data_87N
#

_chem_comp.id                                   87N
_chem_comp.name                                 "[(2~{R},3~{R},4~{S},5~{S},6~{R})-4-acetamido-6-methyl-3,5-bis(oxidanyl)oxan-2-yl] [[(2~{R},3~{S},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] hydrogen phosphate "
_chem_comp.type                                 non-polymer
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C18 H29 N3 O15 P2"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2021-09-09
_chem_comp.pdbx_modified_date                   2021-09-17
_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                       589.381
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    87N
_chem_comp.pdbx_model_coordinates_details       ?
_chem_comp.pdbx_model_coordinates_missing_flag  N
_chem_comp.pdbx_ideal_coordinates_details       Corina
_chem_comp.pdbx_ideal_coordinates_missing_flag  N
_chem_comp.pdbx_model_coordinates_db_code       7S41
_chem_comp.pdbx_subcomponent_list               ?
_chem_comp.pdbx_processing_site                 RCSB
#   #
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
87N  O3     O1   O  0  1  N  N  N  29.662  -14.891  32.616   4.471  -2.349  -2.747  O3     87N   1  
87N  C3     C1   C  0  1  N  N  N  30.726  -14.417  32.408   5.414  -2.973  -2.308  C3     87N   2  
87N  C3M    C2   C  0  1  N  N  N  31.635  -14.999  31.340   6.104  -4.001  -3.168  C3M    87N   3  
87N  N3Q    N1   N  0  1  N  N  N  31.157  -13.328  33.069   5.848  -2.743  -1.053  N3Q    87N   4  
87N  C3Q    C3   C  0  1  N  N  S  30.256  -12.405  33.733   5.181  -1.739  -0.220  C3Q    87N   5  
87N  C4Q    C4   C  0  1  N  N  S  30.667  -12.023  35.162   5.398  -2.076   1.259  C4Q    87N   6  
87N  O4Q    O2   O  0  1  N  N  N  30.751  -13.197  35.958   4.786  -3.332   1.558  O4Q    87N   7  
87N  C2Q    C5   C  0  1  N  N  R  30.077  -11.137  32.900   5.774  -0.357  -0.510  C2Q    87N   8  
87N  O2Q    O3   O  0  1  N  N  N  29.633  -11.390  31.577   5.514  -0.001  -1.869  O2Q    87N   9  
87N  C1Q    C6   C  0  1  N  N  R  29.107  -10.193  33.565   5.127   0.672   0.421  C1Q    87N  10  
87N  O5Q    O4   O  0  1  N  N  N  29.460   -9.965  34.914   5.339   0.283   1.780  O5Q    87N  11  
87N  C5Q    C7   C  0  1  N  N  R  29.581  -11.116  35.721   4.765  -0.980   2.121  C5Q    87N  12  
87N  C6Q    C8   C  0  1  N  N  N  29.919  -10.655  37.141   5.029  -1.278   3.599  C6Q    87N  13  
87N  O3B    O5   O  0  1  N  N  N  27.832  -10.783  33.494   3.724   0.738   0.157  O3B    87N  14  
87N  PB     P1   P  0  1  N  N  N  26.463   -9.920  33.339   2.853   2.076   0.367  PB     87N  15  
87N  O1B    O6   O  0  1  N  N  N  25.920   -9.438  34.657   3.351   3.206  -0.666  O1B    87N  16  
87N  O2B    O7   O  0  1  N  N  N  25.490  -10.703  32.550   3.026   2.564   1.754  O2B    87N  17  
87N  O3A    O8   O  0  1  N  N  N  26.986   -8.654  32.481   1.299   1.752   0.101  O3A    87N  18  
87N  PA     P2   P  0  1  N  N  N  26.251   -7.261  32.073  -0.076   2.524   0.426  PA     87N  19  
87N  O1A    O9   O  0  1  N  N  N  25.197   -6.862  33.008  -0.410   2.389   1.995  O1A    87N  20  
