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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-11 11:42:52 UTC

Update Date

2021-09-26 23:06:28 UTC

HMDB ID

HMDB0253320

Secondary Accession Numbers

None

Metabolite Identification

Common Name

[(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate

Description

[(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate belongs to the class of organic compounds known as pyrimidine 2',3'-dideoxyribonucleosides. Pyrimidine 2',3'-dideoxyribonucleosides are compounds consisting of a pyrimidine linked to a ribose which lacks a hydroxyl group at positions 2 and 3. Based on a literature review very few articles have been published on [(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate. This compound has been identified in human blood as reported by (PMID: 31557052 ). [(2s,3s,5r)-3-azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2s,3s)-2-amino-3-methylpentanoate is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically [(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

  Mrv1652309112113432D          

 27 28  0  0  0  0            999 V2000
    0.4817   -6.0167    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1962   -5.6042    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9106   -6.0167    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9106   -6.8417    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6251   -5.6042    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3396   -6.0167    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3396   -6.8417    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0540   -5.6042    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7685   -6.0167    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4830   -5.6042    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5692   -4.7837    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3762   -4.6122    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7887   -5.3267    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2367   -5.9398    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.6092   -5.4129    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    8.0941   -4.7455    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.9146   -4.8317    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.2501   -5.5854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.0706   -5.6716    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.7652   -6.2528    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    7.9447   -6.1666    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.4598   -6.8340    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.3995   -4.1643    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9561   -4.2317    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.1276   -3.4247    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    5.2992   -2.6178    0.0000 N   0  5  0  0  0  0  0  0  0  0  0  0
    2.6251   -4.7792    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  6  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
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 10 14  1  0  0  0  0
 13 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  2  0  0  0  0
 17 18  1  0  0  0  0
 18 19  2  0  0  0  0
 18 20  1  0  0  0  0
 20 21  1  0  0  0  0
 15 21  1  0  0  0  0
 21 22  2  0  0  0  0
 17 23  1  0  0  0  0
 11 24  1  0  0  0  0
 24 25  2  0  0  0  0
 25 26  2  0  0  0  0
  5 27  1  0  0  0  0
M  CHG  2  25   1  26  -1
M  END

HMDB0253320
     RDKit          3D
[(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2...
 51 52  0  0  0  0  0  0  0  0999 V2000
    6.2197   -1.1419   -1.0467 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7465   -0.7883   -1.2416 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4841    0.4670   -0.4439 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3315    1.6220   -0.8892 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0399    0.8920   -0.5099 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5848    1.1712   -1.8433 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1368   -0.0294    0.2239 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4524   -0.3344    1.3990 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9849   -0.5610   -0.3096 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0889   -1.4340    0.3342 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4840   -0.7378    1.5415 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1592    0.4224    1.2159 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5059    0.2425    1.3559 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2805    0.7832    0.2698 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6212    0.7275    0.3400 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3763    1.2395   -0.6890 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8605    1.1739   -0.6032 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7179    1.7953   -1.7630 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4209    2.2589   -2.6955 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3770    1.8343   -1.8004 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6542    1.3307   -0.7888 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3870    1.3667   -0.8224 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7667   -1.2337    1.5806 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4614   -1.6197    2.2908 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1752   -3.0138    2.1680 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8164   -3.7163    3.1286 N   0  0  0  0  0  4  0  0  0  0  0  0
   -0.6906   -4.4936    4.0935 N   0  0  0  0  0  2  0  0  0  0  0  0
    6.4883   -0.9304    0.0122 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3829   -2.2182   -1.2047 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.8684   -0.5172   -1.6959 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5015   -0.6186   -2.2991 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1772   -1.6247   -0.7894 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7106    0.2457    0.6186 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3794    1.5969   -1.9953 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8744    2.5729   -0.5397 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3462    1.5585   -0.4241 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9861    1.8719    0.0506 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2787    0.3231   -2.3673 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8035    1.8521   -1.7757 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6077   -2.3426    0.7143 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7037   -1.7791   -0.3666 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3326   -0.5194    2.2423 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8438    0.7602    2.3017 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0709    0.2745    1.2179 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1854    2.1335   -0.1337 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2699    1.0346   -1.6097 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1884    0.3214    0.0269 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8820    2.2590   -2.6213 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6463   -1.4315    2.1884 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7570   -1.7793    0.6115 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5048   -1.2666    3.3431 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  3  5  1  0
  5  6  1  0
  5  7  1  0
  7  8  2  0
  7  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  2  0
 16 17  1  0
 16 18  1  0
 18 19  2  0
 18 20  1  0
 20 21  1  0
 21 22  2  0
 13 23  1  0
 23 24  1  0
 24 25  1  0
 25 26  2  0
 26 27  2  0
 24 11  1  0
 21 14  1  0
  1 28  1  0
  1 29  1  0
  1 30  1  0
  2 31  1  0
  2 32  1  0
  3 33  1  0
  4 34  1  0
  4 35  1  0
  4 36  1  0
  5 37  1  0
  6 38  1  0
  6 39  1  0
 10 40  1  0
 10 41  1  0
 11 42  1  0
 13 43  1  0
 15 44  1  0
 17 45  1  0
 17 46  1  0
 17 47  1  0
 20 48  1  0
 23 49  1  0
 23 50  1  0
 24 51  1  0
M  CHG  2  26   1  27  -1
M  END

