NP-MRD: Showing NP-Card for 5-hydroxymethyluridine (NP0011700)

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Record Information

Version

2.0

Created at

2021-01-05 21:18:40 UTC

Updated at

2021-07-15 17:09:40 UTC

NP-MRD ID

NP0011700

Secondary Accession Numbers

None

Natural Product Identification

Common Name

5-hydroxymethyluridine

Provided By

NPAtlas

Description

5-hydroxymethyluridine is found in Serratia plymuthica. It was first documented in 1990 (PMID: 2358410). Based on a literature review very few articles have been published on ACMC-20mt2g.

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306242116583D          

 35 36  0  0  0  0            999 V2000
    3.3340    2.0050    0.6231 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3505    2.2847   -0.5975 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6278    1.2957   -1.5110 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8882   -0.0293   -1.1639 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.7882   -0.7485   -0.5015 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5466   -0.2041   -0.2803 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5430   -0.8979    0.3138 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7580   -0.3660    0.5604 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7668    0.9571    0.0960 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0797    1.3377   -0.0466 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.5086    2.1595    1.1634 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.8256    2.5653    1.0631 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9243    0.1153   -0.1844 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.7015    0.0986   -1.3310 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8595   -0.9901   -0.2171 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.4439   -2.0906    0.4153 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8218   -2.1585    0.6801 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0600   -2.8588    1.2353 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0219   -2.7332    0.4833 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.0248   -2.0649   -0.1008 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1371   -2.6242   -0.2735 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1510    3.2875   -0.9422 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8358   -0.1153   -0.5508 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1012   -0.6072   -2.1140 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2922    0.7941   -0.5756 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0305   -0.3190    1.6293 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1605    1.9256   -0.9810 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4031    1.5240    2.0600 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8752    3.0554    1.2583 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9049    3.5481    0.8511 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5161   -0.0092    0.7466 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4973   -0.4547   -1.1361 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5385   -1.2150   -1.2447 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8190   -2.7333   -0.2122 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2092   -3.7340    0.7855 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  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  2  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
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 10 13  1  0  0  0  0
 13 14  1  0  0  0  0
 13 15  1  0  0  0  0
 15 16  1  0  0  0  0
  7 17  1  0  0  0  0
 17 18  2  0  0  0  0
 17 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  2  0  0  0  0
 20  5  1  0  0  0  0
 15  8  1  0  0  0  0
  2 22  1  0  0  0  0
  4 23  1  0  0  0  0
  4 24  1  0  0  0  0
  6 25  1  0  0  0  0
  8 26  1  1  0  0  0
 10 27  1  6  0  0  0
 11 28  1  0  0  0  0
 11 29  1  0  0  0  0
 12 30  1  0  0  0  0
 13 31  1  1  0  0  0
 14 32  1  0  0  0  0
 15 33  1  6  0  0  0
 16 34  1  0  0  0  0
 19 35  1  0  0  0  0
M  END

     RDKit          3D

 35 36  0  0  0  0  0  0  0  0999 V2000
    3.3340    2.0050    0.6231 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3505    2.2847   -0.5975 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6278    1.2957   -1.5110 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8882   -0.0293   -1.1639 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7882   -0.7485   -0.5015 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5466   -0.2041   -0.2803 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5430   -0.8979    0.3138 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7580   -0.3660    0.5604 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7668    0.9571    0.0960 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0797    1.3377   -0.0466 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.5086    2.1595    1.1634 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8256    2.5653    1.0631 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9243    0.1153   -0.1844 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.7015    0.0986   -1.3310 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8595   -0.9901   -0.2171 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.4439   -2.0906    0.4153 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8218   -2.1585    0.6801 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0600   -2.8588    1.2353 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0219   -2.7332    0.4833 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.0248   -2.0649   -0.1008 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1371   -2.6242   -0.2735 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1510    3.2875   -0.9422 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8358   -0.1153   -0.5508 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1012   -0.6072   -2.1140 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2922    0.7941   -0.5756 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0305   -0.3190    1.6293 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1605    1.9256   -0.9810 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4031    1.5240    2.0600 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8752    3.0554    1.2583 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9049    3.5481    0.8511 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5161   -0.0092    0.7466 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4973   -0.4547   -1.1361 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5385   -1.2150   -1.2447 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8190   -2.7333   -0.2122 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2092   -3.7340    0.7855 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 10 13  1  0
 13 14  1  0
 13 15  1  0
 15 16  1  0
  7 17  1  0
 17 18  2  0
 17 19  1  0
 19 20  1  0
 20 21  2  0
 20  5  1  0
 15  8  1  0
  2 22  1  0
  4 23  1  0
  4 24  1  0
  6 25  1  0
  8 26  1  1
 10 27  1  6
 11 28  1  0
 11 29  1  0
 12 30  1  0
 13 31  1  1
 14 32  1  0
 15 33  1  6
 16 34  1  0
 19 35  1  0
M  END


