data_ZDA
#

_chem_comp.id                                   ZDA
_chem_comp.name                                 "2',5'-dideoxyadenosine 3'-(tetrahydrogen triphosphate)"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C10 H16 N5 O11 P3"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        "2',5'-DIDEOXYADENOSINE 3'-TRIPHOSPHATE"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2014-10-29
_chem_comp.pdbx_modified_date                   2020-06-17
_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                       475.182
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    ZDA
_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       4WP8
_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
ZDA  "C2'"  C1   C  0  1  N  N  N  56.928  -1.447  50.611   2.368  -0.820  -0.658  "C2'"  ZDA   1  
ZDA  "C5'"  C2   C  0  1  N  N  N  59.776  -2.575  52.656   1.766  -4.010   0.756  "C5'"  ZDA   2  
ZDA  "C4'"  C3   C  0  1  N  N  R  58.280  -2.067  52.434   1.744  -2.499   0.996  "C4'"  ZDA   3  
ZDA  "O4'"  O1   O  0  1  N  N  N  58.159  -0.767  52.529   3.078  -2.022   1.235  "O4'"  ZDA   4  
ZDA  "C1'"  C4   C  0  1  N  N  R  56.779  -0.590  51.912   3.160  -0.696   0.669  "C1'"  ZDA   5  
ZDA  N9     N1   N  0  1  Y  N  N  56.609   0.838  51.899   4.555  -0.333   0.404  N9     ZDA   6  
ZDA  C8     C5   C  0  1  Y  N  N  57.480   1.786  51.484   5.604  -1.196   0.288  C8     ZDA   7  
ZDA  N7     N2   N  0  1  Y  N  N  56.891   2.984  51.587   6.700  -0.533   0.053  N7     ZDA   8  
ZDA  C5     C6   C  0  1  Y  N  N  55.624   2.795  52.058   6.423   0.792   0.004  C5     ZDA   9  
ZDA  C6     C7   C  0  1  Y  N  N  54.527   3.623  52.354   7.186   1.953  -0.210  C6     ZDA  10  
ZDA  N6     N3   N  0  1  N  N  N  54.617   5.061  52.199   8.548   1.874  -0.438  N6     ZDA  11  
ZDA  N1     N4   N  0  1  Y  N  N  53.378   3.093  52.805   6.567   3.129  -0.190  N1     ZDA  12  
ZDA  C2     C8   C  0  1  Y  N  N  53.267   1.765  52.977   5.267   3.215   0.026  C2     ZDA  13  
ZDA  N3     N5   N  0  1  Y  N  N  54.278   0.942  52.704   4.514   2.155   0.231  N3     ZDA  14  
ZDA  C4     C9   C  0  1  Y  N  N  55.459   1.443  52.230   5.043   0.936   0.222  C4     ZDA  15  
ZDA  "C3'"  C10  C  0  1  N  N  S  57.747  -2.418  50.928   1.217  -1.777  -0.260  "C3'"  ZDA  16  
ZDA  "O3'"  O2   O  0  1  N  N  N  57.039  -3.650  50.934   0.035  -1.036   0.048  "O3'"  ZDA  17  
ZDA  PA     P1   P  0  1  N  N  N  57.231  -4.685  49.723  -1.359  -1.248  -0.729  PA     ZDA  18  
ZDA  O1A    O3   O  0  1  N  N  N  56.430  -4.244  48.528  -1.749  -2.674  -0.664  O1A    ZDA  19  
ZDA  O2A    O4   O  0  1  N  N  N  56.844  -6.067  50.246  -1.188  -0.809  -2.269  O2A    ZDA  20  
ZDA  O3A    O5   O  0  1  N  N  N  58.755  -4.589  49.357  -2.501  -0.347  -0.038  O3A    ZDA  21  
ZDA  PB     P2   P  0  1  N  N  N  59.481  -5.007  48.025  -4.111  -0.388  -0.038  PB     ZDA  22  