  Mrv1652309112113432D          

 27 28  0  0  0  0            999 V2000
    0.4817   -6.0167    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1962   -5.6042    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9106   -6.0167    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9106   -6.8417    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6251   -5.6042    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3396   -6.0167    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3396   -6.8417    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0540   -5.6042    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7685   -6.0167    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4830   -5.6042    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5692   -4.7837    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3762   -4.6122    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7887   -5.3267    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2367   -5.9398    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.6092   -5.4129    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    8.0941   -4.7455    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.9146   -4.8317    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.2501   -5.5854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.0706   -5.6716    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.7652   -6.2528    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    7.9447   -6.1666    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.4598   -6.8340    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.3995   -4.1643    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9561   -4.2317    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.1276   -3.4247    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    5.2992   -2.6178    0.0000 N   0  5  0  0  0  0  0  0  0  0  0  0
    2.6251   -4.7792    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  6  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
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 10 14  1  0  0  0  0
 13 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  2  0  0  0  0
 17 18  1  0  0  0  0
 18 19  2  0  0  0  0
 18 20  1  0  0  0  0
 20 21  1  0  0  0  0
 15 21  1  0  0  0  0
 21 22  2  0  0  0  0
 17 23  1  0  0  0  0
 11 24  1  0  0  0  0
 24 25  2  0  0  0  0
 25 26  2  0  0  0  0
  5 27  1  0  0  0  0
M  CHG  2  25   1  26  -1
M  END
> <DATABASE_ID>
HMDB0253320

> <DATABASE_NAME>
hmdb

> <SMILES>
CCC(C)C(N)C(=O)OCC1OC(CC1N=[N+]=[N-])N1C=C(C)C(=O)NC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C16H24N6O5/c1-4-8(2)13(17)15(24)26-7-11-10(20-21-18)5-12(27-11)22-6-9(3)14(23)19-16(22)25/h6,8,10-13H,4-5,7,17H2,1-3H3,(H,19,23,25)

> <INCHI_KEY>
QUANSGVUESEHKX-UHFFFAOYSA-N

> <FORMULA>
C16H24N6O5

> <MOLECULAR_WEIGHT>
380.405

> <EXACT_MASS>
380.180817897

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
51

> <JCHEM_AVERAGE_POLARIZABILITY>
38.4729831428821

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
[3-azido-5-(5-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)oxolan-2-yl]methyl 2-amino-3-methylpentanoate

> <ALOGPS_LOGP>
1.44

> <JCHEM_LOGP>
1.1191145379999994

> <ALOGPS_LOGS>
-2.12

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
19.034267259619536

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.961826929165118

> <JCHEM_PKA_STRONGEST_BASIC>
7.4686964504320725

> <JCHEM_POLAR_SURFACE_AREA>
140.39000000000001

> <JCHEM_REFRACTIVITY>
92.30619999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.86e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[3-azido-5-(5-methyl-2,4-dioxo-3H-pyrimidin-1-yl)oxolan-2-yl]methyl 2-amino-3-methylpentanoate

