MiMeDB: Showing metabocard for Se-Adenosylselenohomocysteine (MMDBc0047964)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-23 23:19:14 UTC

Update Date

2024-04-30 20:33:57 UTC

Metabolite ID

MMDBc0047964

Metabolite Identification

Common Name

Se-Adenosylselenohomocysteine

Description

Se-Adenosylselenohomocysteine is an intermediate in Selenoamino acid metabolism. Se-Adenosylselenohomocysteine is the second to last step in the synthesis of Selenohomocystine and is converted from Se-Adenosylselenomethionine via the enzyme Transferases (EC 2.1.1.-). It is then. converted to Selenohomocysteine via the enzyme adenosylhomocysteinase (EC 3.3.1.1).

Structure

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


  Mrv0541 02241201192D          

 26 28  0  0  1  0            999 V2000
    1.8378   -0.0274    0.0000 N   0  0  1  0  0  0  0  0  0  0  0  0
    2.6195    0.2228    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0526   -0.2881    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.3544    0.6411    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6229    1.0492    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3293   -0.1851    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.3840    0.1989    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7955   -1.0732    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.8412    1.3028    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.3293    1.4640    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0390    0.2228    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2881   -0.2881    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.0274   -1.0732    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.2652   -1.8515    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0390    1.0492    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.3258    2.2869    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0698   -0.0274    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5143   -1.7384    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7829   -0.4423    0.0000 Se  0  0  0  0  0  0  0  0  0  0  0  0
   -2.4960   -0.0274    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2092   -0.4423    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9224   -0.0274    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6321   -0.4423    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9224    0.7955    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3487   -0.0274    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6321   -1.2686    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  1  0  0  0
  3  1  1  6  0  0  0
  1  4  1  0  0  0  0
  2  5  1  0  0  0  0
  2  6  2  0  0  0  0
  3  7  1  0  0  0  0
  3  8  1  0  0  0  0
  4  9  2  0  0  0  0
  5 10  2  0  0  0  0
  6 11  1  0  0  0  0
  7 12  1  0  0  0  0
  8 13  1  0  0  0  0
  8 14  1  6  0  0  0
 10 15  1  0  0  0  0
 10 16  1  0  0  0  0
 12 17  1  1  0  0  0
 13 18  1  6  0  0  0
 17 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 22 24  1  0  0  0  0
 23 25  1  0  0  0  0
 23 26  2  0  0  0  0
  5  9  1  0  0  0  0
 11 15  2  0  0  0  0
 12 13  1  0  0  0  0
M  END

HMDB0011117
     RDKit          3D
Se-Adenosylselenohomocysteine
 46 48  0  0  0  0  0  0  0  0999 V2000
    7.4293   -0.1138   -2.0892 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.4347    0.4937   -1.2633 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5565    1.7763   -0.9119 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.5882    2.2994   -0.1305 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5488    1.5456    0.2696 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.4101    0.2408   -0.0787 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3794   -0.3021   -0.8674 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0255   -1.5964   -1.0768 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.8727   -1.7982   -0.4214 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4691   -0.6790    0.2047 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.3242   -0.4107    1.0121 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4747    0.5511    0.5287 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1808    0.2107    0.8203 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.6368    1.3561    1.3798 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4321    0.6944    1.7325 Se  0  0  0  0  0  2  0  0  0  0  0  0
   -3.4608    0.5632    0.0874 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7928   -0.0435    0.4557 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7081   -0.2207   -0.7204 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9378   -0.8195   -0.1764 N   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0326    1.0289   -1.4237 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1983    1.7426   -2.0360 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3683    1.4807   -1.4261 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2195   -0.9499    1.8086 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.8881   -1.7517    1.7144 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4860   -1.6467    1.2817 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.1123   -2.2856    0.0878 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.8608    0.4860   -2.8276 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.6721   -1.1092   -1.9177 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6227    3.3464    0.1972 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3468   -2.7405   -0.4051 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7085   -0.0956    2.0270 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2835   -0.1969   -0.1003 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1803    1.7560    2.3055 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7300    2.1425    0.6082 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6238    1.5599   -0.3691 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9180   -0.0691   -0.6239 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6818   -1.0209    0.9565 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3101    0.6256    1.2033 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2242   -0.9089   -1.4412 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6329   -1.0052   -0.9318 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2986   -0.1019    0.5072 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.5806    2.2402   -0.7632 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4145   -0.5527    2.8153 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3273   -1.7632    2.6218 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9218   -2.3208    2.0156 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1879   -1.6373   -0.6757 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  7  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
 15 16  1  0
 16 17  1  0
 17 18  1  0
 18 19  1  0
 18 20  1  0
 20 21  2  0
 20 22  1  0
 13 23  1  0
 23 24  1  0
 23 25  1  0
 25 26  1  0
  7  2  1  0
 25 11  1  0
 10  6  1  0
  1 27  1  0
  1 28  1  0
  4 29  1  0
  9 30  1  0
 11 31  1  1
 13 32  1  6
 14 33  1  0
 14 34  1  0
 16 35  1  0
 16 36  1  0
 17 37  1  0
 17 38  1  0
 18 39  1  0
 19 40  1  0
 19 41  1  0
 22 42  1  0
 23 43  1  1
 24 44  1  0
 25 45  1  1
 26 46  1  0
M  END


