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Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References enzymes (2) Show 2 proteins XML

Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2021-08-27 00:41:14 UTC

Update Date

2021-10-01 18:15:29 UTC

HMDB ID

HMDB0242130

Secondary Accession Numbers

None

Metabolite Identification

Common Name

3-(3-Amino-3-carboxypropyl)uridine

Description

3-(3-Amino-3-carboxypropyl)uridine, also known as nucleoside X or (acp(3))u, belongs to the class of organic compounds known as pyrimidine nucleosides. Pyrimidine nucleosides are compounds comprising a pyrimidine base attached to a ribosyl or deoxyribosyl moiety. Based on a literature review a significant number of articles have been published on 3-(3-Amino-3-carboxypropyl)uridine.

Structure

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


  Mrv1652308272102512D          

 29 30  0  0  1  0            999 V2000
    1.4289    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6119   -1.5245    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1270   -0.8570    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7145    2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3020   -0.8570    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.0470   -0.0724    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7145    0.4125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.8579    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    3.7125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    2.4750    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2763   -2.2782    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1830   -1.5245    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7376    0.1825    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3819   -0.0724    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    2.0625    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7524   -1.5921    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5129   -0.7280    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0820    0.7424    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4496    0.7870    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  4  2  2  0  0  0  0
  6  1  1  0  0  0  0
  7  5  1  1  0  0  0
  8  2  1  0  0  0  0
  9  7  1  0  0  0  0
 10  9  1  0  0  0  0
 11 10  1  0  0  0  0
 12  6  1  0  0  0  0
 14  6  1  0  0  0  0
 15  3  1  0  0  0  0
 15  8  1  0  0  0  0
 15 13  1  0  0  0  0
 16  4  1  0  0  0  0
 11 16  1  1  0  0  0
 16 13  1  0  0  0  0
 17  5  1  0  0  0  0
 18  8  2  0  0  0  0
  9 19  1  6  0  0  0
 10 20  1  6  0  0  0
 21 12  2  0  0  0  0
 22 12  1  0  0  0  0
 23 13  2  0  0  0  0
 24  7  1  0  0  0  0
 24 11  1  0  0  0  0
 25  6  1  0  0  0  0
  7 26  1  6  0  0  0
  9 27  1  1  0  0  0
 10 28  1  1  0  0  0
 11 29  1  6  0  0  0
M  END

HMDB0242130
     RDKit          3D
3-(3-Amino-3-carboxypropyl)uridine
 43 44  0  0  0  0  0  0  0  0999 V2000
    5.7169   -0.9853    0.3053 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.8986    0.1245    0.7056 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5164    0.0972    0.1103 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7372   -1.1329    0.4904 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4341   -1.0402   -0.1406 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3001   -1.5662   -1.3717 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2908   -2.1220   -1.9488 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0622   -1.4775   -1.9695 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0111   -0.8784   -1.3508 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8250   -0.3684   -0.1214 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9660    0.2647    0.5282 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.9896   -0.6398    0.5757 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1369   -0.0616    0.1124 C   0  0  2  0  0  0  0  0  0  0  0  0
   -5.0487   -1.0477   -0.5974 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4357   -2.0802    0.2493 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7577    1.0898   -0.7569 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.7022    2.1045   -0.6098 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4194    1.4950   -0.1771 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.6070    2.5872    0.6742 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3792   -0.4527    0.4645 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5547    0.0285    1.6244 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.5559    1.3712    0.2536 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6407    1.3921   -0.3682 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9365    2.5733    0.5345 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.1629   -0.8659   -0.6193 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2742   -1.9105    0.4479 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8294    0.1674    1.8218 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9673    0.9694    0.5305 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6061    0.2535   -0.9646 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5970   -1.0943    1.6031 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1943   -2.0731    0.1729 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0836   -1.8891   -2.9589 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9921   -0.8196   -1.8496 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6747    0.5255    1.5850 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7290    0.3474    0.9788 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8754   -0.5543   -1.1139 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4061   -1.5241   -1.3927 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0815   -1.7200    0.9005 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7089    0.8568   -1.8351 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3835    2.9855   -0.8630 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7075    1.7951   -0.9924 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4481    2.5408    1.1719 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3352    2.7342    1.3240 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
  4  5  1  0
  5  6  1  0
  6  7  2  0
  6  8  1  0
  8  9  2  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
 13 16  1  0
 16 17  1  0
 16 18  1  0
 18 19  1  0
 10 20  1  0
 20 21  2  0
  2 22  1  0
 22 23  2  0
 22 24  1  0
 20  5  1  0
 18 11  1  0
  1 25  1  0
  1 26  1  0
  2 27  1  0
  3 28  1  0
  3 29  1  0
  4 30  1  0
  4 31  1  0
  8 32  1  0
  9 33  1  0
 11 34  1  1
 13 35  1  1
 14 36  1  0
 14 37  1  0
 15 38  1  0
 16 39  1  6
 17 40  1  0
 18 41  1  6
 19 42  1  0
 24 43  1  0
M  END