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0253320
     RDKit          3D
[(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2...
 51 52  0  0  0  0  0  0  0  0999 V2000
    6.2197   -1.1419   -1.0467 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7465   -0.7883   -1.2416 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4841    0.4670   -0.4439 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3315    1.6220   -0.8892 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0399    0.8920   -0.5099 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5848    1.1712   -1.8433 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1368   -0.0294    0.2239 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4524   -0.3344    1.3990 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9849   -0.5610   -0.3096 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0889   -1.4340    0.3342 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4840   -0.7378    1.5415 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1592    0.4224    1.2159 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5059    0.2425    1.3559 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2805    0.7832    0.2698 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6212    0.7275    0.3400 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3763    1.2395   -0.6890 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8605    1.1739   -0.6032 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7179    1.7953   -1.7630 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4209    2.2589   -2.6955 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3770    1.8343   -1.8004 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6542    1.3307   -0.7888 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3870    1.3667   -0.8224 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7667   -1.2337    1.5806 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4614   -1.6197    2.2908 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1752   -3.0138    2.1680 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8164   -3.7163    3.1286 N   0  0  0  0  0  4  0  0  0  0  0  0
   -0.6906   -4.4936    4.0935 N   0  0  0  0  0  2  0  0  0  0  0  0
    6.4883   -0.9304    0.0122 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3829   -2.2182   -1.2047 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.8684   -0.5172   -1.6959 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5015   -0.6186   -2.2991 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1772   -1.6247   -0.7894 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7106    0.2457    0.6186 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3794    1.5969   -1.9953 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8744    2.5729   -0.5397 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3462    1.5585   -0.4241 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9861    1.8719    0.0506 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2787    0.3231   -2.3673 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8035    1.8521   -1.7757 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6077   -2.3426    0.7143 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7037   -1.7791   -0.3666 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3326   -0.5194    2.2423 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8438    0.7602    2.3017 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0709    0.2745    1.2179 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1854    2.1335   -0.1337 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2699    1.0346   -1.6097 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1884    0.3214    0.0269 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8820    2.2590   -2.6213 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6463   -1.4315    2.1884 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7570   -1.7793    0.6115 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5048   -1.2666    3.3431 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  3  5  1  0
  5  6  1  0
  5  7  1  0
  7  8  2  0
  7  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  2  0
 16 17  1  0
 16 18  1  0
 18 19  2  0
 18 20  1  0
 20 21  1  0
 21 22  2  0
 13 23  1  0
 23 24  1  0
 24 25  1  0
 25 26  2  0
 26 27  2  0
 24 11  1  0
 21 14  1  0
  1 28  1  0
  1 29  1  0
  1 30  1  0
  2 31  1  0
  2 32  1  0
  3 33  1  0
  4 34  1  0
  4 35  1  0
  4 36  1  0
  5 37  1  0
  6 38  1  0
  6 39  1  0
 10 40  1  0
 10 41  1  0
 11 42  1  0
 13 43  1  0
 15 44  1  0
 17 45  1  0
 17 46  1  0
 17 47  1  0
 20 48  1  0
 23 49  1  0
 23 50  1  0
 24 51  1  0
M  CHG  2  26   1  27  -1
M  END

HEADER    PROTEIN                                 11-SEP-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-21         0                                  
HETATM    1  C   UNK     0       0.899 -11.231   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.233 -10.461   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       3.566 -11.231   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.566 -12.771   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.900 -10.461   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.234 -11.231   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       6.234 -12.771   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       7.568 -10.461   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       8.901 -11.231   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      10.235 -10.461   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      10.396  -8.930   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      11.902  -8.609   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      12.672  -9.943   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      11.642 -11.088   0.000  0.00  0.00           O+0
HETATM   15  N   UNK     0      14.204 -10.104   0.000  0.00  0.00           N+0
HETATM   16  C   UNK     0      15.109  -8.858   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      16.641  -9.019   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      17.267 -10.426   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      18.798 -10.587   0.000  0.00  0.00           O+0
HETATM   20  N   UNK     0      16.362 -11.672   0.000  0.00  0.00           N+0
HETATM   21  C   UNK     0      14.830 -11.511   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      13.925 -12.757   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0      17.546  -7.773   0.000  0.00  0.00           C+0
HETATM   24  N   UNK     0       9.251  -7.899   0.000  0.00  0.00           N+0
HETATM   25  N   UNK     0       9.572  -6.393   0.000  0.00  0.00           N+1
HETATM   26  N   UNK     0       9.892  -4.886   0.000  0.00  0.00           N-1
HETATM   27  N   UNK     0       4.900  -8.921   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6   27                                                  
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11   14                                                  
CONECT   11   10   12   24                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14   15                                                  
CONECT   14   13   10                                                       
CONECT   15   13   16   21                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18   23                                                  
CONECT   18   17   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18   21                                                       
CONECT   21   20   15   22                                                  
CONECT   22   21                                                            
CONECT   23   17                                                            
CONECT   24   11   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25                                                            
CONECT   27    5                                                            
MASTER        0    0    0    0    0    0    0    0   27    0   56    0
END