  Mrv1652306242116583D          

 35 36  0  0  0  0            999 V2000
    3.3340    2.0050    0.6231 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3505    2.2847   -0.5975 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6278    1.2957   -1.5110 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8882   -0.0293   -1.1639 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.7882   -0.7485   -0.5015 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5466   -0.2041   -0.2803 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5430   -0.8979    0.3138 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7580   -0.3660    0.5604 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7668    0.9571    0.0960 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0797    1.3377   -0.0466 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.5086    2.1595    1.1634 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.8256    2.5653    1.0631 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9243    0.1153   -0.1844 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.7015    0.0986   -1.3310 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8595   -0.9901   -0.2171 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.4439   -2.0906    0.4153 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8218   -2.1585    0.6801 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0600   -2.8588    1.2353 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0219   -2.7332    0.4833 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.0248   -2.0649   -0.1008 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1371   -2.6242   -0.2735 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1510    3.2875   -0.9422 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8358   -0.1153   -0.5508 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1012   -0.6072   -2.1140 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2922    0.7941   -0.5756 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0305   -0.3190    1.6293 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1605    1.9256   -0.9810 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4031    1.5240    2.0600 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8752    3.0554    1.2583 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9049    3.5481    0.8511 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5161   -0.0092    0.7466 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4973   -0.4547   -1.1361 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5385   -1.2150   -1.2447 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8190   -2.7333   -0.2122 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2092   -3.7340    0.7855 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  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  2  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
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 10 13  1  0  0  0  0
 13 14  1  0  0  0  0
 13 15  1  0  0  0  0
 15 16  1  0  0  0  0
  7 17  1  0  0  0  0
 17 18  2  0  0  0  0
 17 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  2  0  0  0  0
 20  5  1  0  0  0  0
 15  8  1  0  0  0  0
  2 22  1  0  0  0  0
  4 23  1  0  0  0  0
  4 24  1  0  0  0  0
  6 25  1  0  0  0  0
  8 26  1  1  0  0  0
 10 27  1  6  0  0  0
 11 28  1  0  0  0  0
 11 29  1  0  0  0  0
 12 30  1  0  0  0  0
 13 31  1  1  0  0  0
 14 32  1  0  0  0  0
 15 33  1  6  0  0  0
 16 34  1  0  0  0  0
 19 35  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0011700

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]OC([H])([H])[C@@]1([H])O[C@]([H])(N2C([H])=C(C(=O)N([H])C2=O)C([H])([H])OC([H])=O)[C@@]([H])(O[H])[C@]1([H])O[H]

> <INCHI_IDENTIFIER>
InChI=1S/C11H14N2O8/c14-2-6-7(16)8(17)10(21-6)13-1-5(3-20-4-15)9(18)12-11(13)19/h1,4,6-8,10,14,16-17H,2-3H2,(H,12,18,19)/t6-,7-,8+,10+/m1/s1

> <INCHI_KEY>
JZTZVTCZKZHFNF-UHFFFAOYSA-N

> <FORMULA>
C11H14N2O8

> <MOLECULAR_WEIGHT>
302.239

> <EXACT_MASS>
302.075015419

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
35

> <JCHEM_AVERAGE_POLARIZABILITY>
26.91691410203441

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{1-[(2S,3S,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl}methyl formate

