6551    1.3121 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7614   -2.1673   -1.0922 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5516   -2.1224   -1.3936 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  7 10  1  0
 10 11  1  0
 10 12  1  0
 12 13  1  0
  4 14  1  0
 14 15  2  0
 14 16  1  0
 16 17  1  0
 17 18  2  0
 17  2  1  0
 12  5  1  0
  1 19  1  0
  1 20  1  0
  1 21  1  0
  3 22  1  0
  5 23  1  6
  7 24  1  6
  8 25  1  0
  8 26  1  0
  9 27  1  0
 10 28  1  1
 11 29  1  0
 12 30  1  1
 13 31  1  0
 16 32  1  0
M  END

HEADER    PROTEIN                                 24-JUN-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-JUN-21         0                                  
HETATM    1  C   UNK     0       3.776   1.829   0.684  0.00  0.00           C+0
HETATM    2  N   UNK     0       3.010   0.719   0.181  0.00  0.00           N+0
HETATM    3  C   UNK     0       1.644   0.734   0.239  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.976  -0.306  -0.318  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.487  -0.437  -0.497  0.00  0.00           C+0
HETATM    6  O   UNK     0      -1.128   0.777  -0.158  0.00  0.00           O+0
HETATM    7  C   UNK     0      -2.453   0.377  -0.090  0.00  0.00           C+0
HETATM    8  C   UNK     0      -3.398   1.419   0.466  0.00  0.00           C+0
HETATM    9  O   UNK     0      -3.324   2.572  -0.276  0.00  0.00           O+0
HETATM   10  C   UNK     0      -2.346  -0.776   0.938  0.00  0.00           C+0
HETATM   11  O   UNK     0      -3.424  -1.656   0.819  0.00  0.00           O+0
HETATM   12  C   UNK     0      -1.058  -1.399   0.535  0.00  0.00           C+0
HETATM   13  O   UNK     0      -1.379  -2.575  -0.239  0.00  0.00           O+0
HETATM   14  C   UNK     0       1.723  -1.333  -0.916  0.00  0.00           C+0
HETATM   15  O   UNK     0       1.129  -2.320  -1.445  0.00  0.00           O+0
HETATM   16  N   UNK     0       3.058  -1.313  -0.945  0.00  0.00           N+0
HETATM   17  C   UNK     0       3.695  -0.290  -0.401  0.00  0.00           C+0
HETATM   18  O   UNK     0       4.954  -0.289  -0.448  0.00  0.00           O+0
HETATM   19  H   UNK     0       4.746   1.881   0.084  0.00  0.00           H+0
HETATM   20  H   UNK     0       3.303   2.825   0.509  0.00  0.00           H+0
HETATM   21  H   UNK     0       4.088   1.674   1.727  0.00  0.00           H+0
HETATM   22  H   UNK     0       1.088   1.514   0.691  0.00  0.00           H+0
HETATM   23  H   UNK     0      -0.742  -0.676  -1.516  0.00  0.00           H+0
HETATM   24  H   UNK     0      -2.788  -0.025  -1.062  0.00  0.00           H+0
HETATM   25  H   UNK     0      -3.288   1.514   1.543  0.00  0.00           H+0
HETATM   26  H   UNK     0      -4.423   0.998   0.282  0.00  0.00           H+0
HETATM   27  H   UNK     0      -2.913   3.300   0.288  0.00  0.00           H+0
HETATM   28  H   UNK     0      -2.289  -0.330   1.936  0.00  0.00           H+0
HETATM   29  H   UNK     0      -3.187  -2.460   0.315  0.00  0.00           H+0
HETATM   30  H   UNK     0      -0.351  -1.655   1.312  0.00  0.00           H+0
HETATM   31  H   UNK     0      -1.761  -2.167  -1.092  0.00  0.00           H+0
HETATM   32  H   UNK     0       3.552  -2.122  -1.394  0.00  0.00           H+0
CONECT    1    2   19   20   21                                             
CONECT    2    1    3   17                                                  
CONECT    3    2    4   22                                                  
CONECT    4    3    5   14                                                  
CONECT    5    4    6   12   23                                             
CONECT    6    5    7                                                       
CONECT    7    6    8   10   24                                             
CONECT    8    7    9   25   26                                             
CONECT    9    8   27                                                       
CONECT   10    7   11   12   28                                             
CONECT   11   10   29                                                       
CONECT   12   10   13    5   30                                             
CONECT   13   12   31                                                       
CONECT   14    4   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14   17   32                                                  
CONECT   17   16   18    2                                                  
CONECT   18   17                                                            
CONECT   19    1                                                            
CONECT   20    1                                                            
CONECT   21    1                                                            
CONECT   22    3                                                            
CONECT   23    5                                                            
CONECT   24    7                                                            
CONECT   25    8                                                            
CONECT   26    8                                                            
CONECT   27    9                                                            
CONECT   28   10                                                            
CONECT   29   11                                                            
CONECT   30   12                                                            
CONECT   31   13                                                            
CONECT   32   16                                                            
MASTER        0    0    0    0    0    0    0    0   32    0   66    0
END

