data_9BG
#

_chem_comp.id                                   9BG
_chem_comp.name                                 "2',5'-GpAp"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C20 H26 N10 O14 P2"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        "[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methyl [(2~{R},3~{R},4~{R},5~{R})-2-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-5-(hydroxymethyl)-4-oxidanyl-oxolan-3-yl] hydrogen phosphate"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2017-04-17
_chem_comp.pdbx_modified_date                   2021-03-13
_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                       692.427
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    9BG
_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       5VDQ
_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
9BG  C10  C1   C  0  1  Y  N  N  -25.527   -7.298  -27.175   6.372  -1.113   0.799  C10  9BG   1  
9BG  C17  C2   C  0  1  N  N  R  -27.287   -8.434  -30.657   4.890   2.359  -1.289  C17  9BG   2  
9BG  C24  C3   C  0  1  N  N  R  -28.466  -12.209  -24.787  -2.100   1.507  -0.090  C24  9BG   3  
9BG  C02  C4   C  0  1  N  N  N  -24.680   -9.655  -24.423   4.313  -3.681   2.293  C02  9BG   4  
9BG  C04  C5   C  0  1  N  N  N  -24.621  -11.715  -25.838   2.454  -3.310   0.962  C04  9BG   5  
9BG  C07  C6   C  0  1  Y  N  N  -25.155   -9.448  -26.911   4.345  -1.934   0.577  C07  9BG   6  
9BG  C08  C7   C  0  1  Y  N  N  -25.027   -8.831  -25.670   5.018  -2.605   1.590  C08  9BG   7  
9BG  C12  C8   C  0  1  N  N  R  -25.657   -8.688  -29.113   4.947  -0.058  -0.997  C12  9BG   8  
9BG  C14  C9   C  0  1  N  N  R  -26.060   -7.313  -30.914   5.860   1.635  -2.249  C14  9BG   9  
9BG  C19  C10  C  0  1  N  N  R  -27.157   -8.871  -29.441   4.275   1.219  -0.447  C19  9BG  10  
9BG  C23  C11  C  0  1  N  N  N  -28.976  -12.397  -26.204  -0.847   1.556   0.786  C23  9BG  11  
9BG  C25  C12  C  0  1  N  N  S  -29.751  -12.026  -23.731  -3.342   1.855   0.753  C25  9BG  12  
9BG  N34  N1   N  0  1  Y  N  N  -28.401   -9.162  -23.588  -4.011  -1.481  -0.691  N34  9BG  13  
9BG  O01  O1   O  0  1  N  N  N  -24.571   -9.122  -23.363   4.860  -4.302   3.192  O01  9BG  14  
9BG  N03  N2   N  0  1  N  N  N  -24.487  -11.072  -24.538   3.055  -3.970   1.928  N03  9BG  15  
9BG  N05  N3   N  0  1  N  N  N  -24.432  -13.116  -25.964   1.168  -3.649   0.633  N05  9BG  16  
9BG  N06  N4   N  0  1  N  N  N  -24.955  -10.911  -27.030   3.059  -2.304   0.278  N06  9BG  17  
9BG  N09  N5   N  0  1  Y  N  N  -25.257   -7.517  -25.843   6.252  -2.058   1.688  N09  9BG  18  
9BG  N11  N6   N  0  1  Y  N  N  -25.463   -8.497  -27.817   5.212  -1.004   0.090  N11  9BG  19  
9BG  O13  O2   O  0  1  N  N  N  -25.239   -7.396  -29.942   6.187   0.398  -1.579  O13  9BG  20  
9BG  C15  C13  C  0  1  N  N  N  -26.628   -5.915  -30.982   7.122   2.475  -2.463  C15  9BG  21  
9BG  O16  O3   O  0  1  N  N  N  -26.431   -5.282  -29.691   7.952   1.845  -3.441  O16  9BG  22  
9BG  O18  O4   O  0  1  N  N  N  -27.162   -9.516  -31.580   3.872   3.043  -2.024  O18  9BG  23  
9BG  O20  O5   O  0  1  N  N  N  -27.516  -10.353  -29.368   2.860   1.162  -0.638  O20  9BG  24  