  Mrv0541 02241201192D          

 26 28  0  0  1  0            999 V2000
    1.8378   -0.0274    0.0000 N   0  0  1  0  0  0  0  0  0  0  0  0
    2.6195    0.2228    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0526   -0.2881    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.3544    0.6411    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6229    1.0492    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3293   -0.1851    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.3840    0.1989    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7955   -1.0732    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.8412    1.3028    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.3293    1.4640    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0390    0.2228    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2881   -0.2881    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.0274   -1.0732    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.2652   -1.8515    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0390    1.0492    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.3258    2.2869    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0698   -0.0274    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5143   -1.7384    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7829   -0.4423    0.0000 Se  0  0  0  0  0  0  0  0  0  0  0  0
   -2.4960   -0.0274    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2092   -0.4423    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9224   -0.0274    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6321   -0.4423    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9224    0.7955    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3487   -0.0274    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6321   -1.2686    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  1  0  0  0
  3  1  1  6  0  0  0
  1  4  1  0  0  0  0
  2  5  1  0  0  0  0
  2  6  2  0  0  0  0
  3  7  1  0  0  0  0
  3  8  1  0  0  0  0
  4  9  2  0  0  0  0
  5 10  2  0  0  0  0
  6 11  1  0  0  0  0
  7 12  1  0  0  0  0
  8 13  1  0  0  0  0
  8 14  1  6  0  0  0
 10 15  1  0  0  0  0
 10 16  1  0  0  0  0
 12 17  1  1  0  0  0
 13 18  1  6  0  0  0
 17 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 22 24  1  0  0  0  0
 23 25  1  0  0  0  0
 23 26  2  0  0  0  0
  5  9  1  0  0  0  0
 11 15  2  0  0  0  0
 12 13  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0047964

> <DATABASE_NAME>
MIME

> <SMILES>
NC(CC[Se]C[C@H]1O[C@@H]([C@H](O)[C@@H]1O)N1C=NC2=C(N)N=CN=C12)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C14H20N6O5Se/c15-6(14(23)24)1-2-26-3-7-9(21)10(22)13(25-7)20-5-19-8-11(16)17-4-18-12(8)20/h4-7,9-10,13,21-22H,1-3,15H2,(H,23,24)(H2,16,17,18)/t6?,7-,9-,10-,13+/m1/s1

> <INCHI_KEY>
UVSMMLABJBJNGH-WWJIDFMMSA-N

> <FORMULA>
C14H20N6O5Se

> <MOLECULAR_WEIGHT>
431.31

> <EXACT_MASS>
432.066039608

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_AVERAGE_POLARIZABILITY>
36.905167642975385

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-amino-4-({[(2S,3S,4R,5S)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl}selanyl)butanoic acid