87N  O2A    O10  O  0  1  N  N  N  27.388   -6.394  31.868   0.067   3.955   0.073  O2A    87N  21  
87N  "O5'"  O11  O  0  1  N  N  N  25.467   -7.586  30.695  -1.272   1.876  -0.435  "O5'"  87N  22  
87N  "C5'"  C9   C  0  1  N  N  N  26.191   -8.074  29.584  -2.598   2.408  -0.447  "C5'"  87N  23  
87N  "C4'"  C10  C  0  1  N  N  R  25.626   -9.451  29.136  -3.480   1.556  -1.363  "C4'"  87N  24  
87N  "O4'"  O12  O  0  1  N  N  N  24.321   -9.303  28.620  -3.691   0.247  -0.793  "O4'"  87N  25  
87N  "C3'"  C11  C  0  1  N  N  S  26.410  -10.042  27.989  -4.909   2.151  -1.452  "C3'"  87N  26  
87N  "O3'"  O13  O  0  1  N  N  N  27.545  -10.756  28.497  -4.983   3.149  -2.473  "O3'"  87N  27  
87N  "C2'"  C12  C  0  1  N  N  N  25.359  -11.043  27.511  -5.753   0.910  -1.831  "C2'"  87N  28  
87N  "C1'"  C13  C  0  1  N  N  R  24.031  -10.270  27.656  -4.880  -0.288  -1.399  "C1'"  87N  29  
87N  N1     N2   N  0  1  N  N  N  23.732   -9.568  26.387  -5.607  -1.111  -0.429  N1     87N  30  
87N  C2     C14  C  0  1  N  N  N  23.170  -10.305  25.385  -5.922  -0.599   0.775  C2     87N  31  
87N  O2     O14  O  0  1  N  N  N  22.875  -11.451  25.602  -5.599   0.541   1.045  O2     87N  32  
87N  N3     N3   N  0  1  N  N  N  22.949   -9.683  24.211  -6.589  -1.333   1.685  N3     87N  33  
87N  C6     C15  C  0  1  N  N  N  24.079   -8.285  26.165  -5.964  -2.390  -0.758  C6     87N  34  
87N  C5     C16  C  0  1  N  N  N  23.832   -7.673  24.956  -6.634  -3.148   0.137  C5     87N  35  
87N  C5M    C17  C  0  1  N  N  N  24.235   -6.226  24.684  -7.036  -4.559  -0.208  C5M    87N  36  
87N  C4     C18  C  0  1  N  N  N  23.277   -8.409  23.931  -6.955  -2.599   1.402  C4     87N  37  
87N  O4     O15  O  0  1  N  N  N  23.044   -7.947  22.850  -7.559  -3.263   2.224  O4     87N  38  
87N  H1     H1   H  0  1  N  N  N  31.139  -15.857  30.863   5.620  -4.043  -4.143  H1     87N  39  
87N  H2     H2   H  0  1  N  N  N  31.849  -14.231  30.582   7.151  -3.725  -3.294  H2     87N  40  
87N  H3     H3   H  0  1  N  N  N  32.577  -15.331  31.801   6.041  -4.977  -2.688  H3     87N  41  
87N  H4     H4   H  0  1  N  N  N  32.140  -13.147  33.104   6.602  -3.242  -0.702  H4     87N  42  
87N  H5     H5   H  0  1  N  N  N  29.269  -12.886  33.802   4.114  -1.734  -0.440  H5     87N  43  
87N  H6     H6   H  0  1  N  N  N  31.627  -11.486  35.140   6.466  -2.132   1.467  H6     87N  44  
87N  H7     H7   H  0  1  N  N  N  31.005  -12.963  36.843   4.884  -3.608   2.479  H7     87N  45  
87N  H8     H8   H  0  1  N  N  N  31.054  -10.633  32.855   6.850  -0.378  -0.337  H8     87N  46  
87N  H9     H9   H  0  1  N  N  N  30.237  -11.984  31.148   5.858   0.867  -2.121  H9     87N  47  
87N  H10    H10  H  0  1  N  N  N  29.111   -9.242  33.013   5.575   1.651   0.249  H10    87N  48  
87N  H11    H11  H  0  1  N  N  N  28.631  -11.670  35.745   3.691  -0.952   1.942  H11    87N  49  
87N  H12    H12  H  0  1  N  N  N  30.020  -11.532  37.797   6.104  -1.305   3.777  H12    87N  50  
87N  H13    H13  H  0  1  N  N  N  30.866  -10.095  37.129   4.579  -0.498   4.213  H13    87N  51  