9BG  P21  P1   P  0  1  N  N  N  -28.715  -10.794  -28.300   1.805   1.312   0.570  P21  9BG  25  
9BG  O22  O6   O  0  1  N  N  N  -28.081  -11.798  -27.119   0.309   1.330  -0.024  O22  9BG  26  
9BG  O26  O7   O  0  1  N  N  N  -30.135  -13.328  -23.127  -3.994   3.014   0.229  O26  9BG  27  
9BG  P27  P2   P  0  1  N  N  N  -30.583  -14.666  -24.129  -4.202   4.364   1.081  P27  9BG  28  
9BG  O28  O8   O  0  1  N  N  N  -31.279  -14.177  -25.371  -2.894   4.833   1.590  O28  9BG  29  
9BG  O29  O9   O  0  1  N  N  N  -31.504  -15.554  -23.370  -4.850   5.499   0.140  O29  9BG  30  
9BG  O30  O10  O  0  1  N  N  N  -29.332  -15.455  -24.528  -5.186   4.069   2.321  O30  9BG  31  
9BG  C31  C14  C  0  1  N  N  R  -29.381  -11.217  -22.815  -4.255   0.612   0.616  C31  9BG  32  
9BG  O32  O11  O  0  1  N  N  N  -28.999  -11.969  -21.556  -5.622   0.998   0.458  O32  9BG  33  
9BG  C33  C15  C  0  1  N  N  R  -28.123  -10.448  -23.376  -3.714  -0.046  -0.679  C33  9BG  34  
9BG  C35  C16  C  0  1  Y  N  N  -28.253   -8.129  -22.664  -5.178  -2.064  -1.116  C35  9BG  35  
9BG  N36  N7   N  0  1  Y  N  N  -27.826   -8.091  -21.351  -6.326  -1.614  -1.611  N36  9BG  36  
9BG  C37  C17  C  0  1  Y  N  N  -27.792   -6.959  -20.719  -7.290  -2.449  -1.937  C37  9BG  37  
9BG  N38  N8   N  0  1  Y  N  N  -28.155   -5.832  -21.290  -7.174  -3.757  -1.792  N38  9BG  38  
9BG  C39  C18  C  0  1  Y  N  N  -28.579   -5.797  -22.558  -6.063  -4.299  -1.305  C39  9BG  39  
9BG  N40  N9   N  0  1  N  N  N  -28.980   -4.532  -23.179  -5.951  -5.670  -1.157  N40  9BG  40  
9BG  C41  C19  C  0  1  Y  N  N  -28.632   -6.994  -23.280  -5.005  -3.447  -0.943  C41  9BG  41  
9BG  N42  N10  N  0  1  Y  N  N  -28.995   -7.312  -24.529  -3.765  -3.634  -0.431  N42  9BG  42  
9BG  C43  C20  C  0  1  Y  N  N  -28.840   -8.661  -24.691  -3.178  -2.481  -0.287  C43  9BG  43  
9BG  O44  O12  O  0  1  N  N  N  -27.760  -11.134  -24.718  -2.289   0.176  -0.600  O44  9BG  44  
9BG  O45  O13  O  0  1  N  N  N  -29.779  -11.486  -29.030   2.063   2.576   1.296  O45  9BG  45  
9BG  O46  O14  O  0  1  N  N  N  -29.292   -9.506  -27.625   1.967   0.070   1.581  O46  9BG  46  
9BG  H1   H1   H  0  1  N  N  N  -25.750   -6.344  -27.630   7.252  -0.506   0.650  H1   9BG  47  
9BG  H2   H2   H  0  1  N  N  N  -28.241   -7.910  -30.813   5.432   3.056  -0.651  H2   9BG  48  
9BG  H3   H3   H  0  1  N  N  N  -27.911  -13.107  -24.478  -2.005   2.211  -0.917  H3   9BG  49  
9BG  H4   H4   H  0  1  N  N  N  -25.095   -9.550  -29.501   4.317  -0.522  -1.757  H4   9BG  50  
9BG  H5   H5   H  0  1  N  N  N  -25.598   -7.559  -31.881   5.372   1.433  -3.202  H5   9BG  51  
9BG  H6   H6   H  0  1  N  N  N  -27.760   -8.309  -28.712   4.512   1.354   0.608  H6   9BG  52  
9BG  H7   H7   H  0  1  N  N  N  -29.966  -11.927  -26.301  -0.773   2.534   1.260  H7   9BG  53  
9BG  H8   H8   H  0  1  N  N  N  -29.057  -13.472  -26.423  -0.910   0.784   1.553  H8   9BG  54  
9BG  H9   H9   H  0  1  N  N  N  -30.596  -11.637  -24.319  -3.064   2.014   1.795  H9   9BG  55  
9BG  H10  H10  H  0  1  N  N  N  -24.206  -13.664  -25.159   0.719  -4.364   1.109  H10  9BG  56  
9BG  H11  H11  H  0  1  N  N  N  -24.525  -13.555  -26.858   0.708  -3.174  -0.076  H11  9BG  57  
9BG  H12  H12  H  0  1  N  N  N  -25.047  -11.356  -27.921   2.578  -1.844  -0.428  H12  9BG  58  
9BG  H13  H13  H  0  1  N  N  N  -26.108   -5.339  -31.762   6.841   3.469  -2.810  H13  9BG  59  
9BG  H14  H14  H  0  1  N  N  N  -27.702   -5.960  -31.214   7.666   2.558  -1.523  H14  9BG  60  
9BG  H15  H15  H  0  1  N  N  N  -26.782   -4.400  -29.713   8.772   2.323  -3.628  H15  9BG  61  
9BG  H16  H16  H  0  1  N  N  N  -27.858  -10.144  -31.428   4.203   3.769  -2.571  H16  9BG  62  
9BG  H17  H17  H  0  1  N  N  N  -32.332  -15.621  -23.832  -5.004   6.341   0.589  H17  9BG  63  
9BG  H18  H18  H  0  1  N  N  N  -29.256  -15.471  -25.475  -6.063   3.757   2.062  H18  9BG  64  
9BG  H19  H19  H  0  1  N  N  N  -30.154  -10.475  -22.567  -4.136  -0.053   1.470  H19  9BG  65  
9BG  H20  H20  H  0  1  N  N  N  -28.727  -11.351  -20.888  -6.233   0.254   0.368  H20  9BG  66  
9BG  H21  H21  H  0  1  N  N  N  -27.289  -10.581  -22.671  -4.132   0.439  -1.560  H21  9BG  67  
9BG  H22  H22  H  0  1  N  N  N  -27.455   -6.942  -19.693  -8.211  -2.050  -2.337  H22  9BG  68  
9BG  H23  H23  H  0  1  N  N  N  -28.877   -3.788  -22.518  -6.688  -6.247  -1.410  H23  9BG  69  
9BG  H24  H24  H  0  1  N  N  N  -28.401   -4.353  -23.975  -5.135  -6.054  -0.800  H24  9BG  70  
9BG  H25  H25  H  0  1  N  N  N  -29.051   -9.215  -25.594  -2.181  -2.338   0.101  H25  9BG  71  
9BG  H26  H26  H  0  1  N  N  N  -30.218   -9.431  -27.824   1.812  -0.793   1.172  H26  9BG  72  
#   #
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
9BG  O18  C17  SING  N  N   1  
9BG  C15  C14  SING  N  N   2  
9BG  C15  O16  SING  N  N   3  
9BG  C14  C17  SING  N  N   4  
9BG  C14  O13  SING  N  N   5  
9BG  C17  C19  SING  N  N   6  
9BG  O13  C12  SING  N  N   7  
9BG  C19  O20  SING  N  N   8  
9BG  C19  C12  SING  N  N   9  
9BG  O20  P21  SING  N  N  10  
9BG  C12  N11  SING  N  N  11  
9BG  O45  P21  DOUB  N  N  12  
9BG  P21  O46  SING  N  N  13  
9BG  P21  O22  SING  N  N  14  
9BG  N11  C10  SING  Y  N  15  
9BG  N11  C07  SING  Y  N  16  
9BG  C10  N09  DOUB  Y  N  17  
9BG  O22  C23  SING  N  N  18  
9BG  N06  C07  SING  N  N  19  
9BG  N06  C04  SING  N  N  20  
9BG  C07  C08  DOUB  Y  N  21  
9BG  C23  C24  SING  N  N  22  
9BG  N05  C04  SING  N  N  23  
9BG  N09  C08  SING  Y  N  24  
9BG  C04  N03  DOUB  N  N  25  
9BG  C08  C02  SING  N  N  26  
9BG  O28  P27  DOUB  N  N  27  
9BG  C24  O44  SING  N  N  28  
9BG  C24  C25  SING  N  N  29  
9BG  O44  C33  SING  N  N  30  
9BG  C43  N42  DOUB  Y  N  31  
9BG  C43  N34  SING  Y  N  32  
9BG  N03  C02  SING  N  N  33  
9BG  N42  C41  SING  Y  N  34  
9BG  O30  P27  SING  N  N  35  
9BG  C02  O01  DOUB  N  N  36  
9BG  P27  O29  SING  N  N  37  
9BG  P27  O26  SING  N  N  38  
9BG  C25  O26  SING  N  N  39  
9BG  C25  C31  SING  N  N  40  
9BG  N34  C33  SING  N  N  41  
9BG  N34  C35  SING  Y  N  42  
9BG  C33  C31  SING  N  N  43  
9BG  C41  C35  DOUB  Y  N  44  
9BG  C41  C39  SING  Y  N  45  
9BG  N40  C39  SING  N  N  46  
9BG  C31  O32  SING  N  N  47  
9BG  C35  N36  SING  Y  N  48  
9BG  C39  N38  DOUB  Y  N  49  
9BG  N36  C37  DOUB  Y  N  50  
9BG  N38  C37  SING  Y  N  51  
9BG  C10  H1   SING  N  N  52  
9BG  C17  H2   SING  N  N  53  
9BG  C24  H3   SING  N  N  54  
9BG  C12  H4   SING  N  N  55  
9BG  C14  H5   SING  N  N  56  
