data_A2D
#

_chem_comp.id                                   A2D
_chem_comp.name                                 "BIS{[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL} DIHYDROGEN DIPHOSPHATE"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C20 H26 N10 O13 P2"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        "BIS(ADENOSINE)-5'-DIPHOSPHATE"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2006-10-25
_chem_comp.pdbx_modified_date                   2021-03-01
_chem_comp.pdbx_ambiguous_flag                  ?
_chem_comp.pdbx_release_status                  REL
_chem_comp.pdbx_replaced_by                     ?
_chem_comp.pdbx_replaces                        ?
_chem_comp.formula_weight                       676.427
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    A2D
_chem_comp.pdbx_model_coordinates_details       ?
_chem_comp.pdbx_model_coordinates_missing_flag  N
_chem_comp.pdbx_ideal_coordinates_details       ?
_chem_comp.pdbx_ideal_coordinates_missing_flag  N
_chem_comp.pdbx_model_coordinates_db_code       ?
_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
A2D  PA    PA    P  0  1  N  N  S  14.306   7.549  13.388   4.853   3.286   -1.557  PA    A2D   1  
A2D  O1A   O1A   O  0  1  N  N  N  14.649   8.597  14.574   3.237   3.311   -1.628  O1A   A2D   2  
A2D  O2A   O2A   O  0  1  N  N  N  13.697   6.304  13.461   5.417   3.560   -0.193  O2A   A2D   3  
A2D  O3A   O3A   O  0  1  N  N  N  13.678   8.439  12.658   5.239   1.840   -2.168  O3A   A2D   4  
A2D  PB    PB    P  0  1  N  N  R  12.904   9.645  12.912   4.948   0.346   -1.624  PB    A2D   5  
A2D  O1B   O1B   O  0  1  N  N  N  11.422   9.477  12.862   5.526   0.037   -0.274  O1B   A2D   6  
A2D  O2B   O2B   O  0  1  N  N  N  13.409  10.767  13.768   3.338   0.218   -1.723  O2B   A2D   7  
A2D  O5D   O5*A  O  0  1  N  N  N  15.729   7.529  12.628   5.332   4.309   -2.716  O5D   A2D   8  
A2D  C5D   C5*A  C  0  1  N  N  N  16.702   6.539  12.946   4.862   4.146   -4.043  C5D   A2D   9  
A2D  C4D   C4*A  C  0  1  N  N  R  17.860   7.216  13.655   5.465   5.234   -4.920  C4D   A2D  10  
A2D  O4D   O4*A  O  0  1  N  N  N  18.258   8.362  12.910   6.903   5.079   -4.915  O4D   A2D  11  
A2D  C3D   C3*A  C  0  1  N  N  S  17.509   7.712  15.053   5.025   5.136   -6.377  C3D   A2D  12  
A2D  O3D   O3*A  O  0  1  N  N  N  18.279   6.961  15.994   5.101   6.433   -6.970  O3D   A2D  13  
A2D  C2D   C2*A  C  0  1  N  N  R  17.869   9.195  15.059   6.093   4.243   -6.977  C2D   A2D  14  
A2D  O2D   O2*A  O  0  1  N  N  N  18.548   9.601  16.257   6.218   4.394   -8.377  O2D   A2D  15  
A2D  C1D   C1*A  C  0  1  N  N  R  18.780   9.292  13.847   7.335   4.720   -6.242  C1D   A2D  16  
A2D  N9A   N9A   N  0  1  Y  N  N  18.895  10.622  13.204   8.399   3.722   -6.160  N9A   A2D  17  
A2D  C8A   C8A   C  0  1  Y  N  N  17.931  11.479  12.822   8.523   2.750   -5.202  C8A   A2D  18  
A2D  N7A   N7A   N  0  1  Y  N  N  18.525  12.558  12.267   9.587   1.997   -5.391  N7A   A2D  19  
A2D  C5A   C5A   C  0  1  Y  N  N  19.874  12.364  12.291  10.180   2.503   -6.520  C5A   A2D  20  
A2D  C6A   C6A   C  0  1  Y  N  N  21.002  13.092  11.875  11.326   2.141   -7.221  C6A   A2D  21  
