data_YO7
#

_chem_comp.id                                   YO7
_chem_comp.name                                 "[(2R,3S,4R,5R)-5-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl (2R,3S,4R,5R,6S)-6-[(1R)-1,2-dihydroxyethyl]-3,4,5-trihydroxyoxan-2-yl dihydrogen diphosphate (non-preferred name)"
_chem_comp.type                                 non-polymer
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C17 H27 N5 O17 P2"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2021-03-16
_chem_comp.pdbx_modified_date                   2021-03-19
_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                       635.367
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    YO7
_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       7M15
_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
YO7  O3B    O1   O  0  1  N  N  N  11.481  -27.205  25.254   2.905  -0.049   1.880  O3B    YO7   1  
YO7  PB     P1   P  0  1  N  N  N  11.405  -26.389  23.954   3.061   1.165   0.835  PB     YO7   2  
YO7  O2B    O2   O  0  1  N  N  N  12.478  -25.290  23.760   3.742   2.301   1.496  O2B    YO7   3  
YO7  O1B    O3   O  0  1  N  N  N  11.283  -27.373  22.693   3.933   0.678  -0.428  O1B    YO7   4  
YO7  C11    C1   C  0  1  N  N  R  11.896  -27.220  21.397   5.308   0.300  -0.325  C11    YO7   5  
YO7  C21    C2   C  0  1  N  N  S  10.975  -27.747  20.302   6.022   0.610  -1.643  C21    YO7   6  
YO7  O21    O4   O  0  1  N  N  N   9.863  -26.858  20.151   5.982   2.017  -1.890  O21    YO7   7  
YO7  C31    C3   C  0  1  N  N  R  11.712  -27.910  18.953   7.479   0.148  -1.546  C31    YO7   8  
YO7  O31    O5   O  0  1  N  N  N  10.841  -28.483  17.956   8.134   0.366  -2.797  O31    YO7   9  
YO7  C41    C4   C  0  1  N  N  R  12.978  -28.760  19.161   7.508  -1.346  -1.206  C41    YO7  10  
YO7  O41    O6   O  0  1  N  N  N  13.781  -28.969  17.987   8.862  -1.772  -1.041  O41    YO7  11  
YO7  C51    C5   C  0  1  N  N  S  13.880  -28.160  20.272   6.736  -1.580   0.095  C51    YO7  12  
YO7  C61    C6   C  0  1  N  N  R  15.132  -29.014  20.637   6.709  -3.076   0.411  C61    YO7  13  
YO7  C71    C7   C  0  1  N  N  N  16.185  -28.257  21.463   5.834  -3.323   1.641  C71    YO7  14  
YO7  O71    O7   O  0  1  N  N  N  16.845  -27.411  20.515   5.902  -4.703   2.005  O71    YO7  15  
YO7  O6A    O8   O  0  1  N  N  N  14.743  -30.134  21.423   6.173  -3.789  -0.706  O6A    YO7  16  
YO7  O51    O9   O  0  1  N  N  N  13.075  -28.016  21.432   5.399  -1.100  -0.053  O51    YO7  17  
YO7  O3A    O10  O  0  1  N  N  N  10.021  -25.580  23.792   1.604   1.631   0.332  O3A    YO7  18  
YO7  PA     P2   P  0  1  N  N  N   8.531  -26.208  23.582   0.450   2.562   0.960  PA     YO7  19  
YO7  O1A    O11  O  0  1  N  N  N   8.205  -26.630  22.173   0.336   2.296   2.411  O1A    YO7  20  
YO7  O2A    O12  O  0  1  N  N  N   8.312  -27.291  24.645   0.824   4.111   0.726  O2A    YO7  21  
YO7  "O5'"  O13  O  0  1  N  N  N   7.606  -24.909  23.900  -0.953   2.235   0.241  "O5'"  YO7  22  
