data_5SV
#

_chem_comp.id                                   5SV
_chem_comp.name                                 "[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl icosyl hydrogen phosphate"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C30 H54 N5 O7 P"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2015-11-25
_chem_comp.pdbx_modified_date                   2019-09-04
_chem_comp.pdbx_ambiguous_flag                  N
_chem_comp.pdbx_release_status                  REL
_chem_comp.pdbx_replaced_by                     ?
_chem_comp.pdbx_replaces                        ?
_chem_comp.formula_weight                       627.753
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    5SV
_chem_comp.pdbx_model_coordinates_details       ?
_chem_comp.pdbx_model_coordinates_missing_flag  Y
_chem_comp.pdbx_ideal_coordinates_details       Corina
_chem_comp.pdbx_ideal_coordinates_missing_flag  N
_chem_comp.pdbx_model_coordinates_db_code       5EY8
_chem_comp.pdbx_subcomponent_list               ?
_chem_comp.pdbx_processing_site                 EBI
#   #
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.alt_atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.charge
_chem_comp_atom.pdbx_align
_chem_comp_atom.pdbx_aromatic_flag
_chem_comp_atom.pdbx_leaving_atom_flag
_chem_comp_atom.pdbx_stereo_config
_chem_comp_atom.model_Cartn_x
_chem_comp_atom.model_Cartn_y
_chem_comp_atom.model_Cartn_z
_chem_comp_atom.pdbx_model_Cartn_x_ideal
_chem_comp_atom.pdbx_model_Cartn_y_ideal
_chem_comp_atom.pdbx_model_Cartn_z_ideal
_chem_comp_atom.pdbx_component_atom_id
_chem_comp_atom.pdbx_component_comp_id
_chem_comp_atom.pdbx_ordinal
5SV  C2     C1   C  0  1  Y  N  N  43.352  -1.329  250.245   11.690  -3.842   1.211  C2     5SV   1  
5SV  C4     C2   C  0  1  Y  N  N  43.228   0.916  250.126   10.000  -2.558   0.327  C4     5SV   2  
5SV  C6     C3   C  0  1  Y  N  N  42.726  -0.448  248.173   10.538  -4.724  -0.584  C6     5SV   3  
5SV  C5     C4   C  0  1  Y  N  N  42.840   0.851  248.757    9.751  -3.561  -0.624  C5     5SV   4  
5SV  N1     N1   N  0  1  Y  N  N  42.991  -1.559  248.944   11.489  -4.814   0.340  N1     5SV   5  
5SV  N3     N2   N  0  1  Y  N  N  43.493  -0.166  250.924   10.970  -2.739   1.218  N3     5SV   6  
5SV  C8     C5   C  0  1  Y  N  N  42.961   2.977  249.257    8.340  -1.956  -0.993  C8     5SV   7  
5SV  C9     C6   C  0  1  N  N  N  40.905   7.448  248.145    1.652   2.564  -0.682  C9     5SV   8  
5SV  C10    C7   C  0  1  N  N  N  41.030   6.250  247.174    0.547   1.773   0.021  C10    5SV   9  
5SV  C11    C8   C  0  1  N  N  N  41.434   6.739  245.783   -0.804   2.112  -0.613  C11    5SV  10  
5SV  C12    C9   C  0  1  N  N  N  41.494   5.606  244.742   -1.910   1.322   0.090  C12    5SV  11  
5SV  C13    C10  C  0  1  N  N  N  41.656   6.155  243.301   -3.261   1.661  -0.544  C13    5SV  12  
5SV  C14    C11  C  0  1  N  N  N  40.327   6.697  242.738   -4.366   0.870   0.159  C14    5SV  13  
5SV  C15    C12  C  0  1  N  N  N  40.511   7.360  241.369   -5.717   1.209  -0.475  C15    5SV  14  
5SV  O2P    O1   O  0  1  N  N  N  40.090   8.060  251.663    4.284   4.482  -0.291  O2P    5SV  15  
5SV  P      P1   P  0  1  N  N  N  41.261   7.685  250.834    4.301   2.898  -0.582  P      5SV  16  
5SV  O1P    O2   O  0  1  N  N  N  42.263   8.814  250.327    4.468   2.665  -2.034  O1P    5SV  17  