87N  H14    H14  H  0  1  N  N  N  29.114  -10.007  37.517   4.593  -2.242   3.859  H14    87N  52  
87N  H15    H15  H  0  1  N  N  N  25.021   -9.729  34.755   3.267   2.954  -1.595  H15    87N  53  
87N  H16    H16  H  0  1  N  N  N  25.413   -6.019  33.389  -0.517   1.477   2.297  H16    87N  54  
87N  H17    H17  H  0  1  N  N  N  27.249   -8.189  29.862  -3.005   2.394   0.564  H17    87N  55  
87N  H18    H18  H  0  1  N  N  N  26.106   -7.359  28.753  -2.576   3.433  -0.816  H18    87N  56  
87N  H19    H19  H  0  1  N  N  N  25.640  -10.143  29.991  -3.036   1.476  -2.355  H19    87N  57  
87N  H20    H20  H  0  1  N  N  N  26.660   -9.298  27.219  -5.222   2.557  -0.490  H20    87N  58  
87N  H21    H21  H  0  1  N  N  N  28.201  -10.137  28.795  -5.858   3.551  -2.567  H21    87N  59  
87N  H22    H22  H  0  1  N  N  N  25.360  -11.945  28.141  -6.697   0.910  -1.286  H22    87N  60  
87N  H23    H23  H  0  1  N  N  N  25.535  -11.328  26.463  -5.933   0.884  -2.905  H23    87N  61  
87N  H24    H24  H  0  1  N  N  N  23.215  -10.945  27.951  -4.615  -0.887  -2.270  H24    87N  62  
87N  H25    H25  H  0  1  N  N  N  22.504  -10.212  23.488  -6.808  -0.949   2.549  H25    87N  63  
87N  H26    H26  H  0  1  N  N  N  24.561   -7.724  26.952  -5.712  -2.791  -1.728  H26    87N  64  
87N  H27    H27  H  0  1  N  N  N  24.658   -5.785  25.598  -6.240  -5.245   0.085  H27    87N  65  
87N  H28    H28  H  0  1  N  N  N  24.988   -6.200  23.882  -7.951  -4.816   0.324  H28    87N  66  
87N  H29    H29  H  0  1  N  N  N  23.350   -5.651  24.375  -7.206  -4.637  -1.282  H29    87N  67  
#   #
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
87N  O4     C4     DOUB  N  N   1  
87N  C4     N3     SING  N  N   2  
87N  C4     C5     SING  N  N   3  
87N  N3     C2     SING  N  N   4  
87N  C5M    C5     SING  N  N   5  
87N  C5     C6     DOUB  N  N   6  
87N  C2     O2     DOUB  N  N   7  
87N  C2     N1     SING  N  N   8  
87N  C6     N1     SING  N  N   9  
87N  N1     "C1'"  SING  N  N  10  
87N  "C2'"  "C1'"  SING  N  N  11  
87N  "C2'"  "C3'"  SING  N  N  12  
87N  "C1'"  "O4'"  SING  N  N  13  
87N  "C3'"  "O3'"  SING  N  N  14  
87N  "C3'"  "C4'"  SING  N  N  15  
87N  "O4'"  "C4'"  SING  N  N  16  
87N  "C4'"  "C5'"  SING  N  N  17  
87N  "C5'"  "O5'"  SING  N  N  18  
87N  "O5'"  PA     SING  N  N  19  
87N  C3M    C3     SING  N  N  20  
87N  O2Q    C2Q    SING  N  N  21  
87N  O2A    PA     DOUB  N  N  22  
87N  PA     O3A    SING  N  N  23  
87N  PA     O1A    SING  N  N  24  
87N  C3     O3     DOUB  N  N  25  
87N  C3     N3Q    SING  N  N  26  
87N  O3A    PB     SING  N  N  27  
87N  O2B    PB     DOUB  N  N  28  
87N  C2Q    C1Q    SING  N  N  29  
87N  C2Q    C3Q    SING  N  N  30  
87N  N3Q    C3Q    SING  N  N  31  
87N  PB     O3B    SING  N  N  32  
87N  PB     O1B    SING  N  N  33  
87N  O3B    C1Q    SING  N  N  34  
87N  C1Q    O5Q    SING  N  N  35  
87N  C3Q    C4Q    SING  N  N  36  
87N  O5Q    C5Q    SING  N  N  37  
87N  C4Q    C5Q    SING  N  N  38  
87N  C4Q    O4Q    SING  N  N  39  
87N  C5Q    C6Q    SING  N  N  40  