> <ALOGPS_LOGP>
-2.54

> <JCHEM_LOGP>
-5.3131766740298945

> <ALOGPS_LOGS>
-1.71

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.472280052715373

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.3131055876641091

> <JCHEM_PKA_STRONGEST_BASIC>
9.501861401195526

> <JCHEM_POLAR_SURFACE_AREA>
182.63

> <JCHEM_REFRACTIVITY>
98.04489999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
8.42e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
se-adenosylselenohomocysteine

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0011117
     RDKit          3D
Se-Adenosylselenohomocysteine
 46 48  0  0  0  0  0  0  0  0999 V2000
    7.4293   -0.1138   -2.0892 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.4347    0.4937   -1.2633 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5565    1.7763   -0.9119 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.5882    2.2994   -0.1305 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5488    1.5456    0.2696 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.4101    0.2408   -0.0787 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3794   -0.3021   -0.8674 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0255   -1.5964   -1.0768 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.8727   -1.7982   -0.4214 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4691   -0.6790    0.2047 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.3242   -0.4107    1.0121 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4747    0.5511    0.5287 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1808    0.2107    0.8203 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.6368    1.3561    1.3798 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4321    0.6944    1.7325 Se  0  0  0  0  0  2  0  0  0  0  0  0
   -3.4608    0.5632    0.0874 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7928   -0.0435    0.4557 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7081   -0.2207   -0.7204 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9378   -0.8195   -0.1764 N   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0326    1.0289   -1.4237 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1983    1.7426   -2.0360 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3683    1.4807   -1.4261 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2195   -0.9499    1.8086 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.8881   -1.7517    1.7144 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4860   -1.6467    1.2817 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.1123   -2.2856    0.0878 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.8608    0.4860   -2.8276 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.6721   -1.1092   -1.9177 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6227    3.3464    0.1972 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3468   -2.7405   -0.4051 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7085   -0.0956    2.0270 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2835   -0.1969   -0.1003 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1803    1.7560    2.3055 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7300    2.1425    0.6082 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6238    1.5599   -0.3691 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9180   -0.0691   -0.6239 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6818   -1.0209    0.9565 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3101    0.6256    1.2033 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2242   -0.9089   -1.4412 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6329   -1.0052   -0.9318 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2986   -0.1019    0.5072 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.5806    2.2402   -0.7632 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4145   -0.5527    2.8153 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3273   -1.7632    2.6218 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9218   -2.3208    2.0156 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1879   -1.6373   -0.6757 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  7  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
 15 16  1  0
 16 17  1  0
 17 18  1  0
 18 19  1  0
 18 20  1  0
 20 21  2  0
 20 22  1  0
 13 23  1  0
 23 24  1  0
 23 25  1  0
 25 26  1  0
  7  2  1  0
 25 11  1  0
 10  6  1  0
  1 27  1  0
  1 28  1  0
  4 29  1  0
  9 30  1  0
 11 31  1  1
 13 32  1  6
 14 33  1  0
 14 34  1  0
 16 35  1  0
 16 36  1  0
 17 37  1  0
 17 38  1  0
 18 39  1  0
 19 40  1  0
 19 41  1  0
 22 42  1  0
 23 43  1  1
 24 44  1  0
 25 45  1  1
 26 46  1  0
M  END