> <ALOGPS_LOGP>
-1.72

> <JCHEM_LOGP>
-2.9080361066666667

> <ALOGPS_LOGS>
-0.84

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.619974992324803

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.583882148321345

> <JCHEM_PKA_STRONGEST_BASIC>
-2.980299639939841

> <JCHEM_POLAR_SURFACE_AREA>
145.63

> <JCHEM_REFRACTIVITY>
63.358399999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.40e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
{1-[(2S,3S,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-2,4-dioxo-3H-pyrimidin-5-yl}methyl formate

> <JCHEM_VEBER_RULE>
0

$$$$

     RDKit          3D

 35 36  0  0  0  0  0  0  0  0999 V2000
    3.3340    2.0050    0.6231 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3505    2.2847   -0.5975 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6278    1.2957   -1.5110 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8882   -0.0293   -1.1639 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7882   -0.7485   -0.5015 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5466   -0.2041   -0.2803 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5430   -0.8979    0.3138 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7580   -0.3660    0.5604 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7668    0.9571    0.0960 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0797    1.3377   -0.0466 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.5086    2.1595    1.1634 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8256    2.5653    1.0631 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9243    0.1153   -0.1844 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.7015    0.0986   -1.3310 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8595   -0.9901   -0.2171 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.4439   -2.0906    0.4153 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8218   -2.1585    0.6801 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0600   -2.8588    1.2353 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0219   -2.7332    0.4833 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.0248   -2.0649   -0.1008 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1371   -2.6242   -0.2735 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1510    3.2875   -0.9422 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8358   -0.1153   -0.5508 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1012   -0.6072   -2.1140 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2922    0.7941   -0.5756 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0305   -0.3190    1.6293 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1605    1.9256   -0.9810 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4031    1.5240    2.0600 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8752    3.0554    1.2583 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9049    3.5481    0.8511 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5161   -0.0092    0.7466 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4973   -0.4547   -1.1361 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5385   -1.2150   -1.2447 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8190   -2.7333   -0.2122 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2092   -3.7340    0.7855 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 10 13  1  0
 13 14  1  0
 13 15  1  0
 15 16  1  0
  7 17  1  0
 17 18  2  0
 17 19  1  0
 19 20  1  0
 20 21  2  0
 20  5  1  0
 15  8  1  0
  2 22  1  0
  4 23  1  0
  4 24  1  0
  6 25  1  0
  8 26  1  1
 10 27  1  6
 11 28  1  0
 11 29  1  0
 12 30  1  0
 13 31  1  1
 14 32  1  0
 15 33  1  6
 16 34  1  0
 19 35  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  O   UNK     0       3.334   2.005   0.623  0.00  0.00           O+0
HETATM    2  C   UNK     0       3.350   2.285  -0.598  0.00  0.00           C+0
HETATM    3  O   UNK     0       3.628   1.296  -1.511  0.00  0.00           O+0
HETATM    4  C   UNK     0       3.888  -0.029  -1.164  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.788  -0.749  -0.501  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.547  -0.204  -0.280  0.00  0.00           C+0
HETATM    7  N   UNK     0       0.543  -0.898   0.314  0.00  0.00           N+0
HETATM    8  C   UNK     0      -0.758  -0.366   0.560  0.00  0.00           C+0
HETATM    9  O   UNK     0      -0.767   0.957   0.096  0.00  0.00           O+0
HETATM   10  C   UNK     0      -2.080   1.338  -0.047  0.00  0.00           C+0
HETATM   11  C   UNK     0      -2.509   2.159   1.163  0.00  0.00           C+0
HETATM   12  O   UNK     0      -3.826   2.565   1.063  0.00  0.00           O+0
HETATM   13  C   UNK     0      -2.924   0.115  -0.184  0.00  0.00           C+0
HETATM   14  O   UNK     0      -3.701   0.099  -1.331  0.00  0.00           O+0
HETATM   15  C   UNK     0      -1.859  -0.990  -0.217  0.00  0.00           C+0
HETATM   16  O   UNK     0      -2.444  -2.091   0.415  0.00  0.00           O+0
HETATM   17  C   UNK     0       0.822  -2.159   0.680  0.00  0.00           C+0
HETATM   18  O   UNK     0      -0.060  -2.859   1.235  0.00  0.00           O+0
HETATM   19  N   UNK     0       2.022  -2.733   0.483  0.00  0.00           N+0
HETATM   20  C   UNK     0       3.025  -2.065  -0.101  0.00  0.00           C+0
HETATM   21  O   UNK     0       4.137  -2.624  -0.274  0.00  0.00           O+0
HETATM   22  H   UNK     0       3.151   3.288  -0.942  0.00  0.00           H+0
HETATM   23  H   UNK     0       4.836  -0.115  -0.551  0.00  0.00           H+0
HETATM   24  H   UNK     0       4.101  -0.607  -2.114  0.00  0.00           H+0
HETATM   25  H   UNK     0       1.292   0.794  -0.576  0.00  0.00           H+0
HETATM   26  H   UNK     0      -1.030  -0.319   1.629  0.00  0.00           H+0
HETATM   27  H   UNK     0      -2.160   1.926  -0.981  0.00  0.00           H+0
HETATM   28  H   UNK     0      -2.403   1.524   2.060  0.00  0.00           H+0
HETATM   29  H   UNK     0      -1.875   3.055   1.258  0.00  0.00           H+0
HETATM   30  H   UNK     0      -3.905   3.548   0.851  0.00  0.00           H+0
HETATM   31  H   UNK     0      -3.516  -0.009   0.747  0.00  0.00           H+0
HETATM   32  H   UNK     0      -4.497  -0.455  -1.136  0.00  0.00           H+0
HETATM   33  H   UNK     0      -1.539  -1.215  -1.245  0.00  0.00           H+0
HETATM   34  H   UNK     0      -2.819  -2.733  -0.212  0.00  0.00           H+0
HETATM   35  H   UNK     0       2.209  -3.734   0.786  0.00  0.00           H+0
CONECT    1    2                                                            
CONECT    2    1    3   22                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   23   24                                             
CONECT    5    4    6   20                                                  
CONECT    6    5    7   25                                                  
CONECT    7    6    8   17                                                  
CONECT    8    7    9   15   26                                             
CONECT    9    8   10                                                       
CONECT   10    9   11   13   27                                             
CONECT   11   10   12   28   29                                             
CONECT   12   11   30                                                       
CONECT   13   10   14   15   31                                             
CONECT   14   13   32                                                       
CONECT   15   13   16    8   33                                             
CONECT   16   15   34                                                       
CONECT   17    7   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   20   35                                                  
CONECT   20   19   21    5                                                  
CONECT   21   20                                                            
CONECT   22    2                                                            
CONECT   23    4                                                            
CONECT   24    4                                                            
CONECT   25    6                                                            
CONECT   26    8                                                            
CONECT   27   10                                                            
CONECT   28   11                                                            
CONECT   29   11                                                            
CONECT   30   12                                                            
CONECT   31   13                                                            
CONECT   32   14                                                            
CONECT   33   15                                                            
CONECT   34   16                                                            
CONECT   35   19                                                            
MASTER        0    0    0    0    0    0    0    0   35    0   72    0
END

