data_J2B
#

_chem_comp.id                                   J2B
_chem_comp.name                                 
;O-[(1R,2R,3R)-5-{[(S)-{[(2R,3R,4R,5R)-2-(2-amino-6-oxo-3,6-dihydro-9H-purin-9-yl)-4-hydroxy-5-(hydroxymethyl)tetrahydro
furan-3-yl]oxy}(sulfanyl)phosphoryl]oxy}-1-(6-amino-9H-purin-9-yl)-1,2-dihydroxypentan-3-yl] dihydrogen (R)-phosphorothioate
;

_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C20 H28 N10 O12 P2 S2"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        "cleaved nonhydrolyzable phosphorothioate analog of 2'3' cyclic GMP-AMP"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2018-08-30
_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                       726.574
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    J2B
_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       6EA8
_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
J2B  C02  C1   C  0  1  N  N  R   -8.320  70.866  -72.134    5.677   1.870  -1.706  C02  J2B   1  
J2B  C03  C2   C  0  1  N  N  R   -8.331  69.719  -71.580    4.954   0.844  -0.805  C03  J2B   2  
J2B  C08  C3   C  0  1  N  N  N   -5.529  67.916  -74.077   -0.229   1.018   0.183  C08  J2B   3  
J2B  C09  C4   C  0  1  N  N  N   -5.681  68.536  -75.398   -1.436   0.749  -0.717  C09  J2B   4  
J2B  C11  C5   C  0  1  N  N  R   -5.378  67.366  -77.444   -5.206   0.602   0.054  C11  J2B   5  
J2B  C13  C6   C  0  1  Y  N  N   -4.137  66.230  -79.248   -6.756  -1.192  -0.833  C13  J2B   6  
J2B  C15  C7   C  0  1  Y  N  N   -3.236  66.983  -81.247   -6.981  -3.468  -0.604  C15  J2B   7  
J2B  C17  C8   C  0  1  Y  N  N   -2.994  64.734  -80.708   -8.503  -2.401  -1.972  C17  J2B   8  
J2B  C19  C9   C  0  1  Y  N  N   -3.686  64.953  -79.505   -7.867  -1.179  -1.692  C19  J2B   9  
J2B  C21  C10  C  0  1  Y  N  N   -4.744  64.959  -77.609   -7.171   0.866  -1.507  C21  J2B  10  
J2B  C22  C11  C  0  1  N  N  R   -6.750  67.028  -76.698   -3.918   0.461  -0.760  C22  J2B  11  
J2B  C24  C12  C  0  1  N  N  R   -6.922  68.317  -75.864   -2.720   0.852   0.108  C24  J2B  12  
J2B  C31  C13  C  0  1  N  N  R   -9.525  69.756  -70.553    5.590  -0.510  -1.192  C31  J2B  13  
J2B  C33  C14  C  0  1  Y  N  N  -10.519  67.738  -71.371    4.787  -2.176   0.521  C33  J2B  14  
J2B  C35  C15  C  0  1  N  N  N  -11.012  66.680  -73.654    2.784  -3.372   0.944  C35  J2B  15  
J2B  C38  C16  C  0  1  N  N  N  -11.644  65.482  -71.562    4.550  -3.730   2.400  C38  J2B  16  
J2B  C40  C17  C  0  1  Y  N  N  -11.078  66.639  -70.739    5.364  -2.786   1.628  C40  J2B  17  
J2B  C42  C18  C  0  1  Y  N  N  -10.408  68.026  -69.236    6.857  -1.480   0.763  C42  J2B  18  