5SV  "O5'"  O3   O  0  1  N  N  N  42.283   6.707  251.570    5.525   2.220   0.215  "O5'"  5SV  18  
5SV  "C5'"  C13  C  0  1  N  N  N  43.538   6.272  251.172    6.895   2.510  -0.070  "C5'"  5SV  19  
5SV  "C4'"  C14  C  0  1  N  N  R  43.956   5.101  252.080    7.793   1.699   0.866  "C4'"  5SV  20  
5SV  "O4'"  O4   O  0  1  N  N  N  43.045   4.051  251.861    7.671   0.298   0.568  "O4'"  5SV  21  
5SV  "C3'"  C15  C  0  1  N  N  S  45.389   4.592  251.794    9.267   2.090   0.647  "C3'"  5SV  22  
5SV  "O3'"  O5   O  0  1  N  N  N  46.179   5.098  252.819    9.832   2.605   1.855  "O3'"  5SV  23  
5SV  "C2'"  C16  C  0  1  N  N  R  45.245   3.059  251.851    9.958   0.762   0.250  "C2'"  5SV  24  
5SV  "O2'"  O6   O  0  1  N  N  N  45.720   2.685  253.099   11.235   0.644   0.879  "O2'"  5SV  25  
5SV  "C1'"  C17  C  0  1  N  N  R  43.696   2.819  251.755    8.965  -0.298   0.804  "C1'"  5SV  26  
5SV  N9     N3   N  0  1  Y  N  N  43.307   2.277  250.440    9.096  -1.559   0.070  N9     5SV  27  
5SV  N7     N4   N  0  1  Y  N  N  42.673   2.148  248.234    8.726  -3.131  -1.399  N7     5SV  28  
5SV  N6     N5   N  0  1  N  N  N  42.384  -0.642  246.862   10.339  -5.746  -1.496  N6     5SV  29  
5SV  O3P    O7   O  0  1  N  N  N  40.883   6.958  249.459    2.914   2.247  -0.090  O3P    5SV  30  
5SV  C16    C18  C  0  1  N  N  N  39.327   7.085  240.434   -6.823   0.419   0.228  C16    5SV  31  
5SV  C17    C19  C  0  1  N  N  N  38.816   8.285  239.629   -8.173   0.757  -0.406  C17    5SV  32  
5SV  C18    C20  C  0  1  N  N  N  37.629   7.905  238.738   -9.279  -0.033   0.296  C18    5SV  33  
5SV  C19    C21  C  0  1  N  N  N  36.952   9.168  238.203  -10.630   0.306  -0.338  C19    5SV  34  
5SV  C20    C22  C  0  1  N  N  N  35.821   8.869  237.195  -11.735  -0.484   0.365  C20    5SV  35  
5SV  C21    C23  C  0  1  N  N  N  35.138  10.157  236.722  -13.086  -0.146  -0.269  C21    5SV  36  
5SV  C22    C24  C  0  1  N  N  N  34.391   9.977  235.416  -14.192  -0.936   0.434  C22    5SV  37  
5SV  C23    C25  C  0  1  N  N  N  33.894  11.299  234.926  -15.542  -0.597  -0.200  C23    5SV  38  
5SV  C24    C26  C  0  1  N  N  N  34.332  11.884  233.807  -16.648  -1.388   0.503  C24    5SV  39  
5SV  H1     H1   H  0  1  N  N  N  43.557  -2.218  250.822   12.470  -3.957   1.948  H1     5SV  40  
5SV  H2     H2   H  0  1  N  N  N  42.931   4.054  249.184    7.540  -1.380  -1.433  H2     5SV  41  
5SV  H3     H3   H  0  1  N  N  N  41.765   8.122  248.015    1.671   2.300  -1.739  H3     5SV  42  
5SV  H4     H4   H  0  1  N  N  N  39.974   7.997  247.938    1.459   3.631  -0.576  H4     5SV  43  
5SV  H5     H5   H  0  1  N  N  N  40.062   5.731  247.110    0.740   0.706  -0.084  H5     5SV  44  
5SV  H6     H6   H  0  1  N  N  N  41.794   5.555  247.551    0.528   2.036   1.079  H6     5SV  45  
5SV  H7     H7   H  0  1  N  N  N  42.428   7.206  245.850   -0.998   3.180  -0.507  H7     5SV  46  
5SV  H8     H8   H  0  1  N  N  N  40.700   7.486  245.447   -0.785   1.849  -1.670  H8     5SV  47  
5SV  H9     H9   H  0  1  N  N  N  40.564   5.022  244.798   -1.717   0.254  -0.015  H9     5SV  48  
5SV  H10    H10  H  0  1  N  N  N  42.350   4.955  244.973   -1.929   1.585   1.148  H10    5SV  49  
5SV  H11    H11  H  0  1  N  N  N  42.013   5.344  242.650   -3.454   2.728  -0.439  H11    5SV  50  