ZDA  O2B    O6   O  0  1  N  N  N  60.946  -4.733  48.208  -4.619  -1.505   1.005  O2B    ZDA  23  
ZDA  O1B    O7   O  0  1  N  N  N  58.929  -4.342  46.785  -4.596  -0.724  -1.395  O1B    ZDA  24  
ZDA  O3B    O8   O  0  1  N  N  N  59.227  -6.590  48.024  -4.684   1.052   0.396  O3B    ZDA  25  
ZDA  PG     P3   P  0  1  N  N  N  58.401  -7.478  46.964  -6.130   1.754   0.304  PG     ZDA  26  
ZDA  O2G    O9   O  0  1  N  N  N  58.003  -8.718  47.735  -7.061   1.226   1.507  O2G    ZDA  27  
ZDA  O3G    O10  O  0  1  N  N  N  57.161  -6.726  46.484  -5.960   3.351   0.419  O3G    ZDA  28  
ZDA  O1G    O11  O  0  1  N  N  N  59.326  -7.767  45.804  -6.760   1.417  -0.992  O1G    ZDA  29  
ZDA  H1     H1   H  0  1  N  N  N  57.348  -0.840  49.796   1.978   0.148  -0.970  H1     ZDA  30  
ZDA  H2     H2   H  0  1  N  N  N  55.953  -1.851  50.302   2.986  -1.260  -1.441  H2     ZDA  31  
ZDA  H3     H3   H  0  1  N  N  N  60.102  -2.323  53.676   2.151  -4.512   1.644  H3     ZDA  32  
ZDA  H4     H4   H  0  1  N  N  N  59.817  -3.665  52.517   0.755  -4.360   0.550  H4     ZDA  33  
ZDA  H5     H5   H  0  1  N  N  N  60.441  -2.087  51.928   2.408  -4.233  -0.095  H5     ZDA  34  
ZDA  H6     H6   H  0  1  N  N  N  57.632  -2.597  53.147   1.109  -2.269   1.852  H6     ZDA  35  
ZDA  H7     H7   H  0  1  N  N  N  56.027  -1.061  52.562   2.691   0.033   1.329  H7     ZDA  36  
ZDA  H8     H8   H  0  1  N  N  N  58.484   1.606  51.129   5.537  -2.270   0.378  H8     ZDA  37  
ZDA  H9     H9   H  0  1  N  N  N  53.750   5.481  52.469   8.988   1.010  -0.451  H9     ZDA  38  
ZDA  H10    H10  H  0  1  N  N  N  55.352   5.413  52.778   9.064   2.683  -0.584  H10    ZDA  39  
ZDA  H11    H11  H  0  1  N  N  N  52.338   1.356  53.345   4.804   4.191   0.035  H11    ZDA  40  
ZDA  H12    H12  H  0  1  N  N  N  58.621  -2.472  50.262   1.022  -2.492  -1.059  H12    ZDA  41  
ZDA  H13    H13  H  0  1  N  N  N  56.143  -6.423  49.712  -0.932   0.116  -2.388  H13    ZDA  42  
ZDA  H14    H14  H  0  1  N  N  N  61.257  -4.184  47.498  -4.337  -1.349   1.916  H14    ZDA  43  
ZDA  H15    H15  H  0  1  N  N  N  58.415  -9.480  47.345  -6.709   1.412   2.388  H15    ZDA  44  
ZDA  H16    H16  H  0  1  N  N  N  57.217  -6.588  45.546  -6.793   3.840   0.371  H16    ZDA  45  
#   #
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
ZDA  O1G    PG     DOUB  N  N   1  
ZDA  O3G    PG     SING  N  N   2  
ZDA  O1B    PB     DOUB  N  N   3  
ZDA  PG     O2G    SING  N  N   4  
ZDA  PG     O3B    SING  N  N   5  
ZDA  O3B    PB     SING  N  N   6  
ZDA  PB     O2B    SING  N  N   7  
ZDA  PB     O3A    SING  N  N   8  
ZDA  O1A    PA     DOUB  N  N   9  
ZDA  O3A    PA     SING  N  N  10  
ZDA  PA     O2A    SING  N  N  11  
ZDA  PA     "O3'"  SING  N  N  12  
ZDA  "C2'"  "C3'"  SING  N  N  13  
ZDA  "C2'"  "C1'"  SING  N  N  14  