  Mrv1652308272102512D          

 29 30  0  0  1  0            999 V2000
    1.4289    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6119   -1.5245    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1270   -0.8570    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7145    2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3020   -0.8570    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.0470   -0.0724    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7145    0.4125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.8579    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    3.7125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    2.4750    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2763   -2.2782    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1830   -1.5245    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7376    0.1825    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3819   -0.0724    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    2.0625    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7524   -1.5921    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5129   -0.7280    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0820    0.7424    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4496    0.7870    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  4  2  2  0  0  0  0
  6  1  1  0  0  0  0
  7  5  1  1  0  0  0
  8  2  1  0  0  0  0
  9  7  1  0  0  0  0
 10  9  1  0  0  0  0
 11 10  1  0  0  0  0
 12  6  1  0  0  0  0
 14  6  1  0  0  0  0
 15  3  1  0  0  0  0
 15  8  1  0  0  0  0
 15 13  1  0  0  0  0
 16  4  1  0  0  0  0
 11 16  1  1  0  0  0
 16 13  1  0  0  0  0
 17  5  1  0  0  0  0
 18  8  2  0  0  0  0
  9 19  1  6  0  0  0
 10 20  1  6  0  0  0
 21 12  2  0  0  0  0
 22 12  1  0  0  0  0
 23 13  2  0  0  0  0
 24  7  1  0  0  0  0
 24 11  1  0  0  0  0
 25  6  1  0  0  0  0
  7 26  1  6  0  0  0
  9 27  1  1  0  0  0
 10 28  1  1  0  0  0
 11 29  1  6  0  0  0
M  END
> <DATABASE_ID>
HMDB0242130

> <DATABASE_NAME>
hmdb

> <SMILES>
[H]C(N)(CCN1C(=O)C=CN(C1=O)[C@]1([H])O[C@]([H])(CO)[C@@]([H])(O)[C@@]1([H])O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C13H19N3O8/c14-6(12(21)22)1-3-15-8(18)2-4-16(13(15)23)11-10(20)9(19)7(5-17)24-11/h2,4,6-7,9-11,17,19-20H,1,3,5,14H2,(H,21,22)/t6?,7-,9-,10-,11-/m1/s1

> <INCHI_KEY>
YXNIEZJFCGTDKV-JANFQQFMSA-N

> <FORMULA>
C13H19N3O8

> <MOLECULAR_WEIGHT>
345.308

> <EXACT_MASS>
345.117214584

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
43

> <JCHEM_AVERAGE_POLARIZABILITY>
32.22211080781961

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-2-amino-4-{3-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-2,6-dioxo-1,2,3,6-tetrahydropyrimidin-1-yl}butanoic acid