A2D  N6A   N6A   N  0  1  N  N  N  20.907  14.308  11.279  12.120   1.064   -6.790  N6A   A2D  22  
A2D  N1A   N1A   N  0  1  Y  N  N  22.228  12.556  12.072  11.670   2.842   -8.328  N1A   A2D  23  
A2D  C2A   C2A   C  0  1  Y  N  N  22.402  11.361  12.651  10.866   3.869   -8.694  C2A   A2D  24  
A2D  N3A   N3A   N  0  1  Y  N  N  21.354  10.640  13.059   9.737   4.314   -8.100  N3A   A2D  25  
A2D  C4A   C4A   C  0  1  Y  N  N  20.089  11.126  12.882   9.456   3.577   -7.014  C4A   A2D  26  
A2D  O5E   O5*B  O  0  1  N  N  N  13.267  10.410  11.563   5.497  -0.548   -2.856  O5E   A2D  27  
A2D  C5E   C5*B  C  0  1  N  N  N  13.666   9.672  10.419   6.882  -0.513   -3.152  C5E   A2D  28  
A2D  C4E   C4*B  C  0  1  N  N  R  15.126   9.934  10.140   7.294  -1.849   -3.743  C4E   A2D  29  
A2D  O4E   O4*B  O  0  1  N  N  N  15.853   8.724  10.026   6.588  -2.075   -4.974  O4E   A2D  30  
A2D  C3E   C3*B  C  0  1  N  N  S  15.275  10.609   8.812   8.767  -1.920   -4.110  C3E   A2D  31  
A2D  O3E   O3*B  O  0  1  N  N  N  16.490  11.327   8.890   9.581  -2.192   -2.990  O3E   A2D  32  
A2D  C2E   C2*B  C  0  1  N  N  R  15.622   9.506   7.884   8.786  -3.022   -5.153  C2E   A2D  33  
A2D  O2E   O2*B  O  0  1  N  N  N  16.393  10.140   6.876   8.849  -4.310   -4.543  O2E   A2D  34  
A2D  C1E   C1*B  C  0  1  N  N  R  16.496   8.650   8.767   7.432  -2.858   -5.845  C1E   A2D  35  
A2D  N9B   N9B   N  0  1  Y  N  N  16.533   7.246   8.296   7.516  -2.209   -7.155  N9B   A2D  36  
A2D  C8B   C8B   C  0  1  Y  N  N  15.506   6.569   7.803   7.505  -0.858   -7.389  C8B   A2D  37  
A2D  N7B   N7B   N  0  1  Y  N  N  15.903   5.331   7.474   7.595  -0.575   -8.672  N7B   A2D  38  
A2D  C5B   C5B   C  0  1  Y  N  N  17.197   5.226   7.775   7.668  -1.794   -9.297  C5B   A2D  39  
A2D  C6B   C6B   C  0  1  Y  N  N  18.118   4.202   7.662   7.776  -2.157  -10.636  C6B   A2D  40  
A2D  N6B   N6B   N  0  1  N  N  N  17.780   2.999   7.161   7.830  -1.178  -11.643  N6B   A2D  41  
A2D  N1B   N1B   N  0  1  Y  N  N  19.370   4.419   8.069   7.829  -3.471  -10.960  N1B   A2D  42  
A2D  C2B   C2B   C  0  1  Y  N  N  19.722   5.600   8.563   7.772  -4.369   -9.946  C2B   A2D  43  
A2D  N3B   N3B   N  0  1  Y  N  N  18.857   6.599   8.686   7.668  -4.141   -8.619  N3B   A2D  44  
A2D  C4B   C4B   C  0  1  Y  N  N  17.585   6.439   8.295   7.620  -2.824   -8.371  C4B   A2D  45  
A2D  HO1A  HO1A  H  0  0  N  N  N  14.716   8.131  15.399   2.725   2.836   -0.939  HO1A  A2D  46  
A2D  HO2B  HO2B  H  0  0  N  N  N  13.516  10.461  14.661   2.784   0.648   -1.038  HO2B  A2D  47  
A2D  HD1   1H*A  H  0  1  N  N  N  16.257   5.776  13.602   5.158   3.156   -4.403  HD1   A2D  48  
A2D  HD2   2H*A  H  0  1  N  N  N  17.056   6.049  12.027   3.770   4.215   -4.042  HD2   A2D  49  
A2D  H4D   H4*A  H  0  1  N  N  N  18.652   6.457  13.737   5.237   6.214   -4.488  H4D   A2D  50  
A2D  H3CA  H3CA  H  0  0  N  N  N  16.450   7.585  15.321   4.007   4.764   -6.519  H3CA  A2D  51  
A2D  H3OA  H3OA  H  0  0  N  N  N  19.143   6.794  15.636   4.543   7.013   -6.430  H3OA  A2D  52  
