data_6U4
#

_chem_comp.id                                   6U4
_chem_comp.name                                 "[[(2R,3S,5R)-5-(6-azanyl-2-oxidanylidene-1H-purin-9-yl)-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C10 H16 N5 O13 P3"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        2-oxo-dATP
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2016-06-24
_chem_comp.pdbx_modified_date                   2021-03-01
_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                       507.181
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    6U4
_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       5GHJ
_chem_comp.pdbx_subcomponent_list               ?
_chem_comp.pdbx_processing_site                 PDBJ
#   #
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
6U4  PG     P1   P  0  1  N  N  N  -7.076   -2.247   -9.336   6.411   1.972   0.679  PG     6U4   1  
6U4  O3G    O1   O  0  1  N  N  N  -6.633   -0.808   -9.347   6.164   2.936   1.945  O3G    6U4   2  
6U4  O2G    O2   O  0  1  N  N  N  -7.066   -2.929   -7.982   7.027   2.830  -0.537  O2G    6U4   3  
6U4  O1G    O3   O  0  1  N  N  N  -8.336   -2.479  -10.154   7.357   0.898   1.054  O1G    6U4   4  
6U4  PB     P2   P  0  1  N  N  N  -5.041   -4.313   -9.905   4.613   0.026  -0.651  PB     6U4   5  
6U4  O1B    O4   O  0  1  N  N  N  -5.923   -5.483   -9.601   5.434  -1.128  -0.224  O1B    6U4   6  
6U4  O2B    O5   O  0  1  N  N  N  -3.916   -3.976   -8.964   4.880   0.327  -2.210  O2B    6U4   7  
6U4  O3B    O6   O  0  1  N  N  N  -5.931   -2.982  -10.210   5.012   1.320   0.221  O3B    6U4   8  
6U4  PA     P3   P  0  1  N  N  N  -5.068   -4.841  -12.797   2.153  -1.627  -0.647  PA     6U4   9  
6U4  O2A    O7   O  0  1  N  N  N  -6.096   -5.918  -12.705   1.880  -1.836  -2.220  O2A    6U4  10  
6U4  O1A    O8   O  0  1  N  N  N  -5.411   -3.521  -13.431   2.865  -2.808  -0.109  O1A    6U4  11  
6U4  O3A    O9   O  0  1  N  N  N  -4.394   -4.536  -11.365   3.055  -0.311  -0.428  O3A    6U4  12  
6U4  "O5'"  O10  O  0  1  N  N  N  -3.760   -5.402  -13.509   0.750  -1.450   0.122  "O5'"  6U4  13  
6U4  "C5'"  C1   C  0  1  N  N  N  -3.798   -5.855  -14.870  -0.228  -2.489   0.206  "C5'"  6U4  14  
6U4  "C4'"  C2   C  0  1  N  N  R  -3.264   -7.269  -14.882  -1.435  -1.990   1.003  "C4'"  6U4  15  
6U4  "O4'"  O11  O  0  1  N  N  N  -3.539   -7.814  -16.170  -2.156  -0.990   0.249  "O4'"  6U4  16  
6U4  "C3'"  C3   C  0  1  N  N  S  -1.762   -7.312  -14.709  -2.451  -3.134   1.214  "C3'"  6U4  17  
6U4  "O3'"  O12  O  0  1  N  N  N  -1.399   -8.571  -14.133  -2.291  -3.712   2.511  "O3'"  6U4  18  
6U4  "C2'"  C4   C  0  1  N  N  N  -1.272   -7.276  -16.150  -3.827  -2.441   1.095  "C2'"  6U4  19  
6U4  "C1'"  C5   C  0  1  N  N  R  -2.351   -8.100  -16.871  -3.480  -0.960   0.827  "C1'"  6U4  20  
6U4  N9     N1   N  0  1  N  N  N  -2.459   -7.681  -18.288  -4.435  -0.376  -0.118  N9     6U4  21  
6U4  C8     C6   C  0  1  N  N  N  -2.930   -6.502  -18.730  -4.644  -0.776  -1.407  C8     6U4  22  