J2B  C44  C19  C  0  1  N  N  R   -9.707  71.656  -71.700    6.664   1.015  -2.531  C44  J2B  19  
J2B  C45  C20  C  0  1  N  N  N  -10.368  72.255  -72.911    7.978   1.770  -2.739  C45  J2B  20  
J2B  N12  N1   N  0  1  Y  N  N   -4.773  66.205  -78.064   -6.338   0.111  -0.735  N12  J2B  21  
J2B  N14  N2   N  0  1  Y  N  N   -3.893  67.216  -80.126   -6.352  -2.348  -0.317  N14  J2B  22  
J2B  N16  N3   N  0  1  Y  N  N   -2.797  65.763  -81.519   -8.030  -3.506  -1.405  N16  J2B  23  
J2B  N18  N4   N  0  1  N  N  N   -2.497  63.409  -81.048   -9.603  -2.451  -2.811  N18  J2B  24  
J2B  N20  N5   N  0  1  Y  N  N   -4.078  64.197  -78.463   -8.067   0.107  -2.068  N20  J2B  25  
J2B  N32  N6   N  0  1  Y  N  N  -10.113  68.576  -70.404    5.739  -1.360  -0.008  N32  J2B  26  
J2B  N34  N7   N  0  1  N  N  N  -10.473  67.787  -72.856    3.491  -2.485   0.196  N34  J2B  27  
J2B  N36  N8   N  0  1  N  N  N  -10.960  66.739  -75.105    1.492  -3.653   0.586  N36  J2B  28  
J2B  N37  N9   N  0  1  N  N  N  -11.597  65.530  -72.994    3.292  -3.970   1.999  N37  J2B  29  
J2B  N41  N10  N  0  1  Y  N  N  -10.991  66.854  -69.421    6.632  -2.323   1.730  N41  J2B  30  
J2B  O01  O1   O  0  1  N  N  N   -7.149  71.627  -71.687    4.744   2.526  -2.566  O01  J2B  31  
J2B  O04  O2   O  0  1  N  N  N   -7.030  69.462  -70.875    3.552   0.836  -1.080  O04  J2B  32  
J2B  O07  O3   O  0  1  N  N  N   -5.595  68.916  -73.097    0.971   0.923  -0.589  O07  J2B  33  
J2B  O10  O4   O  0  1  N  N  N   -4.632  67.830  -76.481   -5.414   1.977   0.382  O10  J2B  34  
J2B  O23  O5   O  0  1  N  N  N   -7.725  66.828  -77.566   -3.772  -0.893  -1.191  O23  J2B  35  
J2B  O25  O6   O  0  1  N  N  N   -7.320  69.473  -76.690   -2.884   2.194   0.570  O25  J2B  36  
J2B  O28  O7   O  0  1  N  N  N   -8.806  69.277  -78.768   -1.470   2.185   2.661  O28  J2B  37  
J2B  O29  O8   O  0  1  N  N  N   -9.727  68.553  -76.599   -2.935   4.203   2.266  O29  J2B  38  
J2B  O30  O9   O  0  1  N  N  N   -4.741  68.348  -70.762    2.625   0.238   1.190  O30  J2B  39  
J2B  O39  O10  O  0  1  N  N  N  -12.121  64.541  -71.020    5.010  -4.292   3.382  O39  J2B  40  
J2B  O43  O11  O  0  1  N  N  N  -10.490  70.773  -71.160    6.885  -0.168  -1.732  O43  J2B  41  
J2B  O46  O12  O  0  1  N  N  N  -10.207  71.371  -73.984    8.832   1.013  -3.600  O46  J2B  42  
J2B  P05  P1   P  0  1  N  N  S   -5.957  68.421  -71.568    2.436   1.148   0.038  P05  J2B  43  
J2B  P26  P2   P  0  1  N  N  N   -8.854  69.576  -77.288   -2.783   2.606   2.123  P26  J2B  44  