> <ALOGPS_LOGP>
-2.53

> <JCHEM_LOGP>
-5.5011723806743955

> <ALOGPS_LOGS>
-1.01

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.553974014492223

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.5956782238452512

> <JCHEM_PKA_STRONGEST_BASIC>
9.087768877295623

> <JCHEM_POLAR_SURFACE_AREA>
173.85999999999999

> <JCHEM_REFRACTIVITY>
76.1074

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.41e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S)-2-amino-4-{3-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-2,6-dioxopyrimidin-1-yl}butanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0242130
     RDKit          3D
3-(3-Amino-3-carboxypropyl)uridine
 43 44  0  0  0  0  0  0  0  0999 V2000
    5.7169   -0.9853    0.3053 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.8986    0.1245    0.7056 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5164    0.0972    0.1103 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7372   -1.1329    0.4904 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4341   -1.0402   -0.1406 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3001   -1.5662   -1.3717 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2908   -2.1220   -1.9488 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0622   -1.4775   -1.9695 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0111   -0.8784   -1.3508 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8250   -0.3684   -0.1214 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9660    0.2647    0.5282 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.9896   -0.6398    0.5757 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1369   -0.0616    0.1124 C   0  0  2  0  0  0  0  0  0  0  0  0
   -5.0487   -1.0477   -0.5974 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4357   -2.0802    0.2493 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7577    1.0898   -0.7569 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.7022    2.1045   -0.6098 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4194    1.4950   -0.1771 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.6070    2.5872    0.6742 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3792   -0.4527    0.4645 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5547    0.0285    1.6244 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.5559    1.3712    0.2536 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6407    1.3921   -0.3682 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9365    2.5733    0.5345 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.1629   -0.8659   -0.6193 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2742   -1.9105    0.4479 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8294    0.1674    1.8218 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9673    0.9694    0.5305 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6061    0.2535   -0.9646 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5970   -1.0943    1.6031 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1943   -2.0731    0.1729 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0836   -1.8891   -2.9589 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9921   -0.8196   -1.8496 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6747    0.5255    1.5850 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7290    0.3474    0.9788 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8754   -0.5543   -1.1139 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4061   -1.5241   -1.3927 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0815   -1.7200    0.9005 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7089    0.8568   -1.8351 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3835    2.9855   -0.8630 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7075    1.7951   -0.9924 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4481    2.5408    1.1719 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3352    2.7342    1.3240 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
  4  5  1  0
  5  6  1  0
  6  7  2  0
  6  8  1  0
  8  9  2  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
 13 16  1  0
 16 17  1  0
 16 18  1  0
 18 19  1  0
 10 20  1  0
 20 21  2  0
  2 22  1  0
 22 23  2  0
 22 24  1  0
 20  5  1  0
 18 11  1  0
  1 25  1  0
  1 26  1  0
  2 27  1  0
  3 28  1  0
  3 29  1  0
  4 30  1  0
  4 31  1  0
  8 32  1  0
  9 33  1  0
 11 34  1  1
 13 35  1  1
 14 36  1  0
 14 37  1  0
 15 38  1  0
 16 39  1  6
 17 40  1  0
 18 41  1  6
 19 42  1  0
 24 43  1  0
M  END

HEADER    PROTEIN                                 27-AUG-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-AUG-21         0                                  
HETATM    1  C   UNK     0       2.667   4.620   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -2.667   4.620   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.334   5.390   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -2.667   3.080   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -3.009  -2.846   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.001   5.390   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -2.104  -1.600   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -1.334   5.390   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -0.564  -1.600   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -0.088  -0.135   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -1.334   0.770   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       5.335   4.620   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       0.000   3.080   0.000  0.00  0.00           C+0
HETATM   14  N   UNK     0       4.001   6.930   0.000  0.00  0.00           N+0
HETATM   15  N   UNK     0       0.000   4.620   0.000  0.00  0.00           N+0
HETATM   16  N   UNK     0      -1.334   2.310   0.000  0.00  0.00           N+0
HETATM   17  O   UNK     0      -2.382  -4.253   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0      -1.334   6.930   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       0.342  -2.846   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       1.377   0.341   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       6.668   5.390   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       5.335   3.080   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0       1.334   2.310   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0      -2.580  -0.135   0.000  0.00  0.00           O+0
HETATM   25  H   UNK     0       4.001   3.850   0.000  0.00  0.00           H+0
HETATM   26  H   UNK     0      -1.405  -2.972   0.000  0.00  0.00           H+0
HETATM   27  H   UNK     0       0.957  -1.359   0.000  0.00  0.00           H+0
HETATM   28  H   UNK     0       0.153   1.386   0.000  0.00  0.00           H+0
HETATM   29  H   UNK     0      -2.706   1.469   0.000  0.00  0.00           H+0
CONECT    1    3    6                                                       
CONECT    2    4    8                                                       
CONECT    3    1   15                                                       
CONECT    4    2   16                                                       
CONECT    5    7   17                                                       
CONECT    6    1   12   14   25                                             
CONECT    7    5    9   24   26                                             
CONECT    8    2   15   18                                                  
CONECT    9    7   10   19   27                                             
CONECT   10    9   11   20   28                                             
CONECT   11   10   16   24   29                                             
CONECT   12    6   21   22                                                  
CONECT   13   15   16   23                                                  
CONECT   14    6                                                            
CONECT   15    3    8   13                                                  
CONECT   16    4   11   13                                                  
CONECT   17    5                                                            
CONECT   18    8                                                            
CONECT   19    9                                                            
CONECT   20   10                                                            
CONECT   21   12                                                            
CONECT   22   12                                                            
CONECT   23   13                                                            
CONECT   24    7   11                                                       
CONECT   25    6                                                            
CONECT   26    7                                                            
CONECT   27    9                                                            
CONECT   28   10                                                            
CONECT   29   11                                                            
MASTER        0    0    0    0    0    0    0    0   29    0   60    0
END