6U4  N7     N2   N  0  1  N  N  N  -2.831   -6.462  -20.084  -5.562  -0.041  -1.959  N7     6U4  23  
6U4  C5     C7   C  0  1  N  N  N  -2.301   -7.652  -20.461  -6.002   0.879  -1.062  C5     6U4  24  
6U4  C6     C8   C  0  1  N  N  N  -1.952   -8.185  -21.696  -6.953   1.902  -1.099  C6     6U4  25  
6U4  N6     N3   N  0  1  N  N  N  -2.137   -7.483  -22.841  -7.679   2.141  -2.234  N6     6U4  26  
6U4  N1     N4   N  0  1  N  N  N  -1.381   -9.402  -21.706  -7.141   2.655   0.023  N1     6U4  27  
6U4  C2     C9   C  0  1  N  N  N  -1.208  -10.141  -20.578  -6.424   2.413   1.134  C2     6U4  28  
6U4  N3     N5   N  0  1  N  N  N  -1.545   -9.655  -19.361  -5.517   1.446   1.186  N3     6U4  29  
6U4  C4     C10  C  0  1  N  N  N  -2.067   -8.409  -19.321  -5.285   0.668   0.133  C4     6U4  30  
6U4  O2     O13  O  0  1  N  N  N  -0.750  -11.289  -20.668  -6.613   3.103   2.124  O2     6U4  31  
6U4  H1     H1   H  0  1  N  N  N  -7.234   -0.295   -9.874   6.966   3.364   2.275  H1     6U4  32  
6U4  H2     H2   H  0  1  N  N  N  -7.878   -3.407   -7.862   6.459   3.553  -0.835  H2     6U4  33  
6U4  H3     H3   H  0  1  N  N  N  -3.909   -4.595   -8.244   4.373   1.073  -2.559  H3     6U4  34  
6U4  H4     H4   H  0  1  N  N  N  -6.909   -5.614  -13.090   1.416  -1.099  -2.640  H4     6U4  35  
6U4  H5     H5   H  0  1  N  N  N  -3.170   -5.209  -15.501  -0.546  -2.770  -0.798  H5     6U4  36  
6U4  H6     H6   H  0  1  N  N  N  -4.832   -5.839  -15.244   0.204  -3.355   0.706  H6     6U4  37  
6U4  H7     H7   H  0  1  N  N  N  -3.749   -7.859  -14.090  -1.114  -1.585   1.963  H7     6U4  38  
6U4  H8     H8   H  0  1  N  N  N  -1.392   -6.451  -14.133  -2.336  -3.894   0.441  H8     6U4  39  
6U4  H9     H9   H  0  1  N  N  N  -1.700   -8.606  -13.232  -2.905  -4.437   2.697  H9     6U4  40  
6U4  H10    H10  H  0  1  N  N  N  -0.280   -7.742  -16.247  -4.394  -2.858   0.263  H10    6U4  41  
6U4  H11    H11  H  0  1  N  N  N  -1.232   -6.246  -16.534  -4.386  -2.542   2.025  H11    6U4  42  
6U4  H12    H12  H  0  1  N  N  N  -2.098   -9.169  -16.809  -3.474  -0.397   1.760  H12    6U4  43  
6U4  H13    H13  H  0  1  N  N  N  -3.324   -5.712  -18.108  -4.122  -1.586  -1.896  H13    6U4  44  
6U4  H14    H14  H  0  1  N  N  N  -2.573   -6.608  -22.630  -7.536   1.599  -3.024  H14    6U4  45  
6U4  H15    H15  H  0  1  N  N  N  -1.252   -7.318  -23.277  -8.336   2.855  -2.247  H15    6U4  46  
6U4  H16    H16  H  0  1  N  N  N  -1.071   -9.779  -22.579  -7.797   3.370   0.019  H16    6U4  47  
#   #
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
6U4  N6     C6     SING  N  N   1  
6U4  N1     C6     SING  N  N   2  
6U4  N1     C2     SING  N  N   3  
6U4  C6     C5     DOUB  N  N   4  
6U4  O2     C2     DOUB  N  N   5  
6U4  C2     N3     SING  N  N   6  
6U4  C5     N7     SING  N  N   7  
6U4  C5     C4     SING  N  N   8  
6U4  N7     C8     DOUB  N  N   9  
6U4  N3     C4     DOUB  N  N  10  
6U4  C4     N9     SING  N  N  11  
6U4  C8     N9     SING  N  N  12  
6U4  N9     "C1'"  SING  N  N  13  
6U4  "C1'"  "O4'"  SING  N  N  14  
6U4  "C1'"  "C2'"  SING  N  N  15  