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  N   UNK     0       3.431  -0.051   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       4.890   0.416   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.965  -0.538   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.528   1.197   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.896   1.959   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0       6.215  -0.346   0.000  0.00  0.00           N+0
HETATM    7  O   UNK     0       0.717   0.371   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       1.485  -2.003   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0       3.437   2.432   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0       6.215   2.733   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       7.539   0.416   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -0.538  -0.538   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -0.051  -2.003   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       2.362  -3.456   0.000  0.00  0.00           O+0
HETATM   15  N   UNK     0       7.539   1.959   0.000  0.00  0.00           N+0
HETATM   16  N   UNK     0       6.208   4.269   0.000  0.00  0.00           N+0
HETATM   17  C   UNK     0      -1.997  -0.051   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      -0.960  -3.245   0.000  0.00  0.00           O+0
HETATM   19 Se   UNK     0      -3.328  -0.826   0.000  0.00  0.00          Se+0
HETATM   20  C   UNK     0      -4.659  -0.051   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -5.991  -0.826   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -7.322  -0.051   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -8.647  -0.826   0.000  0.00  0.00           C+0
HETATM   24  N   UNK     0      -7.322   1.485   0.000  0.00  0.00           N+0
HETATM   25  O   UNK     0      -9.984  -0.051   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0      -8.647  -2.368   0.000  0.00  0.00           O+0
CONECT    1    2    3    4                                                  
CONECT    2    1    5    6                                                  
CONECT    3    1    7    8                                                  
CONECT    4    1    9                                                       
CONECT    5    2   10    9                                                  
CONECT    6    2   11                                                       
CONECT    7    3   12                                                       
CONECT    8    3   13   14                                                  
CONECT    9    4    5                                                       
CONECT   10    5   15   16                                                  
CONECT   11    6   15                                                       
CONECT   12    7   17   13                                                  
CONECT   13    8   18   12                                                  
CONECT   14    8                                                            
CONECT   15   10   11                                                       
CONECT   16   10                                                            
CONECT   17   12   19                                                       
CONECT   18   13                                                            
CONECT   19   17   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   23   24                                                  
CONECT   23   22   25   26                                                  
CONECT   24   22                                                            
CONECT   25   23                                                            
CONECT   26   23                                                            
MASTER        0    0    0    0    0    0    0    0   26    0   56    0
END