YO7  "C5'"  C8   C  0  1  N  N  N   7.599  -24.393  25.246  -2.191   2.822   0.648  "C5'"  YO7  23  
YO7  "C4'"  C9   C  0  1  N  N  R   6.471  -23.366  25.331  -3.320   2.297  -0.241  "C4'"  YO7  24  
YO7  "C3'"  C10  C  0  1  N  N  S   5.145  -23.936  24.855  -4.655   2.983   0.124  "C3'"  YO7  25  
YO7  "O3'"  O14  O  0  1  N  N  N   4.150  -23.445  25.747  -4.931   4.055  -0.780  "O3'"  YO7  26  
YO7  "C2'"  C11  C  0  1  N  N  R   4.919  -23.338  23.473  -5.708   1.862  -0.028  "C2'"  YO7  27  
YO7  "O2'"  O15  O  0  1  N  N  N   3.547  -23.039  23.169  -6.667   2.206  -1.030  "O2'"  YO7  28  
YO7  "O4'"  O16  O  0  1  N  N  N   6.756  -22.231  24.469  -3.545   0.892   0.009  "O4'"  YO7  29  
YO7  "C1'"  C12  C  0  1  N  N  R   5.693  -22.024  23.543  -4.884   0.631  -0.467  "C1'"  YO7  30  
YO7  N9     N1   N  0  1  Y  N  N   6.270  -21.631  22.279  -5.417  -0.586   0.150  N9     YO7  31  
YO7  C4     C13  C  0  1  Y  N  N   6.231  -20.411  21.760  -6.450  -1.348  -0.324  C4     YO7  32  
YO7  N3     N2   N  0  1  N  N  N   5.689  -19.251  22.196  -7.252  -1.272  -1.392  N3     YO7  33  
YO7  C2     C14  C  0  1  N  N  N   5.780  -18.082  21.501  -8.188  -2.170  -1.605  C2     YO7  34  
YO7  N2     N3   N  0  1  N  N  N   5.186  -16.987  22.076  -8.987  -2.050  -2.714  N2     YO7  35  
YO7  C8     C15  C  0  1  Y  N  N   6.983  -22.433  21.441  -4.971  -1.170   1.300  C8     YO7  36  
YO7  N7     N4   N  0  1  Y  N  N   7.352  -21.707  20.367  -5.672  -2.235   1.555  N7     YO7  37  
YO7  C5     C16  C  0  1  Y  N  N   6.928  -20.447  20.571  -6.605  -2.401   0.586  C5     YO7  38  
YO7  C6     C17  C  0  1  N  N  N   7.050  -19.171  19.791  -7.619  -3.358   0.347  C6     YO7  39  
YO7  O6     O17  O  0  1  N  N  N   7.673  -19.193  18.709  -7.789  -4.292   1.112  O6     YO7  40  
YO7  N1     N5   N  0  1  N  N  N   6.467  -18.036  20.293  -8.388  -3.217  -0.756  N1     YO7  41  
YO7  H1     H1   H  0  1  N  N  N  12.213  -26.901  25.777   2.466  -0.829   1.514  H1     YO7  42  
YO7  H2     H2   H  0  1  N  N  N  12.137  -26.165  21.201   5.779   0.859   0.484  H2     YO7  43  
YO7  H3     H3   H  0  1  N  N  N  10.610  -28.738  20.609   5.527   0.083  -2.459  H3     YO7  44  
YO7  H4     H4   H  0  1  N  N  N   9.342  -26.864  20.945   5.088   2.378  -1.958  H4     YO7  45  
YO7  H5     H5   H  0  1  N  N  N  12.029  -26.910  18.621   7.989   0.710  -0.763  H5     YO7  46  
YO7  H6     H6   H  0  1  N  N  N  10.072  -27.934  17.854   8.153   1.291  -3.075  H6     YO7  47  
YO7  H7     H7   H  0  1  N  N  N  12.644  -29.743  19.524   7.043  -1.912  -2.012  H7     YO7  48  
YO7  H8     H8   H  0  1  N  N  N  14.536  -29.501  18.210   9.412  -1.648  -1.827  H8     YO7  49  
YO7  H9     H9   H  0  1  N  N  N  14.228  -27.173  19.934   7.226  -1.046   0.910  H9     YO7  50  
YO7  H10    H10  H  0  1  N  N  N  15.601  -29.354  19.702   7.723  -3.424   0.610  H10    YO7  51  
YO7  H11    H11  H  0  1  N  N  N  16.898  -28.959  21.920   6.191  -2.711   2.469  H11    YO7  52  