6U4  "O4'"  "C4'"  SING  N  N  16  
6U4  "C2'"  "C3'"  SING  N  N  17  
6U4  "C4'"  "C5'"  SING  N  N  18  
6U4  "C4'"  "C3'"  SING  N  N  19  
6U4  "C5'"  "O5'"  SING  N  N  20  
6U4  "C3'"  "O3'"  SING  N  N  21  
6U4  "O5'"  PA     SING  N  N  22  
6U4  O1A    PA     DOUB  N  N  23  
6U4  PA     O2A    SING  N  N  24  
6U4  PA     O3A    SING  N  N  25  
6U4  O3A    PB     SING  N  N  26  
6U4  O3B    PB     SING  N  N  27  
6U4  O3B    PG     SING  N  N  28  
6U4  O1G    PG     DOUB  N  N  29  
6U4  PB     O1B    DOUB  N  N  30  
6U4  PB     O2B    SING  N  N  31  
6U4  O3G    PG     SING  N  N  32  
6U4  PG     O2G    SING  N  N  33  
6U4  O3G    H1     SING  N  N  34  
6U4  O2G    H2     SING  N  N  35  
6U4  O2B    H3     SING  N  N  36  
6U4  O2A    H4     SING  N  N  37  
6U4  "C5'"  H5     SING  N  N  38  
6U4  "C5'"  H6     SING  N  N  39  
6U4  "C4'"  H7     SING  N  N  40  
6U4  "C3'"  H8     SING  N  N  41  
6U4  "O3'"  H9     SING  N  N  42  
6U4  "C2'"  H10    SING  N  N  43  
6U4  "C2'"  H11    SING  N  N  44  
6U4  "C1'"  H12    SING  N  N  45  
6U4  C8     H13    SING  N  N  46  
6U4  N6     H14    SING  N  N  47  
6U4  N6     H15    SING  N  N  48  
6U4  N1     H16    SING  N  N  49  
#   #
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
6U4  InChI             InChI                 1.03   "InChI=1S/C10H16N5O13P3/c11-8-7-9(14-10(17)13-8)15(3-12-7)6-1-4(16)5(26-6)2-25-30(21,22)28-31(23,24)27-29(18,19)20/h3-6,16H,1-2H2,(H,21,22)(H,23,24)(H2,18,19,20)(H3,11,13,14,17)/t4-,5+,6+/m0/s1"  
6U4  InChIKey          InChI                 1.03   UOACBPRDWRDEHJ-KVQBGUIXSA-N  
6U4  SMILES_CANONICAL  CACTVS                3.385  "NC1=C2N=CN([C@H]3C[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O3)C2=NC(=O)N1"  
6U4  SMILES            CACTVS                3.385  "NC1=C2N=CN([CH]3C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O3)C2=NC(=O)N1"  
6U4  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.5  "C1[C@@H]([C@H](O[C@H]1N2C=NC3=C(NC(=O)N=C32)N)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O"  
6U4  SMILES            "OpenEye OEToolkits"  2.0.5  "C1C(C(OC1N2C=NC3=C(NC(=O)N=C32)N)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O"  
#
_pdbx_chem_comp_identifier.comp_id          6U4
_pdbx_chem_comp_identifier.type             "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program          "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version  2.0.5
_pdbx_chem_comp_identifier.identifier       "[[(2~{R},3~{S},5~{R})-5-(6-azanyl-2-oxidanylidene-1~{H}-purin-9-yl)-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono 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
6U4  "Create component"    2016-06-24  PDBJ  
6U4  "Other modification"  2016-06-24  PDBJ  
6U4  "Initial release"     2017-01-04  RCSB  
6U4  "Other modification"  2019-09-06  PDBJ  
6U4  "Other modification"  2019-09-17  PDBJ  
6U4  "Modify synonyms"     2021-03-01  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     6U4
_pdbx_chem_comp_synonyms.name        2-oxo-dATP
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