A2D  H2CA  H2CA  H  0  0  N  N  N  16.988   9.853  15.024   5.880   3.191   -6.751  H2CA  A2D  53  
A2D  H2OA  H2OA  H  0  0  N  N  N  19.477   9.691  16.080   6.094   5.338   -8.578  H2OA  A2D  54  
A2D  H1D   H1*A  H  0  1  N  N  N  19.805   9.086  14.188   7.795   5.595   -6.715  H1D   A2D  55  
A2D  H8A   H8A   H  0  1  N  N  N  16.868  11.330  12.939   7.810   2.640   -4.396  H8A   A2D  56  
A2D  H6A1  1H6A  H  0  0  N  N  N  20.884  15.022  11.979  12.770   0.646   -7.428  H6A1  A2D  57  
A2D  H6A2  2H6A  H  0  0  N  N  N  21.698  14.450  10.684  11.961   0.667   -5.884  H6A2  A2D  58  
A2D  H2A   H2A   H  0  1  N  N  N  23.401  10.976  12.790  11.172   4.409   -9.584  H2A   A2D  59  
A2D  HE1   1H*B  H  0  1  N  N  N  13.064   9.984   9.552   7.071   0.296   -3.863  HE1   A2D  60  
A2D  HE2   2H*B  H  0  1  N  N  N  13.513   8.598  10.602   7.435  -0.315   -2.228  HE2   A2D  61  
A2D  H4E   H4*B  H  0  1  N  N  N  15.503  10.547  10.972   7.022  -2.644   -3.039  H4E   A2D  62  
A2D  H3CB  H3CB  H  0  0  N  N  N  14.399  11.214   8.533   9.090  -0.977   -4.567  H3CB  A2D  63  
A2D  H3OB  H3OB  H  0  0  N  N  N  16.820  11.488   8.014   9.521  -1.416   -2.413  H3OB  A2D  64  
A2D  H2CB  H2CB  H  0  0  N  N  N  14.804   8.932   7.423   9.643  -2.947   -5.829  H2CB  A2D  65  
A2D  H2OB  H2OB  H  0  0  N  N  N  15.854  10.282   6.107   9.635  -4.319   -3.969  H2OB  A2D  66  
A2D  H1E   H1*B  H  0  1  N  N  N  17.542   8.990   8.781   6.937  -3.817   -6.032  H1E   A2D  67  
A2D  H8B   H8B   H  0  1  N  N  N  14.504   6.955   7.684   7.429  -0.135   -6.588  H8B   A2D  68  
A2D  H6B1  1H6B  H  0  0  N  N  N  17.696   3.063   6.167   8.705  -0.976  -12.088  H6B1  A2D  69  
A2D  H6B2  2H6B  H  0  0  N  N  N  18.487   2.331   7.393   7.015  -0.627  -11.838  H6B2  A2D  70  
A2D  H2B   H2B   H  0  1  N  N  N  20.745   5.753   8.875   7.816  -5.411  -10.242  H2B   A2D  71  
#   #
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
A2D  PA   O5D   SING  N  N   1  
A2D  PA   O3A   SING  N  N   2  
A2D  PA   O2A   DOUB  N  N   3  
A2D  PA   O1A   SING  N  N   4  
A2D  O1A  HO1A  SING  N  N   5  
A2D  O3A  PB    SING  N  N   6  
A2D  PB   O5E   SING  N  N   7  
A2D  PB   O1B   DOUB  N  N   8  
A2D  PB   O2B   SING  N  N   9  
A2D  O2B  HO2B  SING  N  N  10  
A2D  O5D  C5D   SING  N  N  11  
A2D  C5D  C4D   SING  N  N  12  
A2D  C5D  HD1   SING  N  N  13  
A2D  C5D  HD2   SING  N  N  14  
A2D  C4D  O4D   SING  N  N  15  
A2D  C4D  C3D   SING  N  N  16  
A2D  C4D  H4D   SING  N  N  17  
A2D  O4D  C1D   SING  N  N  18  
A2D  C3D  C2D   SING  N  N  19  
A2D  C3D  O3D   SING  N  N  20  
A2D  C3D  H3CA  SING  N  N  21  
A2D  O3D  H3OA  SING  N  N  22  
A2D  C2D  C1D   SING  N  N  23  
A2D  C2D  O2D   SING  N  N  24  
A2D  C2D  H2CA  SING  N  N  25  
A2D  O2D  H2OA  SING  N  N  26  
A2D  C1D  N9A   SING  N  N  27  
A2D  C1D  H1D   SING  N  N  28  
A2D  N9A  C8A   SING  Y  N  29  
A2D  N9A  C4A   SING  Y  N  30  
A2D  C8A  N7A   DOUB  Y  N  31  
A2D  C8A  H8A   SING  N  N  32  
A2D  N7A  C5A   SING  Y  N  33  
A2D  C5A  C6A   SING  Y  N  34  
A2D  C5A  C4A   DOUB  Y  N  35  
A2D  C6A  N6A   SING  N  N  36  
A2D  C6A  N1A   DOUB  Y  N  37  