YO7  H12    H12  H  0  1  N  N  N  15.704  -27.658  22.250   4.802  -3.058   1.412  H12    YO7  53  
YO7  H13    H13  H  0  1  N  N  N  17.518  -26.905  20.956   5.370  -4.932   2.780  H13    YO7  54  
YO7  H14    H14  H  0  1  N  N  N  15.510  -30.650  21.642   5.271  -3.530  -0.941  H14    YO7  55  
YO7  H15    H15  H  0  1  N  N  N   7.994  -28.084  24.229   0.915   4.358  -0.205  H15    YO7  56  
YO7  H16    H16  H  0  1  N  N  N   7.420  -25.209  25.961  -2.394   2.560   1.686  H16    YO7  57  
YO7  H17    H17  H  0  1  N  N  N   8.563  -23.913  25.471  -2.128   3.906   0.552  H17    YO7  58  
YO7  H18    H18  H  0  1  N  N  N   6.367  -23.032  26.374  -3.083   2.462  -1.292  H18    YO7  59  
YO7  H19    H19  H  0  1  N  N  N   5.175  -25.035  24.813  -4.629   3.348   1.151  H19    YO7  60  
YO7  H20    H20  H  0  1  N  N  N   4.288  -23.816  26.611  -5.758   4.521  -0.597  H20    YO7  61  
YO7  H21    H21  H  0  1  N  N  N   5.361  -23.991  22.706  -6.201   1.671   0.925  H21    YO7  62  
YO7  H22    H22  H  0  1  N  N  N   3.049  -23.847  23.121  -7.212   2.973  -0.807  H22    YO7  63  
YO7  H23    H23  H  0  1  N  N  N   5.019  -21.235  23.909  -4.888   0.539  -1.553  H23    YO7  64  
YO7  H24    H24  H  0  1  N  N  N   4.720  -17.075  22.957  -8.857  -1.310  -3.328  H24    YO7  65  
YO7  H25    H25  H  0  1  N  N  N   5.219  -16.100  21.615  -9.682  -2.705  -2.884  H25    YO7  66  
YO7  H26    H26  H  0  1  N  N  N   7.214  -23.475  21.609  -4.157  -0.802   1.908  H26    YO7  67  
YO7  H27    H27  H  0  1  N  N  N   6.536  -17.175  19.790  -9.089  -3.862  -0.940  H27    YO7  68  
#   #
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
YO7  O31    C31    SING  N  N   1  
YO7  O41    C41    SING  N  N   2  
YO7  O6     C6     DOUB  N  N   3  
YO7  C31    C41    SING  N  N   4  
YO7  C31    C21    SING  N  N   5  
YO7  C41    C51    SING  N  N   6  
YO7  C6     N1     SING  N  N   7  
YO7  C6     C5     SING  N  N   8  
YO7  O21    C21    SING  N  N   9  
YO7  C51    C61    SING  N  N  10  
YO7  C51    O51    SING  N  N  11  
YO7  N1     C2     SING  N  N  12  
YO7  C21    C11    SING  N  N  13  
YO7  N7     C5     SING  Y  N  14  
YO7  N7     C8     DOUB  Y  N  15  
YO7  O71    C71    SING  N  N  16  
YO7  C5     C4     DOUB  Y  N  17  
YO7  C61    O6A    SING  N  N  18  
YO7  C61    C71    SING  N  N  19  
YO7  C11    O51    SING  N  N  20  
YO7  C11    O1B    SING  N  N  21  
YO7  C8     N9     SING  Y  N  22  
YO7  C2     N2     SING  N  N  23  
YO7  C2     N3     DOUB  N  N  24  
YO7  C4     N3     SING  N  N  25  
YO7  C4     N9     SING  Y  N  26  
YO7  O1A    PA     DOUB  N  N  27  
YO7  N9     "C1'"  SING  N  N  28  
YO7  O1B    PB     SING  N  N  29  
YO7  "O2'"  "C2'"  SING  N  N  30  
YO7  "C2'"  "C1'"  SING  N  N  31  
YO7  "C2'"  "C3'"  SING  N  N  32  
YO7  "C1'"  "O4'"  SING  N  N  33  
YO7  PA     O3A    SING  N  N  34  
YO7  PA     "O5'"  SING  N  N  35  
YO7  PA     O2A    SING  N  N  36  
YO7  O2B    PB     DOUB  N  N  37  
YO7  O3A    PB     SING  N  N  38  
YO7  "O5'"  "C5'"  SING  N  N  39  