9BG  C19  H6   SING  N  N  57  
9BG  C23  H7   SING  N  N  58  
9BG  C23  H8   SING  N  N  59  
9BG  C25  H9   SING  N  N  60  
9BG  N05  H10  SING  N  N  61  
9BG  N05  H11  SING  N  N  62  
9BG  N06  H12  SING  N  N  63  
9BG  C15  H13  SING  N  N  64  
9BG  C15  H14  SING  N  N  65  
9BG  O16  H15  SING  N  N  66  
9BG  O18  H16  SING  N  N  67  
9BG  O29  H17  SING  N  N  68  
9BG  O30  H18  SING  N  N  69  
9BG  C31  H19  SING  N  N  70  
9BG  O32  H20  SING  N  N  71  
9BG  C33  H21  SING  N  N  72  
9BG  C37  H22  SING  N  N  73  
9BG  N40  H23  SING  N  N  74  
9BG  N40  H24  SING  N  N  75  
9BG  C43  H25  SING  N  N  76  
9BG  O46  H26  SING  N  N  77  
#   #
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
9BG  SMILES            ACDLabs               12.01  "c2nc1C(=O)N=C(N)Nc1n2C3C(C(C(O3)CO)O)OP(O)(OCC6OC(n5c4ncnc(N)c4nc5)C(C6OP(O)(=O)O)O)=O"  
9BG  InChI             InChI                 1.03   "InChI=1S/C20H26N10O14P2/c21-14-8-15(24-3-23-14)29(4-25-8)18-11(33)12(43-45(35,36)37)7(42-18)2-40-46(38,39)44-13-10(32)6(1-31)41-19(13)30-5-26-9-16(30)27-20(22)28-17(9)34/h3-7,10-13,18-19,31-33H,1-2H2,(H,38,39)(H2,21,23,24)(H2,35,36,37)(H3,22,27,28,34)/t6-,7-,10-,11-,12-,13-,18-,19-/m1/s1"  
9BG  InChIKey          InChI                 1.03   OVXKSNAROFCXFB-INFSMZHSSA-N  
9BG  SMILES_CANONICAL  CACTVS                3.385  "NC1=NC(=O)c2ncn([C@@H]3O[C@H](CO)[C@@H](O)[C@H]3O[P](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O[P](O)(O)=O)n5cnc6c(N)ncnc56)c2N1"  
9BG  SMILES            CACTVS                3.385  "NC1=NC(=O)c2ncn([CH]3O[CH](CO)[CH](O)[CH]3O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O[P](O)(O)=O)n5cnc6c(N)ncnc56)c2N1"  
9BG  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.6  "c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O[C@@H]4[C@@H]([C@H](O[C@H]4n5cnc6c5NC(=NC6=O)N)CO)O)OP(=O)(O)O)O)N"  
9BG  SMILES            "OpenEye OEToolkits"  2.0.6  "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OC4C(C(OC4n5cnc6c5NC(=NC6=O)N)CO)O)OP(=O)(O)O)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
9BG  "SYSTEMATIC NAME"  ACDLabs               12.01  "(2R,3S,4R,5R)-2-({[(R)-{[(2R,3R,4R,5R)-2-(2-amino-6-oxo-3,6-dihydro-9H-purin-9-yl)-4-hydroxy-5-(hydroxymethyl)tetrahydrofuran-3-yl]oxy}(hydroxy)phosphoryl]oxy}methyl)-5-(6-amino-9H-purin-9-yl)-4-hydroxytetrahydrofuran-3-yl dihydrogen phosphate (non-preferred name)"  
9BG  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  2.0.6  "[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methyl [(2~{R},3~{R},4~{R},5~{R})-2-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-5-(hydroxymethyl)-4-oxidanyl-oxolan-3-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
9BG  "Create component"  2017-04-17  RCSB  
9BG  "Initial release"   2017-09-27  RCSB  
9BG  "Modify synonyms"   2021-03-13  RCSB  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     9BG
_pdbx_chem_comp_synonyms.name        "[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methyl [(2~{R},3~{R},4~{R},5~{R})-2-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-5-(hydroxymethyl)-4-oxidanyl-oxolan-3-yl] hydrogen phosphate"
_pdbx_chem_comp_synonyms.provenance  PDB
_pdbx_chem_comp_synonyms.type        ?
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