COMPND    HMDB0253320
HETATM    1  C1  UNL     1       6.220  -1.142  -1.047  1.00  0.00           C  
HETATM    2  C2  UNL     1       4.747  -0.788  -1.242  1.00  0.00           C  
HETATM    3  C3  UNL     1       4.484   0.467  -0.444  1.00  0.00           C  
HETATM    4  C4  UNL     1       5.332   1.622  -0.889  1.00  0.00           C  
HETATM    5  C5  UNL     1       3.040   0.892  -0.510  1.00  0.00           C  
HETATM    6  N1  UNL     1       2.585   1.171  -1.843  1.00  0.00           N  
HETATM    7  C6  UNL     1       2.137  -0.029   0.224  1.00  0.00           C  
HETATM    8  O1  UNL     1       2.452  -0.334   1.399  1.00  0.00           O  
HETATM    9  O2  UNL     1       0.985  -0.561  -0.310  1.00  0.00           O  
HETATM   10  C7  UNL     1       0.089  -1.434   0.334  1.00  0.00           C  
HETATM   11  C8  UNL     1      -0.484  -0.738   1.541  1.00  0.00           C  
HETATM   12  O3  UNL     1      -1.159   0.422   1.216  1.00  0.00           O  
HETATM   13  C9  UNL     1      -2.506   0.243   1.356  1.00  0.00           C  
HETATM   14  N2  UNL     1      -3.280   0.783   0.270  1.00  0.00           N  
HETATM   15  C10 UNL     1      -4.621   0.728   0.340  1.00  0.00           C  
HETATM   16  C11 UNL     1      -5.376   1.239  -0.689  1.00  0.00           C  
HETATM   17  C12 UNL     1      -6.861   1.174  -0.603  1.00  0.00           C  
HETATM   18  C13 UNL     1      -4.718   1.795  -1.763  1.00  0.00           C  
HETATM   19  O4  UNL     1      -5.421   2.259  -2.696  1.00  0.00           O  
HETATM   20  N3  UNL     1      -3.377   1.834  -1.800  1.00  0.00           N  
HETATM   21  C14 UNL     1      -2.654   1.331  -0.789  1.00  0.00           C  
HETATM   22  O5  UNL     1      -1.387   1.367  -0.822  1.00  0.00           O  
HETATM   23  C15 UNL     1      -2.767  -1.234   1.581  1.00  0.00           C  
HETATM   24  C16 UNL     1      -1.461  -1.620   2.291  1.00  0.00           C  
HETATM   25  N4  UNL     1      -1.175  -3.014   2.168  1.00  0.00           N  
HETATM   26  N5  UNL     1      -0.816  -3.716   3.129  1.00  0.00           N1+
HETATM   27  N6  UNL     1      -0.691  -4.494   4.093  1.00  0.00           N1-
HETATM   28  H1  UNL     1       6.488  -0.930   0.012  1.00  0.00           H  
HETATM   29  H2  UNL     1       6.383  -2.218  -1.205  1.00  0.00           H  
HETATM   30  H3  UNL     1       6.868  -0.517  -1.696  1.00  0.00           H  
HETATM   31  H4  UNL     1       4.501  -0.619  -2.299  1.00  0.00           H  
HETATM   32  H5  UNL     1       4.177  -1.625  -0.789  1.00  0.00           H  
HETATM   33  H6  UNL     1       4.711   0.246   0.619  1.00  0.00           H  
HETATM   34  H7  UNL     1       5.379   1.597  -1.995  1.00  0.00           H  
HETATM   35  H8  UNL     1       4.874   2.573  -0.540  1.00  0.00           H  
HETATM   36  H9  UNL     1       6.346   1.558  -0.424  1.00  0.00           H  
HETATM   37  H10 UNL     1       2.986   1.872   0.051  1.00  0.00           H  
HETATM   38  H11 UNL     1       2.279   0.323  -2.367  1.00  0.00           H  
HETATM   39  H12 UNL     1       1.804   1.852  -1.776  1.00  0.00           H  
HETATM   40  H13 UNL     1       0.608  -2.343   0.714  1.00  0.00           H  
HETATM   41  H14 UNL     1      -0.704  -1.779  -0.367  1.00  0.00           H  
HETATM   42  H15 UNL     1       0.333  -0.519   2.242  1.00  0.00           H  
HETATM   43  H16 UNL     1      -2.844   0.760   2.302  1.00  0.00           H  
HETATM   44  H17 UNL     1      -5.071   0.275   1.218  1.00  0.00           H  
HETATM   45  H18 UNL     1      -7.185   2.134  -0.134  1.00  0.00           H  
HETATM   46  H19 UNL     1      -7.270   1.035  -1.610  1.00  0.00           H  
HETATM   47  H20 UNL     1      -7.188   0.321   0.027  1.00  0.00           H  
HETATM   48  H21 UNL     1      -2.882   2.259  -2.621  1.00  0.00           H  
HETATM   49  H22 UNL     1      -3.646  -1.432   2.188  1.00  0.00           H  
HETATM   50  H23 UNL     1      -2.757  -1.779   0.611  1.00  0.00           H  
HETATM   51  H24 UNL     1      -1.505  -1.267   3.343  1.00  0.00           H  
CONECT    1    2   28   29   30
CONECT    2    3   31   32
CONECT    3    4    5   33
CONECT    4   34   35   36
CONECT    5    6    7   37
CONECT    6   38   39
CONECT    7    8    8    9
CONECT    9   10
CONECT   10   11   40   41
CONECT   11   12   24   42
CONECT   12   13
CONECT   13   14   23   43
CONECT   14   15   21
CONECT   15   16   16   44
CONECT   16   17   18
CONECT   17   45   46   47
CONECT   18   19   19   20
CONECT   20   21   48
CONECT   21   22   22
CONECT   23   24   49   50
CONECT   24   25   51
CONECT   25   26   26
CONECT   26   27   27
END