COMPND    HMDB0011117
HETATM    1  N1  UNL     1       7.429  -0.114  -2.089  1.00  0.00           N  
HETATM    2  C1  UNL     1       6.435   0.494  -1.263  1.00  0.00           C  
HETATM    3  N2  UNL     1       6.556   1.776  -0.912  1.00  0.00           N  
HETATM    4  C2  UNL     1       5.588   2.299  -0.130  1.00  0.00           C  
HETATM    5  N3  UNL     1       4.549   1.546   0.270  1.00  0.00           N  
HETATM    6  C3  UNL     1       4.410   0.241  -0.079  1.00  0.00           C  
HETATM    7  C4  UNL     1       5.379  -0.302  -0.867  1.00  0.00           C  
HETATM    8  N4  UNL     1       5.025  -1.596  -1.077  1.00  0.00           N  
HETATM    9  C5  UNL     1       3.873  -1.798  -0.421  1.00  0.00           C  
HETATM   10  N5  UNL     1       3.469  -0.679   0.205  1.00  0.00           N  
HETATM   11  C6  UNL     1       2.324  -0.411   1.012  1.00  0.00           C  
HETATM   12  O1  UNL     1       1.475   0.551   0.529  1.00  0.00           O  
HETATM   13  C7  UNL     1       0.181   0.211   0.820  1.00  0.00           C  
HETATM   14  C8  UNL     1      -0.637   1.356   1.380  1.00  0.00           C  
HETATM   15 SE1  UNL     1      -2.432   0.694   1.732  1.00  0.00          SE  
HETATM   16  C9  UNL     1      -3.461   0.563   0.087  1.00  0.00           C  
HETATM   17  C10 UNL     1      -4.793  -0.044   0.456  1.00  0.00           C  
HETATM   18  C11 UNL     1      -5.708  -0.221  -0.720  1.00  0.00           C  
HETATM   19  N6  UNL     1      -6.938  -0.819  -0.176  1.00  0.00           N  
HETATM   20  C12 UNL     1      -6.033   1.029  -1.424  1.00  0.00           C  
HETATM   21  O2  UNL     1      -5.198   1.743  -2.036  1.00  0.00           O  
HETATM   22  O3  UNL     1      -7.368   1.481  -1.426  1.00  0.00           O  
HETATM   23  C13 UNL     1       0.219  -0.950   1.809  1.00  0.00           C  
HETATM   24  O4  UNL     1      -0.888  -1.752   1.714  1.00  0.00           O  
HETATM   25  C14 UNL     1       1.486  -1.647   1.282  1.00  0.00           C  
HETATM   26  O5  UNL     1       1.112  -2.286   0.088  1.00  0.00           O  
HETATM   27  H1  UNL     1       7.861   0.486  -2.828  1.00  0.00           H  
HETATM   28  H2  UNL     1       7.672  -1.109  -1.918  1.00  0.00           H  
HETATM   29  H3  UNL     1       5.623   3.346   0.197  1.00  0.00           H  
HETATM   30  H4  UNL     1       3.347  -2.741  -0.405  1.00  0.00           H  
HETATM   31  H5  UNL     1       2.709  -0.096   2.027  1.00  0.00           H  
HETATM   32  H6  UNL     1      -0.283  -0.197  -0.100  1.00  0.00           H  
HETATM   33  H7  UNL     1      -0.180   1.756   2.305  1.00  0.00           H  
HETATM   34  H8  UNL     1      -0.730   2.142   0.608  1.00  0.00           H  
HETATM   35  H9  UNL     1      -3.624   1.560  -0.369  1.00  0.00           H  
HETATM   36  H10 UNL     1      -2.918  -0.069  -0.624  1.00  0.00           H  
HETATM   37  H11 UNL     1      -4.682  -1.021   0.957  1.00  0.00           H  
HETATM   38  H12 UNL     1      -5.310   0.626   1.203  1.00  0.00           H  
HETATM   39  H13 UNL     1      -5.224  -0.909  -1.441  1.00  0.00           H  
HETATM   40  H14 UNL     1      -7.633  -1.005  -0.932  1.00  0.00           H  
HETATM   41  H15 UNL     1      -7.299  -0.102   0.507  1.00  0.00           H  
HETATM   42  H16 UNL     1      -7.581   2.240  -0.763  1.00  0.00           H  
HETATM   43  H17 UNL     1       0.414  -0.553   2.815  1.00  0.00           H  
HETATM   44  H18 UNL     1      -1.327  -1.763   2.622  1.00  0.00           H  
HETATM   45  H19 UNL     1       1.922  -2.321   2.016  1.00  0.00           H  
HETATM   46  H20 UNL     1       1.188  -1.637  -0.676  1.00  0.00           H  
CONECT    1    2   27   28
CONECT    2    3    3    7
CONECT    3    4
CONECT    4    5    5   29
CONECT    5    6
CONECT    6    7    7   10
CONECT    7    8
CONECT    8    9    9
CONECT    9   10   30
CONECT   10   11
CONECT   11   12   25   31
CONECT   12   13
CONECT   13   14   23   32
CONECT   14   15   33   34
CONECT   15   16
CONECT   16   17   35   36
CONECT   17   18   37   38
CONECT   18   19   20   39
CONECT   19   40   41
CONECT   20   21   21   22
CONECT   22   42
CONECT   23   24   25   43
CONECT   24   44
CONECT   25   26   45
CONECT   26   46
END