5SV  H12    H12  H  0  1  N  N  N  42.396   6.969  243.312   -3.242   1.397  -1.602  H12    5SV  51  
5SV  H13    H13  H  0  1  N  N  N  39.920   7.440  243.440   -4.173  -0.197   0.053  H13    5SV  52  
5SV  H14    H14  H  0  1  N  N  N  39.618   5.862  242.636   -4.385   1.133   1.216  H14    5SV  53  
5SV  H15    H15  H  0  1  N  N  N  41.428   6.968  240.905   -5.910   2.276  -0.370  H15    5SV  54  
5SV  H16    H16  H  0  1  N  N  N  40.607   8.447  241.511   -5.698   0.946  -1.533  H16    5SV  55  
5SV  H17    H17  H  0  1  N  N  N  40.085   9.000  251.798    4.177   4.709   0.642  H17    5SV  56  
5SV  H18    H18  H  0  1  N  N  N  43.500   5.936  250.125    7.115   2.244  -1.104  H18    5SV  57  
5SV  H19    H19  H  0  1  N  N  N  44.263   7.093  251.267    7.081   3.573   0.079  H19    5SV  58  
5SV  H20    H20  H  0  1  N  N  N  43.909   5.436  253.127    7.510   1.883   1.902  H20    5SV  59  
5SV  H21    H21  H  0  1  N  N  N  45.721   4.914  250.796    9.353   2.820  -0.157  H21    5SV  60  
5SV  H22    H22  H  0  1  N  N  N  46.236   6.043  252.739   10.774   2.814   1.791  H22    5SV  61  
5SV  H23    H23  H  0  1  N  N  N  45.769   2.577  251.013   10.050   0.681  -0.833  H23    5SV  62  
5SV  H24    H24  H  0  1  N  N  N  46.657   2.836  253.140   11.861   1.339   0.633  H24    5SV  63  
5SV  H25    H25  H  0  1  N  N  N  43.390   2.131  252.557    9.127  -0.454   1.870  H25    5SV  64  
5SV  H26    H26  H  0  1  N  N  N  42.381  -1.621  246.659    9.649  -5.664  -2.173  H26    5SV  65  
5SV  H27    H27  H  0  1  N  N  N  41.473  -0.264  246.696   10.888  -6.544  -1.457  H27    5SV  66  
5SV  H28    H28  H  0  1  N  N  N  38.494   6.711  241.047   -6.629  -0.649   0.122  H28    5SV  67  
5SV  H29    H29  H  0  1  N  N  N  39.635   6.307  239.720   -6.841   0.682   1.285  H29    5SV  68  
5SV  H30    H30  H  0  1  N  N  N  39.632   8.662  238.995   -8.367   1.825  -0.301  H30    5SV  69  
5SV  H31    H31  H  0  1  N  N  N  38.500   9.074  240.327   -8.155   0.494  -1.464  H31    5SV  70  
5SV  H32    H32  H  0  1  N  N  N  36.903   7.324  239.326   -9.086  -1.100   0.191  H32    5SV  71  
5SV  H33    H33  H  0  1  N  N  N  37.987   7.298  237.894   -9.298   0.230   1.354  H33    5SV  72  
5SV  H34    H34  H  0  1  N  N  N  37.711   9.787  237.703  -10.823   1.373  -0.232  H34    5SV  73  
5SV  H35    H35  H  0  1  N  N  N  36.527   9.723  239.052  -10.611   0.043  -1.395  H35    5SV  74  
5SV  H36    H36  H  0  1  N  N  N  35.073   8.224  237.678  -11.542  -1.552   0.260  H36    5SV  75  
5SV  H37    H37  H  0  1  N  N  N  36.246   8.349  236.324  -11.754  -0.221   1.423  H37    5SV  76  
5SV  H38    H38  H  0  1  N  N  N  35.906  10.932  236.584  -13.279   0.922  -0.163  H38    5SV  77  
5SV  H39    H39  H  0  1  N  N  N  34.424  10.481  237.494  -13.067  -0.409  -1.326  H39    5SV  78  
5SV  H40    H40  H  0  1  N  N  N  33.537   9.303  235.575  -13.998  -2.003   0.328  H40    5SV  79  
5SV  H41    H41  H  0  1  N  N  N  35.068   9.541  234.666  -14.210  -0.673   1.491  H41    5SV  80  
5SV  H42    H42  H  0  1  N  N  N  34.094  12.015  235.737  -15.736   0.470  -0.095  H42    5SV  81  
5SV  H43    H43  H  0  1  N  N  N  34.110  12.942  234.009  -16.455  -2.455   0.397  H43    5SV  82  
5SV  H44    H44  H  0  1  N  N  N  35.417  11.716  233.880  -16.667  -1.124   1.560  H44    5SV  83  