HMDB0253320
     RDKit          3D
[(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2...
 51 52  0  0  0  0  0  0  0  0999 V2000
    6.2197   -1.1419   -1.0467 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7465   -0.7883   -1.2416 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4841    0.4670   -0.4439 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3315    1.6220   -0.8892 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0399    0.8920   -0.5099 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5848    1.1712   -1.8433 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1368   -0.0294    0.2239 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4524   -0.3344    1.3990 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9849   -0.5610   -0.3096 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0889   -1.4340    0.3342 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4840   -0.7378    1.5415 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1592    0.4224    1.2159 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5059    0.2425    1.3559 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2805    0.7832    0.2698 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6212    0.7275    0.3400 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3763    1.2395   -0.6890 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8605    1.1739   -0.6032 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7179    1.7953   -1.7630 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4209    2.2589   -2.6955 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3770    1.8343   -1.8004 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6542    1.3307   -0.7888 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3870    1.3667   -0.8224 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7667   -1.2337    1.5806 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4614   -1.6197    2.2908 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1752   -3.0138    2.1680 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8164   -3.7163    3.1286 N   0  0  0  0  0  4  0  0  0  0  0  0
   -0.6906   -4.4936    4.0935 N   0  0  0  0  0  2  0  0  0  0  0  0
    6.4883   -0.9304    0.0122 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3829   -2.2182   -1.2047 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.8684   -0.5172   -1.6959 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5015   -0.6186   -2.2991 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1772   -1.6247   -0.7894 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7106    0.2457    0.6186 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3794    1.5969   -1.9953 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8744    2.5729   -0.5397 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3462    1.5585   -0.4241 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9861    1.8719    0.0506 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2787    0.3231   -2.3673 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8035    1.8521   -1.7757 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6077   -2.3426    0.7143 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7037   -1.7791   -0.3666 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3326   -0.5194    2.2423 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8438    0.7602    2.3017 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0709    0.2745    1.2179 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1854    2.1335   -0.1337 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2699    1.0346   -1.6097 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1884    0.3214    0.0269 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8820    2.2590   -2.6213 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6463   -1.4315    2.1884 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7570   -1.7793    0.6115 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5048   -1.2666    3.3431 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  3  5  1  0
  5  6  1  0
  5  7  1  0
  7  8  2  0
  7  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  2  0
 16 17  1  0
 16 18  1  0
 18 19  2  0
 18 20  1  0
 20 21  1  0
 21 22  2  0
 13 23  1  0
 23 24  1  0
 24 25  1  0
 25 26  2  0
 26 27  2  0
 24 11  1  0
 21 14  1  0
  1 28  1  0
  1 29  1  0
  1 30  1  0
  2 31  1  0
  2 32  1  0
  3 33  1  0
  4 34  1  0
  4 35  1  0
  4 36  1  0
  5 37  1  0
  6 38  1  0
  6 39  1  0
 10 40  1  0
 10 41  1  0
 11 42  1  0
 13 43  1  0
 15 44  1  0
 17 45  1  0
 17 46  1  0
 17 47  1  0
 20 48  1  0
 23 49  1  0
 23 50  1  0
 24 51  1  0
M  CHG  2  26   1  27  -1
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
[(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoic acid	Generator
[3-Azido-5-(4-hydroxy-5-methyl-2-oxo-1,2-dihydropyrimidin-1-yl)oxolan-2-yl]methyl 2-amino-3-methylpentanoic acid	HMDB