HMDB0011117
     RDKit          3D
Se-Adenosylselenohomocysteine
 46 48  0  0  0  0  0  0  0  0999 V2000
    7.4293   -0.1138   -2.0892 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.4347    0.4937   -1.2633 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5565    1.7763   -0.9119 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.5882    2.2994   -0.1305 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5488    1.5456    0.2696 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.4101    0.2408   -0.0787 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3794   -0.3021   -0.8674 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0255   -1.5964   -1.0768 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.8727   -1.7982   -0.4214 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4691   -0.6790    0.2047 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.3242   -0.4107    1.0121 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4747    0.5511    0.5287 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1808    0.2107    0.8203 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.6368    1.3561    1.3798 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4321    0.6944    1.7325 Se  0  0  0  0  0  2  0  0  0  0  0  0
   -3.4608    0.5632    0.0874 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7928   -0.0435    0.4557 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7081   -0.2207   -0.7204 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9378   -0.8195   -0.1764 N   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0326    1.0289   -1.4237 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1983    1.7426   -2.0360 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3683    1.4807   -1.4261 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2195   -0.9499    1.8086 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.8881   -1.7517    1.7144 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4860   -1.6467    1.2817 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.1123   -2.2856    0.0878 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.8608    0.4860   -2.8276 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.6721   -1.1092   -1.9177 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6227    3.3464    0.1972 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3468   -2.7405   -0.4051 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7085   -0.0956    2.0270 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2835   -0.1969   -0.1003 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1803    1.7560    2.3055 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7300    2.1425    0.6082 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6238    1.5599   -0.3691 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9180   -0.0691   -0.6239 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6818   -1.0209    0.9565 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3101    0.6256    1.2033 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2242   -0.9089   -1.4412 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6329   -1.0052   -0.9318 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2986   -0.1019    0.5072 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.5806    2.2402   -0.7632 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4145   -0.5527    2.8153 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3273   -1.7632    2.6218 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9218   -2.3208    2.0156 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1879   -1.6373   -0.6757 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  7  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
 15 16  1  0
 16 17  1  0
 17 18  1  0
 18 19  1  0
 18 20  1  0
 20 21  2  0
 20 22  1  0
 13 23  1  0
 23 24  1  0
 23 25  1  0
 25 26  1  0
  7  2  1  0
 25 11  1  0
 10  6  1  0
  1 27  1  0
  1 28  1  0
  4 29  1  0
  9 30  1  0
 11 31  1  1
 13 32  1  6
 14 33  1  0
 14 34  1  0
 16 35  1  0
 16 36  1  0
 17 37  1  0
 17 38  1  0
 18 39  1  0
 19 40  1  0
 19 41  1  0
 22 42  1  0
 23 43  1  1
 24 44  1  0
 25 45  1  1
 26 46  1  0
M  END

Synonyms

Not Available

Molecular Formula

C₁₄H₂₀N₆O₅Se

Average Mass

431.31

Monoisotopic Mass

432.066039608

IUPAC Name

2-amino-4-({[(2S,3S,4R,5S)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl}selanyl)butanoic acid

Traditional Name

se-adenosylselenohomocysteine

CAS Registry Number

Not Available

SMILES

NC(CC[Se]C[C@H]1O[C@@H]([C@H](O)[C@@H]1O)N1C=NC2=C(N)N=CN=C12)C(O)=O

InChI Identifier

InChI=1S/C14H20N6O5Se/c15-6(14(23)24)1-2-26-3-7-9(21)10(22)13(25-7)20-5-19-8-11(16)17-4-18-12(8)20/h4-7,9-10,13,21-22H,1-3,15H2,(H,23,24)(H2,16,17,18)/t6?,7-,9-,10-,13+/m1/s1

InChI Key

UVSMMLABJBJNGH-WWJIDFMMSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 5'-deoxyribonucleosides. These are nucleosides in which the oxygen atom at the 5'position of the ribose moiety has been replaced by another atom. The nucleobases here are limited to purine, pyrimidine, and pyridine derivatives.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

5'-deoxyribonucleosides

Sub Class

Not Available

Direct Parent

5'-deoxyribonucleosides

Alternative Parents

Substituents

5'-deoxyribonucleoside
N-glycosyl compound
Glycosyl compound
Pentose monosaccharide
6-aminopurine
Alpha-amino acid or derivatives
Alpha-amino acid
Purine
Imidazopyrimidine
Aminopyrimidine
Monosaccharide
N-substituted imidazole
Imidolactam
Pyrimidine
Heteroaromatic compound
Tetrahydrofuran
Azole
Imidazole
1,2-diol
Amino acid
Amino acid or derivatives
Secondary alcohol
Organoheterocyclic compound
Azacycle
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Selenoether
Oxacycle
Organic nitrogen compound
Primary aliphatic amine
Organonitrogen compound
Organooxygen compound
Carbonyl group
Organoselenium compound
Primary amine
Hydrocarbon derivative
Amine
Organic oxide
Organopnictogen compound
Alcohol
Organic oxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Solid