J2B  S06  S1   S  0  1  N  N  N   -6.840  66.496  -71.701    2.627   3.158   0.685  S06  J2B  45  
J2B  S27  S2   S  0  1  N  N  N   -9.659  71.517  -76.978   -4.332   1.649   3.210  S27  J2B  46  
J2B  H1   H1   H  0  1  N  N  N   -8.315  70.801  -73.232    6.217   2.597  -1.099  H1   J2B  47  
J2B  H2   H2   H  0  1  N  N  N   -8.519  68.905  -72.295    5.136   1.064   0.247  H2   J2B  48  
J2B  H3   H3   H  0  1  N  N  N   -6.337  67.187  -73.916   -0.308   2.019   0.608  H3   J2B  49  
J2B  H4   H4   H  0  1  N  N  N   -4.557  67.405  -74.018   -0.203   0.283   0.986  H4   J2B  50  
J2B  H5   H5   H  0  1  N  N  N   -5.508  69.619  -75.315   -1.462   1.485  -1.521  H5   J2B  51  
J2B  H6   H6   H  0  1  N  N  N   -4.948  68.100  -76.093   -1.357  -0.251  -1.143  H6   J2B  52  
J2B  H7   H7   H  0  1  N  N  N   -5.589  68.129  -78.208   -5.122   0.018   0.970  H7   J2B  53  
J2B  H8   H8   H  0  1  N  N  N   -3.056  67.788  -81.944   -6.627  -4.390  -0.167  H8   J2B  54  
J2B  H9   H9   H  0  1  N  N  N   -5.193  64.620  -76.687   -7.097   1.936  -1.635  H9   J2B  55  
J2B  H10  H10  H  0  1  N  N  N   -6.589  66.172  -76.026   -3.965   1.116  -1.630  H10  J2B  56  
J2B  H11  H11  H  0  1  N  N  N   -7.654  68.144  -75.061   -2.657   0.179   0.964  H11  J2B  57  
J2B  H12  H12  H  0  1  N  N  N   -9.147  70.150  -69.598    4.983  -1.012  -1.945  H12  J2B  58  
J2B  H13  H13  H  0  1  N  N  N  -10.202  68.470  -68.273    7.786  -0.955   0.598  H13  J2B  59  
J2B  H14  H14  H  0  1  N  N  N   -9.428  72.458  -71.001    6.224   0.748  -3.492  H14  J2B  60  
J2B  H15  H15  H  0  1  N  N  N  -11.439  72.407  -72.713    7.772   2.739  -3.192  H15  J2B  61  
J2B  H16  H16  H  0  1  N  N  N   -9.899  73.220  -73.151    8.470   1.916  -1.777  H16  J2B  62  
J2B  H17  H17  H  0  1  N  N  N   -2.027  63.445  -81.930   -9.943  -1.636  -3.213  H17  J2B  63  
J2B  H18  H18  H  0  1  N  N  N   -1.858  63.102  -80.343  -10.033  -3.300  -2.997  H18  J2B  64  
J2B  H19  H19  H  0  1  N  N  N  -10.072  68.580  -73.314    3.075  -2.066  -0.574  H19  J2B  65  
J2B  H20  H20  H  0  1  N  N  N  -11.328  65.985  -75.650    1.099  -3.222  -0.189  H20  J2B  66  
J2B  H21  H21  H  0  1  N  N  N  -10.556  67.533  -75.559    0.971  -4.283   1.107  H21  J2B  67  
J2B  H22  H22  H  0  1  N  N  N   -7.147  72.481  -72.104    5.144   3.182  -3.153  H22  J2B  68  
J2B  H23  H23  H  0  1  N  N  N   -3.779  68.065  -76.826   -5.498   2.557  -0.387  H23  J2B  69  
J2B  H24  H24  H  0  1  N  N  N   -8.020  67.663  -77.909   -3.724  -1.533  -0.468  H24  J2B  70  
J2B  H25  H25  H  0  1  N  N  N  -10.062  67.938  -77.241   -2.884   4.523   3.177  H25  J2B  71  