Chemical Formula

C₁₆H₂₄N₆O₅

Average Molecular Weight

380.405

Monoisotopic Molecular Weight

380.180817897

IUPAC Name

[3-azido-5-(5-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)oxolan-2-yl]methyl 2-amino-3-methylpentanoate

Traditional Name

[3-azido-5-(5-methyl-2,4-dioxo-3H-pyrimidin-1-yl)oxolan-2-yl]methyl 2-amino-3-methylpentanoate

CAS Registry Number

Not Available

SMILES

CCC(C)C(N)C(=O)OCC1OC(CC1N=[N+]=[N-])N1C=C(C)C(=O)NC1=O

InChI Identifier

InChI=1S/C16H24N6O5/c1-4-8(2)13(17)15(24)26-7-11-10(20-21-18)5-12(27-11)22-6-9(3)14(23)19-16(22)25/h6,8,10-13H,4-5,7,17H2,1-3H3,(H,19,23,25)

InChI Key

QUANSGVUESEHKX-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyrimidine 2',3'-dideoxyribonucleosides. Pyrimidine 2',3'-dideoxyribonucleosides are compounds consisting of a pyrimidine linked to a ribose which lacks a hydroxyl group at positions 2 and 3.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Pyrimidine nucleosides

Sub Class

Pyrimidine 2',3'-dideoxyribonucleosides

Direct Parent

Pyrimidine 2',3'-dideoxyribonucleosides

Alternative Parents

Substituents

Pyrimidine 2',3'-dideoxyribonucleoside
Isoleucine or derivatives
Alpha-amino acid ester
Alpha-amino acid or derivatives
Fatty acid ester
Pyrimidone
Hydropyrimidine
Fatty acyl
Pyrimidine
Heteroaromatic compound
Oxolane
Vinylogous amide
Amino acid or derivatives
Azo compound
Azo imide
Carboxylic acid ester
Lactam
Urea
Oxacycle
Organoheterocyclic compound
Azacycle
Monocarboxylic acid or derivatives
Carboxylic acid derivative
Organic zwitterion
Hydrocarbon derivative
Organic oxide
Organic nitrogen compound
Primary aliphatic amine
Carbonyl group
Amine
Primary amine
Organonitrogen compound
Organooxygen compound
Organic salt
Organic oxygen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 31557052)

Source

Exogenous

Exogenous (PMID: 31557052)

Process

Not Available

Role

Not Available

Physical Properties

State

Not Available

Experimental Molecular 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

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
logP	1.44	ALOGPS
logP	1.12	ChemAxon
logS	-2.1	ALOGPS
pKa (Strongest Acidic)	9.96	ChemAxon
pKa (Strongest Basic)	7.47	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	140.39 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	92.31 m³·mol⁻¹	ChemAxon
Polarizability	38.47 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DeepCCS	[M+H]+	193.707	30932474
DeepCCS	[M-H]-	191.349	30932474
DeepCCS	[M-2H]-	225.337	30932474
DeepCCS	[M+Na]+	200.972	30932474