RDKit          3D

32 33  0  0  0  0  0  0  0  0999 V2000
    3.7755    1.8287    0.6844 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0097    0.7191    0.1809 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6437    0.7337    0.2392 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9760   -0.3064   -0.3178 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4865   -0.4374   -0.4967 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.1284    0.7769   -0.1582 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4531    0.3771   -0.0902 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.3984    1.4191    0.4661 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3243    2.5720   -0.2755 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3462   -0.7764    0.9382 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.4237   -1.6559    0.8188 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0580   -1.3994    0.5352 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.3789   -2.5750   -0.2388 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7227   -1.3335   -0.9158 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1291   -2.3201   -1.4448 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0576   -1.3131   -0.9454 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.6945   -0.2904   -0.4009 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9536   -0.2887   -0.4479 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7464    1.8809    0.0844 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3031    2.8249    0.5089 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0881    1.6744    1.7272 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0877    1.5140    0.6907 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7415   -0.6762   -1.5163 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7875   -0.0254   -1.0616 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2881    1.5144    1.5432 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4231    0.9982    0.2815 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9134    3.2999    0.2878 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2890   -0.3304    1.9361 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1866   -2.4597    0.3147 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3511   -1.6551    1.3121 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7614   -2.1673   -1.0922 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5516   -2.1224   -1.3936 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  7 10  1  0
 10 11  1  0
 10 12  1  0
 12 13  1  0
  4 14  1  0
 14 15  2  0
 14 16  1  0
 16 17  1  0
 17 18  2  0
 17  2  1  0
 12  5  1  0
  1 19  1  0
  1 20  1  0
  1 21  1  0
  3 22  1  0
  5 23  1  6
  7 24  1  6
  8 25  1  0
  8 26  1  0
  9 27  1  0
 10 28  1  1
 11 29  1  0
 12 30  1  1
 13 31  1  0
 16 32  1  0
M  END

View in JSmol View NMR Assignments

Synonyms

Value	Source
m(1)F	ChEBI
N1-Methyl-pseudouridine	MeSH

Chemical Formula

C₁₀H₁₄N₂O₆

Average Mass

258.2300 Da

Monoisotopic Mass

258.08519 Da

IUPAC Name

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

Traditional Name

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

CAS Registry Number

Not Available

SMILES

CN1C=C([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)C(=O)NC1=O

InChI Identifier

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

InChI Key

UVBYMVOUBXYSFV-XUTVFYLZSA-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
Streptomyces lincolnensis	NPAtlas	993120

Species Where Detected

Species Name	Source	Reference
Streptomyces platensis	KNApSAcK Database	22123792

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	-1.8	ALOGPS
logP	-2.9	ChemAxon
logS	-0.27	ALOGPS
pKa (Strongest Acidic)	9.64	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	57.34 m³·mol⁻¹	ChemAxon
Polarizability	24.12 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

NPAtlas ID

NPA005708

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00018102

Chemspider ID

89930

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

N1-Methylpseudouridine

METLIN ID

Not Available

PubChem Compound

99543

PDB ID

Not Available

ChEBI ID

19068

Good Scents ID

Not Available

References

General References

Argoudelis AD, Mizsak SA: 1-methylpseudouridine, a metabolite of Streptomyces platensis. J Antibiot (Tokyo). 1976 Aug;29(8):818-23. doi: 10.7164/antibiotics.29.818. [PubMed:993120 ]
Chatterjee K, Blaby IK, Thiaville PC, Majumder M, Grosjean H, Yuan YA, Gupta R, de Crecy-Lagard V: The archaeal COG1901/DUF358 SPOUT-methyltransferase members, together with pseudouridine synthase Pus10, catalyze the formation of 1-methylpseudouridine at position 54 of tRNA. RNA. 2012 Mar;18(3):421-33. doi: 10.1261/rna.030841.111. Epub 2012 Jan 24. [PubMed:22274953 ]
Pang H, Ihara M, Kuchino Y, Nishimura S, Gupta R, Woese CR, McCloskey JA: Structure of a modified nucleoside in archaebacterial tRNA which replaces ribosylthymine. 1-Methylpseudouridine. J Biol Chem. 1982 Apr 10;257(7):3589-92. [PubMed:7061499 ]
Parr CJC, Wada S, Kotake K, Kameda S, Matsuura S, Sakashita S, Park S, Sugiyama H, Kuang Y, Saito H: N 1-Methylpseudouridine substitution enhances the performance of synthetic mRNA switches in cells. Nucleic Acids Res. 2020 Apr 6;48(6):e35. doi: 10.1093/nar/gkaa070. [PubMed:32090264 ]

Showing NP-Card for 1-methyl-pseudouridine (NP0023937)

MOL for NP0023937 (1-methyl-pseudouridine)

3D MOL for NP0023937 (1-methyl-pseudouridine)

3D SDF for NP0023937 (1-methyl-pseudouridine)

3D-SDF for NP0023937 (1-methyl-pseudouridine)

PDB for NP0023937 (1-methyl-pseudouridine)

3D PDB for NP0023937 (1-methyl-pseudouridine)

SMILES for NP0023937 (1-methyl-pseudouridine)

INCHI for NP0023937 (1-methyl-pseudouridine)

Structure for NP0023937 (1-methyl-pseudouridine)

3D Structure for NP0023937 (1-methyl-pseudouridine)