RDKit          3D

35 36  0  0  0  0  0  0  0  0999 V2000
    3.3340    2.0050    0.6231 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3505    2.2847   -0.5975 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6278    1.2957   -1.5110 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8882   -0.0293   -1.1639 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7882   -0.7485   -0.5015 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5466   -0.2041   -0.2803 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5430   -0.8979    0.3138 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7580   -0.3660    0.5604 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7668    0.9571    0.0960 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0797    1.3377   -0.0466 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.5086    2.1595    1.1634 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8256    2.5653    1.0631 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9243    0.1153   -0.1844 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.7015    0.0986   -1.3310 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8595   -0.9901   -0.2171 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.4439   -2.0906    0.4153 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8218   -2.1585    0.6801 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0600   -2.8588    1.2353 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0219   -2.7332    0.4833 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.0248   -2.0649   -0.1008 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1371   -2.6242   -0.2735 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1510    3.2875   -0.9422 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8358   -0.1153   -0.5508 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1012   -0.6072   -2.1140 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2922    0.7941   -0.5756 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0305   -0.3190    1.6293 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1605    1.9256   -0.9810 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4031    1.5240    2.0600 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8752    3.0554    1.2583 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9049    3.5481    0.8511 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5161   -0.0092    0.7466 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4973   -0.4547   -1.1361 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5385   -1.2150   -1.2447 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8190   -2.7333   -0.2122 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2092   -3.7340    0.7855 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 10 13  1  0
 13 14  1  0
 13 15  1  0
 15 16  1  0
  7 17  1  0
 17 18  2  0
 17 19  1  0
 19 20  1  0
 20 21  2  0
 20  5  1  0
 15  8  1  0
  2 22  1  0
  4 23  1  0
  4 24  1  0
  6 25  1  0
  8 26  1  1
 10 27  1  6
 11 28  1  0
 11 29  1  0
 12 30  1  0
 13 31  1  1
 14 32  1  0
 15 33  1  6
 16 34  1  0
 19 35  1  0
M  END