5SV  C25    C27  C  0  1  N  N  N       ?       ?        ?  -17.999  -1.049  -0.131  C25    5SV  84  
5SV  C26    C28  C  0  1  N  N  N       ?       ?        ?  -19.104  -1.839   0.571  C26    5SV  85  
5SV  C27    C29  C  0  1  N  N  N       ?       ?        ?  -20.455  -1.500  -0.062  C27    5SV  86  
5SV  C28    C30  C  0  1  N  N  N       ?       ?        ?  -21.561  -2.291   0.640  C28    5SV  87  
5SV  H45    H45  H  0  1  N  N  N  32.808  11.183  234.799  -15.524  -0.860  -1.258  H45    5SV  88  
5SV  H46    H46  H  0  1  N  N  N       ?       ?        ?  -18.192   0.019  -0.026  H46    5SV  89  
5SV  H47    H47  H  0  1  N  N  N       ?       ?        ?  -17.980  -1.312  -1.189  H47    5SV  90  
5SV  H48    H48  H  0  1  N  N  N       ?       ?        ?  -18.911  -2.907   0.466  H48    5SV  91  
5SV  H49    H49  H  0  1  N  N  N       ?       ?        ?  -19.123  -1.576   1.629  H49    5SV  92  
5SV  H50    H50  H  0  1  N  N  N       ?       ?        ?  -20.649  -0.433   0.043  H50    5SV  93  
5SV  H51    H51  H  0  1  N  N  N       ?       ?        ?  -20.436  -1.763  -1.120  H51    5SV  94  
5SV  H52    H52  H  0  1  N  N  N       ?       ?        ?  -21.580  -2.027   1.698  H52    5SV  95  
5SV  H53    H53  H  0  1  N  N  N       ?       ?        ?  -22.523  -2.049   0.189  H53    5SV  96  
5SV  H54    H54  H  0  1  N  N  N       ?       ?        ?  -21.368  -3.358   0.535  H54    5SV  97  
#   #
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_aromatic_flag
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_ordinal
5SV  C24    C23    SING  N  N   1  
5SV  C23    C22    SING  N  N   2  
5SV  C22    C21    SING  N  N   3  
5SV  C21    C20    SING  N  N   4  
5SV  C20    C19    SING  N  N   5  
5SV  C19    C18    SING  N  N   6  
5SV  C18    C17    SING  N  N   7  
5SV  C17    C16    SING  N  N   8  
5SV  C16    C15    SING  N  N   9  
5SV  C15    C14    SING  N  N  10  
5SV  C14    C13    SING  N  N  11  
5SV  C13    C12    SING  N  N  12  
5SV  C12    C11    SING  N  N  13  
5SV  C11    C10    SING  N  N  14  
5SV  N6     C6     SING  N  N  15  
5SV  C10    C9     SING  N  N  16  
5SV  C9     O3P    SING  N  N  17  
5SV  C6     C5     DOUB  Y  N  18  
5SV  C6     N1     SING  Y  N  19  
5SV  N7     C5     SING  Y  N  20  
5SV  N7     C8     DOUB  Y  N  21  
5SV  C5     C4     SING  Y  N  22  
5SV  N1     C2     DOUB  Y  N  23  
5SV  C8     N9     SING  Y  N  24  
5SV  O3P    P      SING  N  N  25  
5SV  C4     N9     SING  Y  N  26  
5SV  C4     N3     DOUB  Y  N  27  
5SV  C2     N3     SING  Y  N  28  
5SV  O1P    P      DOUB  N  N  29  
5SV  N9     "C1'"  SING  N  N  30  
5SV  P      "O5'"  SING  N  N  31  
5SV  P      O2P    SING  N  N  32  
5SV  "C5'"  "O5'"  SING  N  N  33  
5SV  "C5'"  "C4'"  SING  N  N  34  
5SV  "C1'"  "C2'"  SING  N  N  35  
5SV  "C1'"  "O4'"  SING  N  N  36  
5SV  "C3'"  "C2'"  SING  N  N  37  
5SV  "C3'"  "C4'"  SING  N  N  38  
5SV  "C3'"  "O3'"  SING  N  N  39  
5SV  "C2'"  "O2'"  SING  N  N  40  
5SV  "O4'"  "C4'"  SING  N  N  41  
5SV  C2     H1     SING  N  N  42  
5SV  C8     H2     SING  N  N  43  
5SV  C9     H3     SING  N  N  44  
5SV  C9     H4     SING  N  N  45  
5SV  C10    H5     SING  N  N  46  
5SV  C10    H6     SING  N  N  47  
5SV  C11    H7     SING  N  N  48  
5SV  C11    H8     SING  N  N  49  
5SV  C12    H9     SING  N  N  50  
5SV  C12    H10    SING  N  N  51  
5SV  C13    H11    SING  N  N  52  