87N  C3M    H1     SING  N  N  41  
87N  C3M    H2     SING  N  N  42  
87N  C3M    H3     SING  N  N  43  
87N  N3Q    H4     SING  N  N  44  
87N  C3Q    H5     SING  N  N  45  
87N  C4Q    H6     SING  N  N  46  
87N  O4Q    H7     SING  N  N  47  
87N  C2Q    H8     SING  N  N  48  
87N  O2Q    H9     SING  N  N  49  
87N  C1Q    H10    SING  N  N  50  
87N  C5Q    H11    SING  N  N  51  
87N  C6Q    H12    SING  N  N  52  
87N  C6Q    H13    SING  N  N  53  
87N  C6Q    H14    SING  N  N  54  
87N  O1B    H15    SING  N  N  55  
87N  O1A    H16    SING  N  N  56  
87N  "C5'"  H17    SING  N  N  57  
87N  "C5'"  H18    SING  N  N  58  
87N  "C4'"  H19    SING  N  N  59  
87N  "C3'"  H20    SING  N  N  60  
87N  "O3'"  H21    SING  N  N  61  
87N  "C2'"  H22    SING  N  N  62  
87N  "C2'"  H23    SING  N  N  63  
87N  "C1'"  H24    SING  N  N  64  
87N  N3     H25    SING  N  N  65  
87N  C6     H26    SING  N  N  66  
87N  C5M    H27    SING  N  N  67  
87N  C5M    H28    SING  N  N  68  
87N  C5M    H29    SING  N  N  69  
#   #
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
87N  SMILES            ACDLabs               12.01  "CC1=CN(C(=O)NC1=O)C1CC(O)C(O1)COP(=O)(O)OP(=O)(O)OC1OC(C)C(O)C(NC(C)=O)C1O"  
87N  InChI             InChI                 1.03   "InChI=1S/C18H29N3O15P2/c1-7-5-21(18(27)20-16(7)26)12-4-10(23)11(34-12)6-32-37(28,29)36-38(30,31)35-17-15(25)13(19-9(3)22)14(24)8(2)33-17/h5,8,10-15,17,23-25H,4,6H2,1-3H3,(H,19,22)(H,28,29)(H,30,31)(H,20,26,27)/t8-,10+,11-,12-,13+,14-,15-,17-/m1/s1"  
87N  InChIKey          InChI                 1.03   CWQDRZJUANNJKC-NMSPNFBVSA-N  
87N  SMILES_CANONICAL  CACTVS                3.385  "C[C@H]1O[C@H](O[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H](C[C@@H]2O)N3C=C(C)C(=O)NC3=O)[C@H](O)[C@@H](NC(C)=O)[C@@H]1O"  
87N  SMILES            CACTVS                3.385  "C[CH]1O[CH](O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH](C[CH]2O)N3C=C(C)C(=O)NC3=O)[CH](O)[CH](NC(C)=O)[CH]1O"  
87N  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "C[C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)OP(=O)(O)OP(=O)(O)OC[C@@H]2[C@H](C[C@@H](O2)N3C=C(C(=O)NC3=O)C)O)O)NC(=O)C)O"  
87N  SMILES            "OpenEye OEToolkits"  2.0.7  "CC1C(C(C(C(O1)OP(=O)(O)OP(=O)(O)OCC2C(CC(O2)N3C=C(C(=O)NC3=O)C)O)O)NC(=O)C)O"  
#   #
loop_
_pdbx_chem_comp_identifier.comp_id
_pdbx_chem_comp_identifier.type
_pdbx_chem_comp_identifier.program
_pdbx_chem_comp_identifier.program_version
_pdbx_chem_comp_identifier.identifier
87N  "SYSTEMATIC NAME"  ACDLabs               12.01  "(2R,3R,4S,5S,6R)-4-acetamido-3,5-dihydroxy-6-methyloxan-2-yl [(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)oxolan-2-yl]methyl dihydrogen diphosphate (non-preferred name)"  
87N  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  2.0.7  "[(2~{R},3~{R},4~{S},5~{S},6~{R})-4-acetamido-6-methyl-3,5-bis(oxidanyl)oxan-2-yl] [[(2~{R},3~{S},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] 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
87N  "Create component"  2021-09-09  RCSB  
87N  "Initial release"   2021-09-22  RCSB  
##