View in JSmol View NMR Assignments

Synonyms

Value	Source
5-Formyloxymethyluridine	MeSH
{1-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-hydroxy-2-oxo-1,2-dihydropyrimidin-5-yl}methyl formic acid	Generator

Chemical Formula

C₁₁H₁₄N₂O₈

Average Mass

302.2390 Da

Monoisotopic Mass

302.07502 Da

IUPAC Name

{1-[(2S,3S,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl}methyl formate

Traditional Name

{1-[(2S,3S,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-2,4-dioxo-3H-pyrimidin-5-yl}methyl formate

CAS Registry Number

Not Available

SMILES

OCC1OC(C(O)C1O)N1C=C(COC=O)C(=O)NC1=O

InChI Identifier

InChI=1S/C11H14N2O8/c14-2-6-7(16)8(17)10(21-6)13-1-5(3-20-4-15)9(18)12-11(13)19/h1,4,6-8,10,14,16-17H,2-3H2,(H,12,18,19)

InChI Key

JZTZVTCZKZHFNF-UHFFFAOYSA-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
Serratia plymuthica	NPAtlas	2358410

Chemical Taxonomy

Description

This compound belongs to the class of organic compounds known as pyrimidine nucleosides. These are compounds comprising a pyrimidine base attached to a ribosyl or deoxyribosyl moiety.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Pyrimidine nucleosides

Sub Class

Not Available

Direct Parent

Pyrimidine nucleosides

Alternative Parents

Substituents

Pyrimidine nucleoside
Glycosyl compound
N-glycosyl compound
Pentose monosaccharide
Hydroxypyrimidine
Pyrimidone
Hydropyrimidine
Monosaccharide
Pyrimidine
Tetrahydrofuran
Heteroaromatic compound
Secondary alcohol
Carboxylic acid ester
Organoheterocyclic compound
Oxacycle
Azacycle
Carboxylic acid derivative
Monocarboxylic acid or derivatives
Hydrocarbon derivative
Organonitrogen compound
Organooxygen compound
Alcohol
Organic oxygen compound
Organic nitrogen compound
Organopnictogen compound
Primary alcohol
Organic oxide
Carbonyl group
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic 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	-1.7	ALOGPS
logP	-2.9	ChemAxon
logS	-0.84	ALOGPS
pKa (Strongest Acidic)	9.58	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	145.63 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	63.36 m³·mol⁻¹	ChemAxon
Polarizability	26.92 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

NPA002501

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

26502603

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

53461941

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Isshiki K, Sawa T, Naganawa H, Hattori S, Ikeda T, Homma Y, Hamada M, Takeuchi T: A novel nucleoside antibiotic, 5-formyloxymethyluridine. J Antibiot (Tokyo). 1990 May;43(5):584-5. doi: 10.7164/antibiotics.43.584. [PubMed:2358410 ]

Showing NP-Card for 5-hydroxymethyluridine (NP0011700)

MOL for NP0011700 (5-hydroxymethyluridine)

3D MOL for NP0011700 (5-hydroxymethyluridine)

3D SDF for NP0011700 (5-hydroxymethyluridine)

3D-SDF for NP0011700 (5-hydroxymethyluridine)

PDB for NP0011700 (5-hydroxymethyluridine)

3D PDB for NP0011700 (5-hydroxymethyluridine)

SMILES for NP0011700 (5-hydroxymethyluridine)

INCHI for NP0011700 (5-hydroxymethyluridine)

Structure for NP0011700 (5-hydroxymethyluridine)

3D Structure for NP0011700 (5-hydroxymethyluridine)