5SV  C13    H12    SING  N  N  53  
5SV  C14    H13    SING  N  N  54  
5SV  C14    H14    SING  N  N  55  
5SV  C15    H15    SING  N  N  56  
5SV  C15    H16    SING  N  N  57  
5SV  O2P    H17    SING  N  N  58  
5SV  "C5'"  H18    SING  N  N  59  
5SV  "C5'"  H19    SING  N  N  60  
5SV  "C4'"  H20    SING  N  N  61  
5SV  "C3'"  H21    SING  N  N  62  
5SV  "O3'"  H22    SING  N  N  63  
5SV  "C2'"  H23    SING  N  N  64  
5SV  "O2'"  H24    SING  N  N  65  
5SV  "C1'"  H25    SING  N  N  66  
5SV  N6     H26    SING  N  N  67  
5SV  N6     H27    SING  N  N  68  
5SV  C16    H28    SING  N  N  69  
5SV  C16    H29    SING  N  N  70  
5SV  C17    H30    SING  N  N  71  
5SV  C17    H31    SING  N  N  72  
5SV  C18    H32    SING  N  N  73  
5SV  C18    H33    SING  N  N  74  
5SV  C19    H34    SING  N  N  75  
5SV  C19    H35    SING  N  N  76  
5SV  C20    H36    SING  N  N  77  
5SV  C20    H37    SING  N  N  78  
5SV  C21    H38    SING  N  N  79  
5SV  C21    H39    SING  N  N  80  
5SV  C22    H40    SING  N  N  81  
5SV  C22    H41    SING  N  N  82  
5SV  C23    H42    SING  N  N  83  
5SV  C24    H43    SING  N  N  84  
5SV  C24    H44    SING  N  N  85  
5SV  C24    C25    SING  N  N  86  
5SV  C25    C26    SING  N  N  87  
5SV  C26    C27    SING  N  N  88  
5SV  C27    C28    SING  N  N  89  
5SV  C23    H45    SING  N  N  90  
5SV  C25    H46    SING  N  N  91  
5SV  C25    H47    SING  N  N  92  
5SV  C26    H48    SING  N  N  93  
5SV  C26    H49    SING  N  N  94  
5SV  C27    H50    SING  N  N  95  
5SV  C27    H51    SING  N  N  96  
5SV  C28    H52    SING  N  N  97  
5SV  C28    H53    SING  N  N  98  
5SV  C28    H54    SING  N  N  99  
#   #
loop_
_pdbx_chem_comp_descriptor.comp_id
_pdbx_chem_comp_descriptor.type
_pdbx_chem_comp_descriptor.program
_pdbx_chem_comp_descriptor.program_version
_pdbx_chem_comp_descriptor.descriptor
5SV  InChI             InChI                 1.03   "InChI=1S/C30H54N5O7P/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18-19-20-40-43(38,39)41-21-24-26(36)27(37)30(42-24)35-23-34-25-28(31)32-22-33-29(25)35/h22-24,26-27,30,36-37H,2-21H2,1H3,(H,38,39)(H2,31,32,33)/t24-,26-,27-,30-/m1/s1"  
5SV  InChIKey          InChI                 1.03   JFYKNVSLLXBVHG-BQOYKFDPSA-N  
5SV  SMILES_CANONICAL  CACTVS                3.385  "CCCCCCCCCCCCCCCCCCCCO[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23"  
5SV  SMILES            CACTVS                3.385  "CCCCCCCCCCCCCCCCCCCCO[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23"  
5SV  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.4  "CCCCCCCCCCCCCCCCCCCCOP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O"  
5SV  SMILES            "OpenEye OEToolkits"  2.0.4  "CCCCCCCCCCCCCCCCCCCCOP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)O"  
#
_pdbx_chem_comp_identifier.comp_id          5SV
_pdbx_chem_comp_identifier.type             "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program          "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version  2.0.4
_pdbx_chem_comp_identifier.identifier       "[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl icosyl hydrogen phosphate"
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
5SV  "Create component"    2015-11-25  EBI   
5SV  "Initial release"     2015-12-16  RCSB  
5SV  "Other modification"  2019-09-04  EBI   
##