A2D  N6A  H6A1  SING  N  N  38  
A2D  N6A  H6A2  SING  N  N  39  
A2D  N1A  C2A   SING  Y  N  40  
A2D  C2A  N3A   DOUB  Y  N  41  
A2D  C2A  H2A   SING  N  N  42  
A2D  N3A  C4A   SING  Y  N  43  
A2D  O5E  C5E   SING  N  N  44  
A2D  C5E  C4E   SING  N  N  45  
A2D  C5E  HE1   SING  N  N  46  
A2D  C5E  HE2   SING  N  N  47  
A2D  C4E  C3E   SING  N  N  48  
A2D  C4E  O4E   SING  N  N  49  
A2D  C4E  H4E   SING  N  N  50  
A2D  O4E  C1E   SING  N  N  51  
A2D  C3E  C2E   SING  N  N  52  
A2D  C3E  O3E   SING  N  N  53  
A2D  C3E  H3CB  SING  N  N  54  
A2D  O3E  H3OB  SING  N  N  55  
A2D  C2E  O2E   SING  N  N  56  
A2D  C2E  C1E   SING  N  N  57  
A2D  C2E  H2CB  SING  N  N  58  
A2D  O2E  H2OB  SING  N  N  59  
A2D  C1E  N9B   SING  N  N  60  
A2D  C1E  H1E   SING  N  N  61  
A2D  N9B  C8B   SING  Y  N  62  
A2D  N9B  C4B   SING  Y  N  63  
A2D  C8B  N7B   DOUB  Y  N  64  
A2D  C8B  H8B   SING  N  N  65  
A2D  N7B  C5B   SING  Y  N  66  
A2D  C5B  C6B   DOUB  Y  N  67  
A2D  C5B  C4B   SING  Y  N  68  
A2D  C6B  N6B   SING  N  N  69  
A2D  C6B  N1B   SING  Y  N  70  
A2D  N6B  H6B1  SING  N  N  71  
A2D  N6B  H6B2  SING  N  N  72  
A2D  N1B  C2B   DOUB  Y  N  73  
A2D  C2B  N3B   SING  Y  N  74  
A2D  C2B  H2B   SING  N  N  75  
A2D  N3B  C4B   DOUB  Y  N  76  
#   #
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
A2D  SMILES            ACDLabs               10.04  "O=P(O)(OCC3OC(n1c2ncnc(N)c2nc1)C(O)C3O)OP(=O)(O)OCC6OC(n5cnc4c(ncnc45)N)C(O)C6O"  
A2D  SMILES_CANONICAL  CACTVS                3.341  "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6c(N)ncnc56)[C@@H](O)[C@H]3O"  
A2D  SMILES            CACTVS                3.341  "Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)[CH](O)[CH]3O"  
A2D  SMILES_CANONICAL  "OpenEye OEToolkits"  1.5.0  "c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)O)O)N"  
A2D  SMILES            "OpenEye OEToolkits"  1.5.0  "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)N"  
A2D  InChI             InChI                 1.03   "InChI=1S/C20H26N10O13P2/c21-15-9-17(25-3-23-15)29(5-27-9)19-13(33)11(31)7(41-19)1-39-44(35,36)43-45(37,38)40-2-8-12(32)14(34)20(42-8)30-6-28-10-16(22)24-4-26-18(10)30/h3-8,11-14,19-20,31-34H,1-2H2,(H,35,36)(H,37,38)(H2,21,23,25)(H2,22,24,26)/t7-,8-,11-,12-,13-,14-,19-,20-/m1/s1"  
A2D  InChIKey          InChI                 1.03   AKDJDUXNKGWGAZ-XPWFQUROSA-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
A2D  "SYSTEMATIC NAME"  ACDLabs               10.04  "bis{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl} dihydrogen diphosphate (non-preferred name)"  
A2D  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.5.0  "[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl] [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl 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
A2D  "Create component"   2006-10-25  RCSB  
A2D  "Modify descriptor"  2011-06-04  RCSB  
A2D  "Modify synonyms"    2021-03-01  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     A2D
_pdbx_chem_comp_synonyms.name        "BIS(ADENOSINE)-5'-DIPHOSPHATE"
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