Predicted Properties

Property	Value	Source
Water Solubility	8.42 g/L	ALOGPS
logP	-2.5	ALOGPS
logP	-5.3	ChemAxon
logS	-1.7	ALOGPS
pKa (Strongest Acidic)	1.31	ChemAxon
pKa (Strongest Basic)	9.5	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	182.63 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	98.04 m³·mol⁻¹	ChemAxon
Polarizability	36.91 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Spectra

Not Available

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Feces

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species
MMDBp0192132	Protein arginine N-methyltransferase 3	Unknown	O60678	Homo sapiens
MMDBp0192301	Putative adenosylhomocysteinase 3	Unknown	Q96HN2	Homo sapiens
MMDBp0192302	Adenosylhomocysteinase	Unknown	P23526	Homo sapiens
MMDBp0192303	Putative adenosylhomocysteinase 2	Unknown	O43865	Homo sapiens
MMDBp0196837	HemK methyltransferase family member 1	Unknown	Q9Y5R4
MMDBp0196881	Methyltransferase-like protein 2B	Unknown	Q6P1Q9
MMDBp0196882	Methyltransferase-like protein 6	Unknown	Q8TCB7
MMDBp0197020	Uncharacterized methyltransferase WBSCR22	Unknown	O43709

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria/Eubacteria	Firmicutes	107	Human feces; Human ; Human stool; Human subgingival plaque	Metabolic reconstruction
Bacteria/Eubacteria	Proteobacteria	89	Human feces; Human sputum; Human ; Human unknown; Human pleural fluid plaque	Metabolic reconstruction
Bacteria/Eubacteria	Actinobacteria	14	Human feces	Metabolic reconstruction
Bacteria/Eubacteria	Bacteroidetes	8	Human feces; Human ; Human supragingival plaque; Human subgingival plaque; Human saliva	Metabolic reconstruction
Bacteria/Eubacteria	Spirochaetes	1	Human feces	Metabolic reconstruction
Bacteria	Firmicutes	5	Human feces; Human ; Human stool; Human subgingival plaque	Metabolic reconstruction
Bacteria	Proteobacteria	4	Human feces; Human sputum; Human ; Human unknown; Human pleural fluid plaque	Metabolic reconstruction
Archaea	Euryarchaeota	1		Metabolic reconstruction
Bacteria	Actinobacteria	3	Human feces	Metabolic reconstruction
Bacteria/Eubacteria	Synergistetes	1	Human feces	Metabolic reconstruction
Bacteria/Eubacteria	Planctomycetes	1	Human feces	Metabolic reconstruction
Archaea	Crenarchaeota	1		Metabolic reconstruction

Exposure Sources

Other Exposures

Source Type	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference
Human Feces	Detected but not Quantified									HMDB

External Links

HMDB ID

HMDB0011117

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB027899

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

16682731

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Noronha A, Modamio J, Jarosz Y, Guerard E, Sompairac N, Preciat G, Danielsdottir AD, Krecke M, Merten D, Haraldsdottir HS, Heinken A, Heirendt L, Magnusdottir S, Ravcheev DA, Sahoo S, Gawron P, Friscioni L, Garcia B, Prendergast M, Puente A, Rodrigues M, Roy A, Rouquaya M, Wiltgen L, Zagare A, John E, Krueger M, Kuperstein I, Zinovyev A, Schneider R, Fleming RMT, Thiele I: The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease. Nucleic Acids Res. 2019 Jan 8;47(D1):D614-D624. doi: 10.1093/nar/gky992. [PubMed:30371894 ]

Showing metabocard for Se-Adenosylselenohomocysteine (MMDBc0047964)

MOL for #<Metabolite:0x00007f9222123e58>

3D MOL for #<Metabolite:0x00007f9222123e58>

3D SDF for #<Metabolite:0x00007f9222123e58>

3D-SDF for #<Metabolite:0x00007f9222123e58>

PDB for #<Metabolite:0x00007f9222123e58>

3D PDB for #<Metabolite:0x00007f9222123e58>

SMILES for #<Metabolite:0x00007f9222123e58>

INCHI for #<Metabolite:0x00007f9222123e58>

Structure for #<Metabolite:0x00007f9222123e58>

3D Structure for #<Metabolite:0x00007f9222123e58>