COMPND    HMDB0242130
HETATM    1  N1  UNL     1       5.717  -0.985   0.305  1.00  0.00           N  
HETATM    2  C1  UNL     1       4.899   0.124   0.706  1.00  0.00           C  
HETATM    3  C2  UNL     1       3.516   0.097   0.110  1.00  0.00           C  
HETATM    4  C3  UNL     1       2.737  -1.133   0.490  1.00  0.00           C  
HETATM    5  N2  UNL     1       1.434  -1.040  -0.141  1.00  0.00           N  
HETATM    6  C4  UNL     1       1.300  -1.566  -1.372  1.00  0.00           C  
HETATM    7  O1  UNL     1       2.291  -2.122  -1.949  1.00  0.00           O  
HETATM    8  C5  UNL     1       0.062  -1.478  -1.970  1.00  0.00           C  
HETATM    9  C6  UNL     1      -1.011  -0.878  -1.351  1.00  0.00           C  
HETATM   10  N3  UNL     1      -0.825  -0.368  -0.121  1.00  0.00           N  
HETATM   11  C7  UNL     1      -1.966   0.265   0.528  1.00  0.00           C  
HETATM   12  O2  UNL     1      -2.990  -0.640   0.576  1.00  0.00           O  
HETATM   13  C8  UNL     1      -4.137  -0.062   0.112  1.00  0.00           C  
HETATM   14  C9  UNL     1      -5.049  -1.048  -0.597  1.00  0.00           C  
HETATM   15  O3  UNL     1      -5.436  -2.080   0.249  1.00  0.00           O  
HETATM   16  C10 UNL     1      -3.758   1.090  -0.757  1.00  0.00           C  
HETATM   17  O4  UNL     1      -4.702   2.104  -0.610  1.00  0.00           O  
HETATM   18  C11 UNL     1      -2.419   1.495  -0.177  1.00  0.00           C  
HETATM   19  O5  UNL     1      -2.607   2.587   0.674  1.00  0.00           O  
HETATM   20  C12 UNL     1       0.379  -0.453   0.464  1.00  0.00           C  
HETATM   21  O6  UNL     1       0.555   0.028   1.624  1.00  0.00           O  
HETATM   22  C13 UNL     1       5.556   1.371   0.254  1.00  0.00           C  
HETATM   23  O7  UNL     1       6.641   1.392  -0.368  1.00  0.00           O  
HETATM   24  O8  UNL     1       4.936   2.573   0.535  1.00  0.00           O  
HETATM   25  H1  UNL     1       6.163  -0.866  -0.619  1.00  0.00           H  
HETATM   26  H2  UNL     1       5.274  -1.910   0.448  1.00  0.00           H  
HETATM   27  H3  UNL     1       4.829   0.167   1.822  1.00  0.00           H  
HETATM   28  H4  UNL     1       2.967   0.969   0.531  1.00  0.00           H  
HETATM   29  H5  UNL     1       3.606   0.254  -0.965  1.00  0.00           H  
HETATM   30  H6  UNL     1       2.597  -1.094   1.603  1.00  0.00           H  
HETATM   31  H7  UNL     1       3.194  -2.073   0.173  1.00  0.00           H  
HETATM   32  H8  UNL     1      -0.084  -1.889  -2.959  1.00  0.00           H  
HETATM   33  H9  UNL     1      -1.992  -0.820  -1.850  1.00  0.00           H  
HETATM   34  H10 UNL     1      -1.675   0.525   1.585  1.00  0.00           H  
HETATM   35  H11 UNL     1      -4.729   0.347   0.979  1.00  0.00           H  
HETATM   36  H12 UNL     1      -5.875  -0.554  -1.114  1.00  0.00           H  
HETATM   37  H13 UNL     1      -4.406  -1.524  -1.393  1.00  0.00           H  
HETATM   38  H14 UNL     1      -6.081  -1.720   0.900  1.00  0.00           H  
HETATM   39  H15 UNL     1      -3.709   0.857  -1.835  1.00  0.00           H  
HETATM   40  H16 UNL     1      -4.384   2.986  -0.863  1.00  0.00           H  
HETATM   41  H17 UNL     1      -1.708   1.795  -0.992  1.00  0.00           H  
HETATM   42  H18 UNL     1      -3.448   2.541   1.172  1.00  0.00           H  
HETATM   43  H19 UNL     1       4.335   2.734   1.324  1.00  0.00           H  
CONECT    1    2   25   26
CONECT    2    3   22   27
CONECT    3    4   28   29
CONECT    4    5   30   31
CONECT    5    6   20
CONECT    6    7    7    8
CONECT    8    9    9   32
CONECT    9   10   33
CONECT   10   11   20
CONECT   11   12   18   34
CONECT   12   13
CONECT   13   14   16   35
CONECT   14   15   36   37
CONECT   15   38
CONECT   16   17   18   39
CONECT   17   40
CONECT   18   19   41
CONECT   19   42
CONECT   20   21   21
CONECT   22   23   23   24
CONECT   24   43
END