ZDA  "C3'"  "O3'"  SING  N  N  15  
ZDA  "C3'"  "C4'"  SING  N  N  16  
ZDA  C8     N7     DOUB  Y  N  17  
ZDA  C8     N9     SING  Y  N  18  
ZDA  N7     C5     SING  Y  N  19  
ZDA  N9     "C1'"  SING  N  N  20  
ZDA  N9     C4     SING  Y  N  21  
ZDA  "C1'"  "O4'"  SING  N  N  22  
ZDA  C5     C4     DOUB  Y  N  23  
ZDA  C5     C6     SING  Y  N  24  
ZDA  N6     C6     SING  N  N  25  
ZDA  C4     N3     SING  Y  N  26  
ZDA  C6     N1     DOUB  Y  N  27  
ZDA  "C4'"  "O4'"  SING  N  N  28  
ZDA  "C4'"  "C5'"  SING  N  N  29  
ZDA  N3     C2     DOUB  Y  N  30  
ZDA  N1     C2     SING  Y  N  31  
ZDA  "C2'"  H1     SING  N  N  32  
ZDA  "C2'"  H2     SING  N  N  33  
ZDA  "C5'"  H3     SING  N  N  34  
ZDA  "C5'"  H4     SING  N  N  35  
ZDA  "C5'"  H5     SING  N  N  36  
ZDA  "C4'"  H6     SING  N  N  37  
ZDA  "C1'"  H7     SING  N  N  38  
ZDA  C8     H8     SING  N  N  39  
ZDA  N6     H9     SING  N  N  40  
ZDA  N6     H10    SING  N  N  41  
ZDA  C2     H11    SING  N  N  42  
ZDA  "C3'"  H12    SING  N  N  43  
ZDA  O2A    H13    SING  N  N  44  
ZDA  O2B    H14    SING  N  N  45  
ZDA  O2G    H15    SING  N  N  46  
ZDA  O3G    H16    SING  N  N  47  
#   #
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
ZDA  SMILES            ACDLabs               12.01  "O=P(O)(O)OP(=O)(O)OP(=O)(O)OC3C(OC(n2cnc1c(ncnc12)N)C3)C"  
ZDA  InChI             InChI                 1.03   "InChI=1S/C10H16N5O11P3/c1-5-6(24-28(19,20)26-29(21,22)25-27(16,17)18)2-7(23-5)15-4-14-8-9(11)12-3-13-10(8)15/h3-7H,2H2,1H3,(H,19,20)(H,21,22)(H2,11,12,13)(H2,16,17,18)/t5-,6+,7-/m1/s1"  
ZDA  InChIKey          InChI                 1.03   ZJGUOEYCABTFNH-DSYKOEDSSA-N  
ZDA  SMILES_CANONICAL  CACTVS                3.385  "C[C@H]1O[C@H](C[C@@H]1O[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)n2cnc3c(N)ncnc23"  
ZDA  SMILES            CACTVS                3.385  "C[CH]1O[CH](C[CH]1O[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)n2cnc3c(N)ncnc23"  
ZDA  SMILES_CANONICAL  "OpenEye OEToolkits"  1.9.2  "C[C@@H]1[C@H](C[C@@H](O1)n2cnc3c2ncnc3N)OP(=O)(O)OP(=O)(O)OP(=O)(O)O"  
ZDA  SMILES            "OpenEye OEToolkits"  1.9.2  "CC1C(CC(O1)n2cnc3c2ncnc3N)OP(=O)(O)OP(=O)(O)OP(=O)(O)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
ZDA  "SYSTEMATIC NAME"  ACDLabs               12.01  "2',5'-dideoxyadenosine 3'-(tetrahydrogen triphosphate)"  
ZDA  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.9.2  "[(2R,3S,5R)-5-(6-aminopurin-9-yl)-2-methyl-oxolan-3-yl] [oxidanyl(phosphonooxy)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
ZDA  "Create component"  2014-10-29  PDBJ  
ZDA  "Initial release"   2015-09-02  RCSB  
ZDA  "Modify synonyms"   2020-06-05  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     ZDA
_pdbx_chem_comp_synonyms.name        "2',5'-DIDEOXYADENOSINE 3'-TRIPHOSPHATE"
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