YO7  PB     O3B    SING  N  N  40  
YO7  "O4'"  "C4'"  SING  N  N  41  
YO7  "C3'"  "C4'"  SING  N  N  42  
YO7  "C3'"  "O3'"  SING  N  N  43  
YO7  "C5'"  "C4'"  SING  N  N  44  
YO7  O3B    H1     SING  N  N  45  
YO7  C11    H2     SING  N  N  46  
YO7  C21    H3     SING  N  N  47  
YO7  O21    H4     SING  N  N  48  
YO7  C31    H5     SING  N  N  49  
YO7  O31    H6     SING  N  N  50  
YO7  C41    H7     SING  N  N  51  
YO7  O41    H8     SING  N  N  52  
YO7  C51    H9     SING  N  N  53  
YO7  C61    H10    SING  N  N  54  
YO7  C71    H11    SING  N  N  55  
YO7  C71    H12    SING  N  N  56  
YO7  O71    H13    SING  N  N  57  
YO7  O6A    H14    SING  N  N  58  
YO7  O2A    H15    SING  N  N  59  
YO7  "C5'"  H16    SING  N  N  60  
YO7  "C5'"  H17    SING  N  N  61  
YO7  "C4'"  H18    SING  N  N  62  
YO7  "C3'"  H19    SING  N  N  63  
YO7  "O3'"  H20    SING  N  N  64  
YO7  "C2'"  H21    SING  N  N  65  
YO7  "O2'"  H22    SING  N  N  66  
YO7  "C1'"  H23    SING  N  N  67  
YO7  N2     H24    SING  N  N  68  
YO7  N2     H25    SING  N  N  69  
YO7  C8     H26    SING  N  N  70  
YO7  N1     H27    SING  N  N  71  
#   #
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
YO7  SMILES            ACDLabs               12.01  "NC1=Nc2c(ncn2C2OC(COP(=O)(O)OP(=O)(O)OC3OC(C(O)C(O)C3O)C(O)CO)C(O)C2O)C(=O)N1"  
YO7  InChI             InChI                 1.03   "InChI=1S/C17H27N5O17P2/c18-17-20-13-6(14(30)21-17)19-3-22(13)15-10(28)7(25)5(36-15)2-35-40(31,32)39-41(33,34)38-16-11(29)8(26)9(27)12(37-16)4(24)1-23/h3-5,7-12,15-16,23-29H,1-2H2,(H,31,32)(H,33,34)(H3,18,20,21,30)/t4-,5-,7-,8-,9-,10-,11+,12+,15-,16-/m1/s1"  
YO7  InChIKey          InChI                 1.03   HRUXIQZFNLQZQA-GVGRRHNDSA-N  
YO7  SMILES_CANONICAL  CACTVS                3.385  "NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[C@H]4O[C@@H]([C@H](O)CO)[C@H](O)[C@@H](O)[C@@H]4O)[C@@H](O)[C@H]3O"  
YO7  SMILES            CACTVS                3.385  "NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[CH]4O[CH]([CH](O)CO)[CH](O)[CH](O)[CH]4O)[CH](O)[CH]3O"  
YO7  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)O[C@@H]4[C@H]([C@@H]([C@H]([C@@H](O4)[C@@H](CO)O)O)O)O)O)O)N=C(NC2=O)N"  
YO7  SMILES            "OpenEye OEToolkits"  2.0.7  "c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OC4C(C(C(C(O4)C(CO)O)O)O)O)O)O)N=C(NC2=O)N"  
#   #
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
YO7  "SYSTEMATIC NAME"  ACDLabs               12.01  "[(2R,3S,4R,5R)-5-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl (2R,3S,4R,5R,6S)-6-[(1R)-1,2-dihydroxyethyl]-3,4,5-trihydroxyoxan-2-yl dihydrogen diphosphate (non-preferred name)"  
YO7  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  2.0.7  "[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R},6~{S})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-3,4,5-tris(oxidanyl)oxan-2-yl] 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
YO7  "Create component"  2021-03-16  RCSB  
YO7  "Initial release"   2021-03-24  RCSB  
##