HMDB0242130
     RDKit          3D
3-(3-Amino-3-carboxypropyl)uridine
 43 44  0  0  0  0  0  0  0  0999 V2000
    5.7169   -0.9853    0.3053 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.8986    0.1245    0.7056 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5164    0.0972    0.1103 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7372   -1.1329    0.4904 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4341   -1.0402   -0.1406 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3001   -1.5662   -1.3717 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2908   -2.1220   -1.9488 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0622   -1.4775   -1.9695 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0111   -0.8784   -1.3508 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8250   -0.3684   -0.1214 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9660    0.2647    0.5282 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.9896   -0.6398    0.5757 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1369   -0.0616    0.1124 C   0  0  2  0  0  0  0  0  0  0  0  0
   -5.0487   -1.0477   -0.5974 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4357   -2.0802    0.2493 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7577    1.0898   -0.7569 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.7022    2.1045   -0.6098 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4194    1.4950   -0.1771 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.6070    2.5872    0.6742 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3792   -0.4527    0.4645 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5547    0.0285    1.6244 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.5559    1.3712    0.2536 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6407    1.3921   -0.3682 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9365    2.5733    0.5345 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.1629   -0.8659   -0.6193 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2742   -1.9105    0.4479 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8294    0.1674    1.8218 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9673    0.9694    0.5305 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6061    0.2535   -0.9646 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5970   -1.0943    1.6031 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1943   -2.0731    0.1729 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0836   -1.8891   -2.9589 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9921   -0.8196   -1.8496 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6747    0.5255    1.5850 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7290    0.3474    0.9788 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8754   -0.5543   -1.1139 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4061   -1.5241   -1.3927 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0815   -1.7200    0.9005 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7089    0.8568   -1.8351 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3835    2.9855   -0.8630 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7075    1.7951   -0.9924 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4481    2.5408    1.1719 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3352    2.7342    1.3240 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
  4  5  1  0
  5  6  1  0
  6  7  2  0
  6  8  1  0
  8  9  2  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
 13 16  1  0
 16 17  1  0
 16 18  1  0
 18 19  1  0
 10 20  1  0
 20 21  2  0
  2 22  1  0
 22 23  2  0
 22 24  1  0
 20  5  1  0
 18 11  1  0
  1 25  1  0
  1 26  1  0
  2 27  1  0
  3 28  1  0
  3 29  1  0
  4 30  1  0
  4 31  1  0
  8 32  1  0
  9 33  1  0
 11 34  1  1
 13 35  1  1
 14 36  1  0
 14 37  1  0
 15 38  1  0
 16 39  1  6
 17 40  1  0
 18 41  1  6
 19 42  1  0
 24 43  1  0
M  END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
(Acp(3))u	ChEBI
Nucleoside X	ChEBI