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
[(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate	CCC(C)C(N)C(=O)OCC1OC(CC1N=[N+]=[N-])N1C=C(C)C(=O)NC1=O	4253.3	Standard polar	33892256
[(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate	CCC(C)C(N)C(=O)OCC1OC(CC1N=[N+]=[N-])N1C=C(C)C(=O)NC1=O	2685.6	Standard non polar	33892256
[(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate	CCC(C)C(N)C(=O)OCC1OC(CC1N=[N+]=[N-])N1C=C(C)C(=O)NC1=O	2951.4	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
[(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,1TMS,isomer #1	CCC(C)C(N[Si](C)(C)C)C(=O)OCC1OC(N2C=C(C)C(=O)[NH]C2=O)CC1N=[N+]=[N-]	3147.7	Semi standard non polar	33892256
[(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,1TMS,isomer #1	CCC(C)C(N[Si](C)(C)C)C(=O)OCC1OC(N2C=C(C)C(=O)[NH]C2=O)CC1N=[N+]=[N-]	3070.0	Standard non polar	33892256
[(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,1TMS,isomer #1	CCC(C)C(N[Si](C)(C)C)C(=O)OCC1OC(N2C=C(C)C(=O)[NH]C2=O)CC1N=[N+]=[N-]	4825.0	Standard polar	33892256
[(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,1TMS,isomer #2	CCC(C)C(N)C(=O)OCC1OC(N2C=C(C)C(=O)N([Si](C)(C)C)C2=O)CC1N=[N+]=[N-]	3116.1	Semi standard non polar	33892256
[(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,1TMS,isomer #2	CCC(C)C(N)C(=O)OCC1OC(N2C=C(C)C(=O)N([Si](C)(C)C)C2=O)CC1N=[N+]=[N-]	3127.1	Standard non polar	33892256
[(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,1TMS,isomer #2	CCC(C)C(N)C(=O)OCC1OC(N2C=C(C)C(=O)N([Si](C)(C)C)C2=O)CC1N=[N+]=[N-]	5254.4	Standard polar	33892256
[(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,2TMS,isomer #1	CCC(C)C(C(=O)OCC1OC(N2C=C(C)C(=O)[NH]C2=O)CC1N=[N+]=[N-])N([Si](C)(C)C)[Si](C)(C)C	3171.3	Semi standard non polar	33892256
[(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,2TMS,isomer #1	CCC(C)C(C(=O)OCC1OC(N2C=C(C)C(=O)[NH]C2=O)CC1N=[N+]=[N-])N([Si](C)(C)C)[Si](C)(C)C	3195.4	Standard non polar	33892256
[(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,2TMS,isomer #1	CCC(C)C(C(=O)OCC1OC(N2C=C(C)C(=O)[NH]C2=O)CC1N=[N+]=[N-])N([Si](C)(C)C)[Si](C)(C)C	4604.2	Standard polar	33892256
[(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,2TMS,isomer #2	CCC(C)C(N[Si](C)(C)C)C(=O)OCC1OC(N2C=C(C)C(=O)N([Si](C)(C)C)C2=O)CC1N=[N+]=[N-]	3119.7	Semi standard non polar	33892256
[(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,2TMS,isomer #2	CCC(C)C(N[Si](C)(C)C)C(=O)OCC1OC(N2C=C(C)C(=O)N([Si](C)(C)C)C2=O)CC1N=[N+]=[N-]	3110.8	Standard non polar	33892256
[(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,2TMS,isomer #2	CCC(C)C(N[Si](C)(C)C)C(=O)OCC1OC(N2C=C(C)C(=O)N([Si](C)(C)C)C2=O)CC1N=[N+]=[N-]	4575.3	Standard polar	33892256
[(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,3TMS,isomer #1	CCC(C)C(C(=O)OCC1OC(N2C=C(C)C(=O)N([Si](C)(C)C)C2=O)CC1N=[N+]=[N-])N([Si](C)(C)C)[Si](C)(C)C	3223.4	Semi standard non polar	33892256
[(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,3TMS,isomer #1	CCC(C)C(C(=O)OCC1OC(N2C=C(C)C(=O)N([Si](C)(C)C)C2=O)CC1N=[N+]=[N-])N([Si](C)(C)C)[Si](C)(C)C	3227.1	Standard non polar	33892256
[(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,3TMS,isomer #1	CCC(C)C(C(=O)OCC1OC(N2C=C(C)C(=O)N([Si](C)(C)C)C2=O)CC1N=[N+]=[N-])N([Si](C)(C)C)[Si](C)(C)C	4346.6	Standard polar	33892256
[(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,1TBDMS,isomer #1	CCC(C)C(N[Si](C)(C)C(C)(C)C)C(=O)OCC1OC(N2C=C(C)C(=O)[NH]C2=O)CC1N=[N+]=[N-]	3370.4	Semi standard non polar	33892256
[(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,1TBDMS,isomer #1	CCC(C)C(N[Si](C)(C)C(C)(C)C)C(=O)OCC1OC(N2C=C(C)C(=O)[NH]C2=O)CC1N=[N+]=[N-]	3290.1	Standard non polar	33892256
[(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,1TBDMS,isomer #1	CCC(C)C(N[Si](C)(C)C(C)(C)C)C(=O)OCC1OC(N2C=C(C)C(=O)[NH]C2=O)CC1N=[N+]=[N-]	4820.3	Standard polar	33892256
[(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,1TBDMS,isomer #2	CCC(C)C(N)C(=O)OCC1OC(N2C=C(C)C(=O)N([Si](C)(C)C(C)(C)C)C2=O)CC1N=[N+]=[N-]	3317.2	Semi standard non polar	33892256