J2B  H26  H26  H  0  1  N  N  N  -10.619  71.734  -74.759    9.685   1.432  -3.776  H26  J2B  72  
J2B  H27  H27  H  0  1  N  N  N   -6.017  65.772  -71.001    2.435   3.859  -0.446  H27  J2B  73  
J2B  H28  H28  H  0  1  N  N  N   -9.890  71.911  -78.195   -5.445   2.229   2.725  H28  J2B  74  
#   #
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
J2B  C02  C03  SING  N  N   1  
J2B  C02  C44  SING  N  N   2  
J2B  C02  O01  SING  N  N   3  
J2B  C03  C31  SING  N  N   4  
J2B  C03  O04  SING  N  N   5  
J2B  C08  C09  SING  N  N   6  
J2B  C08  O07  SING  N  N   7  
J2B  C09  C24  SING  N  N   8  
J2B  C11  C22  SING  N  N   9  
J2B  C11  N12  SING  N  N  10  
J2B  C11  O10  SING  N  N  11  
J2B  C13  C19  DOUB  Y  N  12  
J2B  C13  N12  SING  Y  N  13  
J2B  C13  N14  SING  Y  N  14  
J2B  C15  N14  DOUB  Y  N  15  
J2B  C15  N16  SING  Y  N  16  
J2B  C17  C19  SING  Y  N  17  
J2B  C17  N16  DOUB  Y  N  18  
J2B  C17  N18  SING  N  N  19  
J2B  C19  N20  SING  Y  N  20  
J2B  C21  N12  SING  Y  N  21  
J2B  C21  N20  DOUB  Y  N  22  
J2B  C22  C24  SING  N  N  23  
J2B  C22  O23  SING  N  N  24  
J2B  C24  O25  SING  N  N  25  
J2B  C31  N32  SING  N  N  26  
J2B  C31  O43  SING  N  N  27  
J2B  C33  C40  DOUB  Y  N  28  
J2B  C33  N32  SING  Y  N  29  
J2B  C33  N34  SING  N  N  30  
J2B  C35  N34  SING  N  N  31  
J2B  C35  N36  SING  N  N  32  
J2B  C35  N37  DOUB  N  N  33  
J2B  C38  C40  SING  N  N  34  
J2B  C38  N37  SING  N  N  35  
J2B  C38  O39  DOUB  N  N  36  
J2B  C40  N41  SING  Y  N  37  
J2B  C42  N32  SING  Y  N  38  
J2B  C42  N41  DOUB  Y  N  39  
J2B  C44  C45  SING  N  N  40  
J2B  C44  O43  SING  N  N  41  
J2B  C45  O46  SING  N  N  42  
J2B  O04  P05  SING  N  N  43  
J2B  O07  P05  SING  N  N  44  
J2B  O25  P26  SING  N  N  45  
J2B  O28  P26  DOUB  N  N  46  
J2B  O29  P26  SING  N  N  47  
J2B  O30  P05  DOUB  N  N  48  
J2B  P05  S06  SING  N  N  49  
J2B  P26  S27  SING  N  N  50  
J2B  C02  H1   SING  N  N  51  
J2B  C03  H2   SING  N  N  52  
J2B  C08  H3   SING  N  N  53  
J2B  C08  H4   SING  N  N  54  
J2B  C09  H5   SING  N  N  55  
J2B  C09  H6   SING  N  N  56  
J2B  C11  H7   SING  N  N  57  
J2B  C15  H8   SING  N  N  58  
J2B  C21  H9   SING  N  N  59  
J2B  C22  H10  SING  N  N  60  
J2B  C24  H11  SING  N  N  61  
J2B  C31  H12  SING  N  N  62  
J2B  C42  H13  SING  N  N  63  
J2B  C44  H14  SING  N  N  64  
J2B  C45  H15  SING  N  N  65  
J2B  C45  H16  SING  N  N  66  
J2B  N18  H17  SING  N  N  67  
J2B  N18  H18  SING  N  N  68  
J2B  N34  H19  SING  N  N  69  
J2B  N36  H20  SING  N  N  70  
J2B  N36  H21  SING  N  N  71  
J2B  O01  H22  SING  N  N  72  
J2B  O10  H23  SING  N  N  73  
J2B  O23  H24  SING  N  N  74  
J2B  O29  H25  SING  N  N  75  
J2B  O46  H26  SING  N  N  76  
J2B  S06  H27  SING  N  N  77  
J2B  S27  H28  SING  N  N  78  
#   #
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
J2B  SMILES            ACDLabs               12.01  "C3(C(C(n2c1c(C(N=C(N1)N)=O)nc2)OC3CO)OP(OCCC(C(C(n5c4c(c(ncn4)N)nc5)O)O)OP(=O)(O)S)(=O)S)O"  
J2B  InChI             InChI                 1.03   "InChI=1S/C20H28N10O12P2S2/c21-14-9-15(24-4-23-14)29(5-25-9)18(35)12(33)7(41-43(36,37)45)1-2-39-44(38,46)42-13-11(32)8(3-31)40-19(13)30-6-26-10-16(30)27-20(22)28-17(10)34/h4-8,11-13,18-19,31-33,35H,1-3H2,(H,38,46)(H2,21,23,24)(H2,36,37,45)(H3,22,27,28,34)/t7-,8-,11-,12-,13-,18-,19-,44+/m1/s1"  
J2B  InChIKey          InChI                 1.03   WDMUGQSSXDUMIY-MHPWAGLLSA-N  
J2B  SMILES_CANONICAL  CACTVS                3.385  "NC1=NC(=O)c2ncn([C@@H]3O[C@H](CO)[C@@H](O)[C@H]3O[P@](S)(=O)OCC[C@@H](O[P](O)(S)=O)[C@@H](O)[C@@H](O)n4cnc5c(N)ncnc45)c2N1"  
J2B  SMILES            CACTVS                3.385  "NC1=NC(=O)c2ncn([CH]3O[CH](CO)[CH](O)[CH]3O[P](S)(=O)OCC[CH](O[P](O)(S)=O)[CH](O)[CH](O)n4cnc5c(N)ncnc45)c2N1"  
J2B  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.6  "c1nc(c2c(n1)n(cn2)[C@@H]([C@@H]([C@@H](CCO[P@@](=O)(O[C@@H]3[C@@H]([C@H](O[C@H]3n4cnc5c4NC(=NC5=O)N)CO)O)S)OP(=O)(O)S)O)O)N"  
J2B  SMILES            "OpenEye OEToolkits"  2.0.6  "c1nc(c2c(n1)n(cn2)C(C(C(CCOP(=O)(OC3C(C(OC3n4cnc5c4NC(=NC5=O)N)CO)O)S)OP(=O)(O)S)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
J2B  "SYSTEMATIC NAME"  ACDLabs               12.01  "O-[(1R,2R,3R)-5-{[(S)-{[(2R,3R,4R,5R)-2-(2-amino-6-oxo-3,6-dihydro-9H-purin-9-yl)-4-hydroxy-5-(hydroxymethyl)tetrahydrofuran-3-yl]oxy}(sulfanyl)phosphoryl]oxy}-1-(6-amino-9H-purin-9-yl)-1,2-dihydroxypentan-3-yl] dihydrogen (R)-phosphorothioate (non-preferred name)"  
J2B  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  2.0.6  "[(1~{R},2~{R},3~{R})-1-(6-aminopurin-9-yl)-5-[[(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]oxy-sulfanyl-phosphoryl]oxy-1,2-bis(oxidanyl)pentan-3-yl]oxy-sulfanyl-phosphinic acid"  
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
J2B  "Create component"  2018-08-30  RCSB  
J2B  "Modify synonyms"   2018-08-31  RCSB  
J2B  "Modify synonyms"   2018-09-04  RCSB  
J2B  "Initial release"   2019-02-06  RCSB  
J2B  "Modify synonyms"   2020-06-05  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     J2B
_pdbx_chem_comp_synonyms.name        "cleaved nonhydrolyzable phosphorothioate analog of 2'3' cyclic GMP-AMP"
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