Chemical Formula

C₁₃H₁₉N₃O₈

Average Molecular Weight

345.308

Monoisotopic Molecular Weight

345.117214584

IUPAC Name

(2S)-2-amino-4-{3-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-2,6-dioxo-1,2,3,6-tetrahydropyrimidin-1-yl}butanoic acid

Traditional Name

(2S)-2-amino-4-{3-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-2,6-dioxopyrimidin-1-yl}butanoic acid

CAS Registry Number

Not Available

SMILES

[H]C(N)(CCN1C(=O)C=CN(C1=O)[C@]1([H])O[C@]([H])(CO)[C@@]([H])(O)[C@@]1([H])O)C(O)=O

InChI Identifier

InChI=1S/C13H19N3O8/c14-6(12(21)22)1-3-15-8(18)2-4-16(13(15)23)11-10(20)9(19)7(5-17)24-11/h2,4,6-7,9-11,17,19-20H,1,3,5,14H2,(H,21,22)/t6?,7-,9-,10-,11-/m1/s1

InChI Key

YXNIEZJFCGTDKV-JANFQQFMSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyrimidine nucleosides. Pyrimidine nucleosides 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
Alpha-amino acid
Alpha-amino acid or derivatives
Pentose monosaccharide
Pyrimidone
Hydropyrimidine
Pyrimidine
Monosaccharide
Heteroaromatic compound
Vinylogous amide
Tetrahydrofuran
Secondary alcohol
Urea
Lactam
Amino acid
Amino acid or derivatives
Carboxylic acid derivative
Carboxylic acid
Oxacycle
Azacycle
Monocarboxylic acid or derivatives
Organoheterocyclic compound
Primary aliphatic amine
Amine
Organic oxygen compound
Hydrocarbon derivative
Organic oxide
Organic nitrogen compound
Alcohol
Carbonyl group
Organopnictogen compound
Organonitrogen compound
Organooxygen compound
Primary amine
Primary alcohol
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

uridines (CHEBI:19928 )

Ontology

Not Available

Not Available

Not Available

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	-2.5	ALOGPS
logP	-5.5	ChemAxon
logS	-1	ALOGPS
pKa (Strongest Acidic)	1.6	ChemAxon
pKa (Strongest Basic)	9.09	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	173.86 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	76.11 m³·mol⁻¹	ChemAxon
Polarizability	32.22 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

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DeepCCS	[M+H]+	174.782	30932474
DeepCCS	[M-H]-	172.592	30932474
DeepCCS	[M-2H]-	205.833	30932474
DeepCCS	[M+Na]+	181.521	30932474