[(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,1TBDMS,isomer #2	CCC(C)C(N)C(=O)OCC1OC(N2C=C(C)C(=O)N([Si](C)(C)C(C)(C)C)C2=O)CC1N=[N+]=[N-]	3340.7	Standard non polar	33892256
[(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,1TBDMS,isomer #2	CCC(C)C(N)C(=O)OCC1OC(N2C=C(C)C(=O)N([Si](C)(C)C(C)(C)C)C2=O)CC1N=[N+]=[N-]	5207.4	Standard polar	33892256
[(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,2TBDMS,isomer #1	CCC(C)C(C(=O)OCC1OC(N2C=C(C)C(=O)[NH]C2=O)CC1N=[N+]=[N-])N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	3632.6	Semi standard non polar	33892256
[(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,2TBDMS,isomer #1	CCC(C)C(C(=O)OCC1OC(N2C=C(C)C(=O)[NH]C2=O)CC1N=[N+]=[N-])N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	3568.9	Standard non polar	33892256
[(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,2TBDMS,isomer #1	CCC(C)C(C(=O)OCC1OC(N2C=C(C)C(=O)[NH]C2=O)CC1N=[N+]=[N-])N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	4573.6	Standard polar	33892256
[(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,2TBDMS,isomer #2	CCC(C)C(N[Si](C)(C)C(C)(C)C)C(=O)OCC1OC(N2C=C(C)C(=O)N([Si](C)(C)C(C)(C)C)C2=O)CC1N=[N+]=[N-]	3556.0	Semi standard non polar	33892256
[(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,2TBDMS,isomer #2	CCC(C)C(N[Si](C)(C)C(C)(C)C)C(=O)OCC1OC(N2C=C(C)C(=O)N([Si](C)(C)C(C)(C)C)C2=O)CC1N=[N+]=[N-]	3509.5	Standard non polar	33892256
[(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,2TBDMS,isomer #2	CCC(C)C(N[Si](C)(C)C(C)(C)C)C(=O)OCC1OC(N2C=C(C)C(=O)N([Si](C)(C)C(C)(C)C)C2=O)CC1N=[N+]=[N-]	4534.4	Standard polar	33892256
[(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,3TBDMS,isomer #1	CCC(C)C(C(=O)OCC1OC(N2C=C(C)C(=O)N([Si](C)(C)C(C)(C)C)C2=O)CC1N=[N+]=[N-])N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	3860.9	Semi standard non polar	33892256
[(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,3TBDMS,isomer #1	CCC(C)C(C(=O)OCC1OC(N2C=C(C)C(=O)N([Si](C)(C)C(C)(C)C)C2=O)CC1N=[N+]=[N-])N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	3757.2	Standard non polar	33892256
[(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate,3TBDMS,isomer #1	CCC(C)C(C(=O)OCC1OC(N2C=C(C)C(=O)N([Si](C)(C)C(C)(C)C)C2=O)CC1N=[N+]=[N-])N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	4327.8	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - [(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate GC-MS (Non-derivatized) - 70eV, Positive	splash10-0019-9110000000-17b6389cf9971dc1631c	2021-09-24	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - [(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	31557052	details

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

25043410

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

44284846

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]

Showing metabocard for [(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate (HMDB0253320)

MOL for HMDB0253320 ([(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate)

3D MOL for HMDB0253320 ([(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate)

3D SDF for HMDB0253320 ([(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate)

3D-SDF for HMDB0253320 ([(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate)

PDB for HMDB0253320 ([(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate)

3D PDB for HMDB0253320 ([(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate)

SMILES for HMDB0253320 ([(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate)

INCHI for HMDB0253320 ([(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate)

Structure for HMDB0253320 ([(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate)

3D Structure for HMDB0253320 ([(2S,3S,5R)-3-Azido-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl (2S,3S)-2-amino-3-methylpentanoate)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra