data_87Z
#

_chem_comp.id                                   87Z
_chem_comp.name                                 "[(2~{R},3~{R},4~{S},5~{R},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                    87Z
_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       7S42
_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
87Z  C2     C1   C  0  1  N  N  N  23.115  -10.486  25.668   5.975   0.605   0.812  C2     87Z   1  
87Z  O3     O1   O  0  1  N  N  N  29.604  -15.032  33.010  -4.400   2.443  -2.718  O3     87Z   2  
87Z  C3     C2   C  0  1  N  N  N  30.631  -14.467  32.858  -5.344   3.060  -2.271  C3     87Z   3  
87Z  C3M    C3   C  0  1  N  N  N  31.630  -14.978  31.821  -6.024   4.109  -3.111  C3M    87Z   4  
87Z  N3Q    N1   N  0  1  N  N  N  30.999  -13.387  33.543  -5.783   2.806  -1.022  N3Q    87Z   5  
87Z  C3Q    C4   C  0  1  N  N  S  30.015  -12.526  34.185  -5.122   1.786  -0.206  C3Q    87Z   6  
87Z  C4Q    C5   C  0  1  N  N  R  30.318  -12.226  35.658  -5.343   2.094   1.278  C4Q    87Z   7  
87Z  O4Q    O2   O  0  1  N  N  N  31.601  -11.588  35.814  -6.745   2.165   1.547  O4Q    87Z   8  
87Z  C2Q    C6   C  0  1  N  N  R  29.896  -11.192  33.424  -5.715   0.410  -0.524  C2Q    87Z   9  
87Z  O2Q    O3   O  0  1  N  N  N  29.528  -11.450  32.071  -5.451   0.080  -1.889  O2Q    87Z  10  
87Z  C1Q    C7   C  0  1  N  N  R  28.885  -10.335  34.092  -5.074  -0.638   0.389  C1Q    87Z  11  
87Z  O5Q    O4   O  0  1  N  N  N  29.073  -10.126  35.478  -5.291  -0.274   1.754  O5Q    87Z  12  
87Z  C5Q    C8   C  0  1  N  N  R  29.202  -11.368  36.223  -4.716   0.981   2.122  C5Q    87Z  13  
87Z  C6Q    C9   C  0  1  N  N  N  29.426  -10.963  37.682  -4.985   1.251   3.604  C6Q    87Z  14  
87Z  O3B    O5   O  0  1  N  N  N  27.620  -10.961  33.837  -3.670  -0.701   0.130  O3B    87Z  15  
87Z  PB     P1   P  0  1  N  N  N  26.214  -10.150  33.666  -2.803  -2.044   0.317  PB     87Z  16  
87Z  O1B    O6   O  0  1  N  N  N  25.633   -9.666  35.004  -3.298  -3.154  -0.739  O1B    87Z  17  
87Z  O2B    O7   O  0  1  N  N  N  25.339  -11.034  32.782  -2.982  -2.559   1.694  O2B    87Z  18  
87Z  O3A    O8   O  0  1  N  N  N  26.782   -8.915  32.734  -1.247  -1.719   0.064  O3A    87Z  19  
87Z  PA     P2   P  0  1  N  N  N  26.089   -7.495  32.372   0.125  -2.500   0.379  PA     87Z  20  
87Z  O1A    O9   O  0  1  N  N  N  24.991   -7.114  33.359   0.453  -2.395   1.952  O1A    87Z  21  
87Z  O2A    O10  O  0  1  N  N  N  27.267   -6.541  32.207  -0.019  -3.923  -0.001  O2A    87Z  22  
87Z  "O5'"  O11  O  0  1  N  N  N  25.346   -7.764  30.955   1.326  -1.838  -0.464  "O5'"  87Z  23  
87Z  "C5'"  C10  C  0  1  N  N  N  26.092   -8.134  29.764   2.651  -2.371  -0.482  "C5'"  87Z  24  
87Z  "C4'"  C11  C  0  1  N  N  R  25.589   -9.551  29.492   3.538  -1.505  -1.378  "C4'"  87Z  25  
87Z  "O4'"  O12  O  0  1  N  N  N  24.271   -9.472  28.962   3.750  -0.207  -0.781  "O4'"  87Z  26  
87Z  "C3'"  C12  C  0  1  N  N  S  26.342  -10.177  28.368   4.966  -2.100  -1.472  "C3'"  87Z  27  
87Z  "O3'"  O13  O  0  1  N  N  N  27.491  -10.910  28.822   5.043  -3.079  -2.511  "O3'"  87Z  28  
87Z  "C2'"  C13  C  0  1  N  N  N  25.346  -11.196  27.817   5.815  -0.854  -1.823  "C2'"  87Z  29  
87Z  "C1'"  C14  C  0  1  N  N  R  24.014  -10.447  27.966   4.942   0.338  -1.372  "C1'"  87Z  30  
87Z  N1     N2   N  0  1  N  N  N  23.684   -9.743  26.699   5.666   1.140  -0.384  N1     87Z  31  
87Z  O2     O14  O  0  1  N  N  N  22.921  -11.641  25.841   5.649  -0.540   1.058  O2     87Z  32  
87Z  N3     N3   N  0  1  N  N  N  22.931   -9.918  24.485   6.645   1.318   1.736  N3     87Z  33  
87Z  C6     C15  C  0  1  N  N  N  24.021   -8.418  26.491   6.022   2.427  -0.684  C6     87Z  34  
87Z  C5     C16  C  0  1  N  N  N  23.733   -7.826  25.270   6.690   3.166   0.227  C5     87Z  35  
87Z  C5M    C17  C  0  1  N  N  N  24.070   -6.302  25.061   7.090   4.585  -0.086  C5M    87Z  36  
87Z  C4     C18  C  0  1  N  N  N  23.210   -8.627  24.254   7.014   2.589   1.479  C4     87Z  37  
87Z  O4     O15  O  0  1  N  N  N  22.978   -8.163  23.137   7.620   3.235   2.315  O4     87Z  38  
87Z  H1     H1   H  0  1  N  N  N  31.220  -15.869  31.324  -5.533   4.172  -4.082  H1     87Z  39  
87Z  H2     H2   H  0  1  N  N  N  31.815  -14.193  31.073  -7.071   3.841  -3.250  H2     87Z  40  
87Z  H3     H3   H  0  1  N  N  N  32.575  -15.239  32.320  -5.960   5.075  -2.609  H3     87Z  41  
87Z  H4     H4   H  0  1  N  N  N  31.970  -13.162  33.618  -6.538   3.300  -0.664  H4     87Z  42  
87Z  H5     H5   H  0  1  N  N  N  29.034  -13.021  34.141  -4.053   1.782  -0.421  H5     87Z  43  
87Z  H6     H6   H  0  1  N  N  N  30.323  -13.181  36.203  -4.876   3.048   1.526  H6     87Z  44  
87Z  H7     H7   H  0  1  N  N  N  31.760  -11.415  36.735  -6.959   2.358   2.470  H7     87Z  45  
87Z  H8     H8   H  0  1  N  N  N  30.873  -10.687  33.456  -6.792   0.431  -0.356  H8     87Z  46  
87Z  H9     H9   H  0  1  N  N  N  30.187  -11.999  31.662  -5.795  -0.782  -2.159  H9     87Z  47  
87Z  H10    H10  H  0  1  N  N  N  28.893   -9.357  33.588  -5.523  -1.612   0.197  H10    87Z  48  
87Z  H11    H11  H  0  1  N  N  N  28.260  -11.932  36.160  -3.641   0.955   1.947  H11    87Z  49  
87Z  H12    H12  H  0  1  N  N  N  29.532  -11.866  38.302  -6.061   1.277   3.779  H12    87Z  50  
87Z  H13    H13  H  0  1  N  N  N  30.341  -10.357  37.758  -4.539   0.458   4.204  H13    87Z  51  
87Z  H14    H14  H  0  1  N  N  N  28.566  -10.375  38.035  -4.548   2.209   3.884  H14    87Z  52  
87Z  H15    H15  H  0  1  N  N  N  24.751  -10.004  35.107  -3.210  -2.884  -1.663  H15    87Z  53  
87Z  H16    H16  H  0  1  N  N  N  25.203   -6.281  33.763   0.560  -1.489   2.272  H16    87Z  54  
87Z  H17    H17  H  0  1  N  N  N  27.175   -8.125  29.954   3.054  -2.378   0.531  H17    87Z  55  
87Z  H18    H18  H  0  1  N  N  N  25.862   -7.461  28.925   2.628  -3.390  -0.869  H18    87Z  56  
87Z  H19    H19  H  0  1  N  N  N  25.640  -10.167  30.402   3.098  -1.404  -2.370  H19    87Z  57  
87Z  H20    H20  H  0  1  N  N  N  26.603   -9.434  27.600   5.275  -2.525  -0.517  H20    87Z  58  
87Z  H21    H21  H  0  1  N  N  N  28.134  -10.306  29.173   5.917  -3.480  -2.609  H21    87Z  59  
87Z  H22    H22  H  0  1  N  N  N  25.353  -12.123  28.409   6.756  -0.866  -1.275  H22    87Z  60  
87Z  H23    H23  H  0  1  N  N  N  25.557  -11.433  26.764   5.998  -0.807  -2.897  H23    87Z  61  
87Z  H24    H24  H  0  1  N  N  N  23.212  -11.141  28.257   4.681   0.953  -2.233  H24    87Z  62  
87Z  H25    H25  H  0  1  N  N  N  22.570  -10.473  23.736   6.863   0.916   2.592  H25    87Z  63  
87Z  H26    H26  H  0  1  N  N  N  24.504   -7.849  27.272   5.771   2.848  -1.646  H26    87Z  64  
87Z  H27    H27  H  0  1  N  N  N  24.468   -5.882  25.997   6.293   5.263   0.220  H27    87Z  65  
87Z  H28    H28  H  0  1  N  N  N  24.821   -6.199  24.264   8.004   4.832   0.453  H28    87Z  66  
87Z  H29    H29  H  0  1  N  N  N  23.156   -5.760  24.776   7.261   4.686  -1.158  H29    87Z  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
87Z  O4     C4     DOUB  N  N   1  
87Z  C4     N3     SING  N  N   2  
87Z  C4     C5     SING  N  N   3  
87Z  N3     C2     SING  N  N   4  
87Z  C5M    C5     SING  N  N   5  
87Z  C5     C6     DOUB  N  N   6  
87Z  C2     O2     DOUB  N  N   7  
87Z  C2     N1     SING  N  N   8  
87Z  C6     N1     SING  N  N   9  
87Z  N1     "C1'"  SING  N  N  10  
87Z  "C2'"  "C1'"  SING  N  N  11  
87Z  "C2'"  "C3'"  SING  N  N  12  
87Z  "C1'"  "O4'"  SING  N  N  13  
87Z  "C3'"  "O3'"  SING  N  N  14  
87Z  "C3'"  "C4'"  SING  N  N  15  
87Z  "O4'"  "C4'"  SING  N  N  16  
87Z  "C4'"  "C5'"  SING  N  N  17  
87Z  "C5'"  "O5'"  SING  N  N  18  
87Z  "O5'"  PA     SING  N  N  19  
87Z  C3M    C3     SING  N  N  20  
87Z  O2Q    C2Q    SING  N  N  21  
87Z  O2A    PA     DOUB  N  N  22  
87Z  PA     O3A    SING  N  N  23  
87Z  PA     O1A    SING  N  N  24  
87Z  O3A    PB     SING  N  N  25  
87Z  O2B    PB     DOUB  N  N  26  
87Z  C3     O3     DOUB  N  N  27  
87Z  C3     N3Q    SING  N  N  28  
87Z  C2Q    C1Q    SING  N  N  29  
87Z  C2Q    C3Q    SING  N  N  30  
87Z  N3Q    C3Q    SING  N  N  31  
87Z  PB     O3B    SING  N  N  32  
87Z  PB     O1B    SING  N  N  33  
87Z  O3B    C1Q    SING  N  N  34  
87Z  C1Q    O5Q    SING  N  N  35  
87Z  C3Q    C4Q    SING  N  N  36  
87Z  O5Q    C5Q    SING  N  N  37  
87Z  C4Q    O4Q    SING  N  N  38  
87Z  C4Q    C5Q    SING  N  N  39  
87Z  C5Q    C6Q    SING  N  N  40  
87Z  C3M    H1     SING  N  N  41  
87Z  C3M    H2     SING  N  N  42  
87Z  C3M    H3     SING  N  N  43  
87Z  N3Q    H4     SING  N  N  44  
87Z  C3Q    H5     SING  N  N  45  
87Z  C4Q    H6     SING  N  N  46  
87Z  O4Q    H7     SING  N  N  47  
87Z  C2Q    H8     SING  N  N  48  
87Z  O2Q    H9     SING  N  N  49  
87Z  C1Q    H10    SING  N  N  50  
87Z  C5Q    H11    SING  N  N  51  
87Z  C6Q    H12    SING  N  N  52  
87Z  C6Q    H13    SING  N  N  53  
87Z  C6Q    H14    SING  N  N  54  
87Z  O1B    H15    SING  N  N  55  
87Z  O1A    H16    SING  N  N  56  
87Z  "C5'"  H17    SING  N  N  57  
87Z  "C5'"  H18    SING  N  N  58  
87Z  "C4'"  H19    SING  N  N  59  
87Z  "C3'"  H20    SING  N  N  60  
87Z  "O3'"  H21    SING  N  N  61  
87Z  "C2'"  H22    SING  N  N  62  
87Z  "C2'"  H23    SING  N  N  63  
87Z  "C1'"  H24    SING  N  N  64  
87Z  N3     H25    SING  N  N  65  
87Z  C6     H26    SING  N  N  66  
87Z  C5M    H27    SING  N  N  67  
87Z  C5M    H28    SING  N  N  68  
87Z  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
87Z  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"  
87Z  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"  
87Z  InChIKey          InChI                 1.03   CWQDRZJUANNJKC-HYPDDMKDSA-N  
87Z  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"  
87Z  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"  
87Z  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"  
87Z  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
87Z  "SYSTEMATIC NAME"  ACDLabs               12.01  "(2R,3R,4S,5R,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)"  
87Z  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  2.0.7  "[(2~{R},3~{R},4~{S},5~{R},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
87Z  "Create component"  2021-09-09  RCSB  
87Z  "Initial release"   2021-09-22  RCSB  
##