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Predicted by Siyang on May 30, 2022	9.2243 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	9.06 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	412.6 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	224.3 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	55.3 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	163.3 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	45.1 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	304.6 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	246.6 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	845.8 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	553.1 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	48.9 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	715.1 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	181.7 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	247.7 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	691.0 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	553.4 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	423.5 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
3-(3-Amino-3-carboxypropyl)uridine	[H]C(N)(CCN1C(=O)C=CN(C1=O)[C@]1([H])O[C@]([H])(CO)[C@@]([H])(O)[C@@]1([H])O)C(O)=O	3643.8	Standard polar	33892256
3-(3-Amino-3-carboxypropyl)uridine	[H]C(N)(CCN1C(=O)C=CN(C1=O)[C@]1([H])O[C@]([H])(CO)[C@@]([H])(O)[C@@]1([H])O)C(O)=O	2518.6	Standard non polar	33892256
3-(3-Amino-3-carboxypropyl)uridine	[H]C(N)(CCN1C(=O)C=CN(C1=O)[C@]1([H])O[C@]([H])(CO)[C@@]([H])(O)[C@@]1([H])O)C(O)=O	3160.2	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
3-(3-Amino-3-carboxypropyl)uridine,5TMS,isomer #1	C[Si](C)(C)NC(CCN1C(=O)C=CN([C@@H]2O[C@H](CO[Si](C)(C)C)[C@@H](O[Si](C)(C)C)[C@H]2O[Si](C)(C)C)C1=O)C(=O)O[Si](C)(C)C	2995.4	Semi standard non polar	33892256
3-(3-Amino-3-carboxypropyl)uridine,5TMS,isomer #1	C[Si](C)(C)NC(CCN1C(=O)C=CN([C@@H]2O[C@H](CO[Si](C)(C)C)[C@@H](O[Si](C)(C)C)[C@H]2O[Si](C)(C)C)C1=O)C(=O)O[Si](C)(C)C	3136.9	Standard non polar	33892256
3-(3-Amino-3-carboxypropyl)uridine,5TMS,isomer #1	C[Si](C)(C)NC(CCN1C(=O)C=CN([C@@H]2O[C@H](CO[Si](C)(C)C)[C@@H](O[Si](C)(C)C)[C@H]2O[Si](C)(C)C)C1=O)C(=O)O[Si](C)(C)C	3452.1	Standard polar	33892256
3-(3-Amino-3-carboxypropyl)uridine,5TMS,isomer #2	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(=O)N(CCC(C(=O)O[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C)C2=O)[C@H](O[Si](C)(C)C)[C@@H]1O	3151.0	Semi standard non polar	33892256
3-(3-Amino-3-carboxypropyl)uridine,5TMS,isomer #2	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(=O)N(CCC(C(=O)O[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C)C2=O)[C@H](O[Si](C)(C)C)[C@@H]1O	3223.2	Standard non polar	33892256
3-(3-Amino-3-carboxypropyl)uridine,5TMS,isomer #2	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(=O)N(CCC(C(=O)O[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C)C2=O)[C@H](O[Si](C)(C)C)[C@@H]1O	3597.0	Standard polar	33892256
3-(3-Amino-3-carboxypropyl)uridine,5TMS,isomer #3	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(=O)N(CCC(C(=O)O[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C)C2=O)[C@H](O)[C@@H]1O[Si](C)(C)C	3143.2	Semi standard non polar	33892256
3-(3-Amino-3-carboxypropyl)uridine,5TMS,isomer #3	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(=O)N(CCC(C(=O)O[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C)C2=O)[C@H](O)[C@@H]1O[Si](C)(C)C	3213.2	Standard non polar	33892256
3-(3-Amino-3-carboxypropyl)uridine,5TMS,isomer #3	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(=O)N(CCC(C(=O)O[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C)C2=O)[C@H](O)[C@@H]1O[Si](C)(C)C	3538.2	Standard polar	33892256
3-(3-Amino-3-carboxypropyl)uridine,5TMS,isomer #4	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(=O)N(CCC(C(=O)O)N([Si](C)(C)C)[Si](C)(C)C)C2=O)[C@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C	3137.6	Semi standard non polar	33892256
3-(3-Amino-3-carboxypropyl)uridine,5TMS,isomer #4	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(=O)N(CCC(C(=O)O)N([Si](C)(C)C)[Si](C)(C)C)C2=O)[C@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C	3256.5	Standard non polar	33892256
3-(3-Amino-3-carboxypropyl)uridine,5TMS,isomer #4	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(=O)N(CCC(C(=O)O)N([Si](C)(C)C)[Si](C)(C)C)C2=O)[C@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C	3615.6	Standard polar	33892256
3-(3-Amino-3-carboxypropyl)uridine,5TMS,isomer #5	C[Si](C)(C)OC(=O)C(CCN1C(=O)C=CN([C@@H]2O[C@H](CO)[C@@H](O[Si](C)(C)C)[C@H]2O[Si](C)(C)C)C1=O)N([Si](C)(C)C)[Si](C)(C)C	3170.1	Semi standard non polar	33892256
3-(3-Amino-3-carboxypropyl)uridine,5TMS,isomer #5	C[Si](C)(C)OC(=O)C(CCN1C(=O)C=CN([C@@H]2O[C@H](CO)[C@@H](O[Si](C)(C)C)[C@H]2O[Si](C)(C)C)C1=O)N([Si](C)(C)C)[Si](C)(C)C	3218.5	Standard non polar	33892256
3-(3-Amino-3-carboxypropyl)uridine,5TMS,isomer #5	C[Si](C)(C)OC(=O)C(CCN1C(=O)C=CN([C@@H]2O[C@H](CO)[C@@H](O[Si](C)(C)C)[C@H]2O[Si](C)(C)C)C1=O)N([Si](C)(C)C)[Si](C)(C)C	3527.8	Standard polar	33892256
3-(3-Amino-3-carboxypropyl)uridine,6TMS,isomer #1	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(=O)N(CCC(C(=O)O[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C)C2=O)[C@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C	3171.1	Semi standard non polar	33892256
3-(3-Amino-3-carboxypropyl)uridine,6TMS,isomer #1	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(=O)N(CCC(C(=O)O[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C)C2=O)[C@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C	3227.2	Standard non polar	33892256
3-(3-Amino-3-carboxypropyl)uridine,6TMS,isomer #1	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(=O)N(CCC(C(=O)O[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C)C2=O)[C@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C	3357.8	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - 3-(3-Amino-3-carboxypropyl)uridine GC-MS (Non-derivatized) - 70eV, Positive	splash10-05br-9233000000-be8359607c245de22835	2021-09-24	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3-(3-Amino-3-carboxypropyl)uridine GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-(3-Amino-3-carboxypropyl)uridine 10V, Positive-QTOF	splash10-002b-0439000000-6e914f020aa6dd0d89c4	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-(3-Amino-3-carboxypropyl)uridine 20V, Positive-QTOF	splash10-004j-1900000000-f601caed4ee3467ba55c	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-(3-Amino-3-carboxypropyl)uridine 40V, Positive-QTOF	splash10-0a4i-9600000000-42aefea9da00432de564	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-(3-Amino-3-carboxypropyl)uridine 10V, Negative-QTOF	splash10-0udl-0395000000-7b1360a7814d81e2bf75	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-(3-Amino-3-carboxypropyl)uridine 20V, Negative-QTOF	splash10-00di-3980000000-44660531c1a0a51f6773	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-(3-Amino-3-carboxypropyl)uridine 40V, Negative-QTOF	splash10-00kr-2900000000-4b7e536636b4e3ff1430	2021-10-12	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

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

149669

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

171198

PDB ID

Not Available

ChEBI ID

19928

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

Kong SW, Hernandez-Ferrer C: Assessment of coverage for endogenous metabolites and exogenous chemical compounds using an untargeted metabolomics platform. Pac Symp Biocomput. 2020;25:587-598. [PubMed:31797630 ]

Enzymes

Enzyme Details

1. tRNA-uridine aminocarboxypropyltransferase 2

General function:: Not Available
Specific function:: Catalyzes the formation of 3-(3-amino-3-carboxypropyl)uridine (acp3U) at position 20a in the D-loop of several cytoplasmic tRNAs (acp3U(20a)) (PubMed:31804502). Also has a weak activity to form acp3U at position 20 in the D-loop of tRNAs (acp3U(20)) (PubMed:31804502).
Gene Name:: DTWD2
Uniprot ID:: Q8NBA8
Molecular weight:: 33415.285

Enzyme Details

2. tRNA-uridine aminocarboxypropyltransferase 1

General function:: Not Available
Specific function:: Catalyzes the formation of 3-(3-amino-3-carboxypropyl)uridine (acp3U) at position 20 in the D-loop of several cytoplasmic tRNAs (acp3U(20)).
Gene Name:: DTWD1
Uniprot ID:: Q8N5C7
Molecular weight:: 35248.125

Showing metabocard for 3-(3-Amino-3-carboxypropyl)uridine (HMDB0242130)

MOL for HMDB0242130 (3-(3-Amino-3-carboxypropyl)uridine)

3D MOL for HMDB0242130 (3-(3-Amino-3-carboxypropyl)uridine)

3D SDF for HMDB0242130 (3-(3-Amino-3-carboxypropyl)uridine)

3D-SDF for HMDB0242130 (3-(3-Amino-3-carboxypropyl)uridine)

PDB for HMDB0242130 (3-(3-Amino-3-carboxypropyl)uridine)

3D PDB for HMDB0242130 (3-(3-Amino-3-carboxypropyl)uridine)

SMILES for HMDB0242130 (3-(3-Amino-3-carboxypropyl)uridine)

INCHI for HMDB0242130 (3-(3-Amino-3-carboxypropyl)uridine)

Structure for HMDB0242130 (3-(3-Amino-3-carboxypropyl)uridine)

3D Structure for HMDB0242130 (3-(3-Amino-3-carboxypropyl)uridine)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

Enzymes