data_8JD
#

_chem_comp.id                                   8JD
_chem_comp.name                                 "[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (3R)-4-[(3-{[2-(ethylsulfanyl)ethyl]amino}-3-oxopropyl)amino]-3-hydroxy-2,2-dimethyl-4-oxobutyl dihydrogen diphosphate (non-preferred name)"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C23 H39 N7 O13 P2 S"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        "Ethyl Coenzyme A"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2017-02-09
_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                       715.607
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    8JD
_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       5UQR
_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
8JD  N6A  N1   N  0  1  N  N  N  42.769  -35.668  -33.255    8.481   6.421   2.177  N6A  8JD   1  
8JD  C6A  C1   C  0  1  Y  N  N  43.087  -35.621  -31.946    8.251   5.724   1.003  C6A  8JD   2  
8JD  N1A  N2   N  0  1  Y  N  N  44.043  -34.804  -31.456    8.413   6.310  -0.178  N1A  8JD   3  
8JD  C2A  C2   C  0  1  Y  N  N  44.336  -34.796  -30.138    8.196   5.653  -1.303  C2A  8JD   4  
8JD  N3A  N3   N  0  1  Y  N  N  43.723  -35.569  -29.206    7.812   4.395  -1.324  N3A  8JD   5  
8JD  C4A  C3   C  0  1  Y  N  N  42.735  -36.426  -29.589    7.624   3.725  -0.191  C4A  8JD   6  
8JD  C5A  C4   C  0  1  Y  N  N  42.370  -36.508  -31.011    7.847   4.378   1.033  C5A  8JD   7  
8JD  N9A  N4   N  0  1  Y  N  N  41.960  -37.320  -28.987    7.239   2.448   0.127  N9A  8JD   8  
8JD  N7A  N5   N  0  1  Y  N  N  41.390  -37.419  -31.137    7.594   3.481   2.016  N7A  8JD   9  
8JD  C8A  C5   C  0  1  Y  N  N  41.145  -37.902  -29.900    7.228   2.350   1.487  C8A  8JD  10  
8JD  C1M  C6   C  0  1  N  N  N  33.230  -34.874  -40.174  -14.824   5.677   0.745  C1M  8JD  11  
8JD  CP   C7   C  0  1  N  N  N  33.207  -34.112  -38.875  -13.826   4.625   1.233  CP   8JD  12  
8JD  O3X  O1   O  0  1  N  N  N  41.192  -37.131  -24.658    7.868  -1.347  -2.673  O3X  8JD  13  
8JD  S1   S1   S  0  1  N  N  N  33.672  -34.918  -37.502  -12.794   4.080  -0.155  S1   8JD  14  
8JD  N4   N6   N  0  1  N  N  N  36.672  -33.764  -35.185   -9.857   1.304   0.168  N4   8JD  15  
8JD  C5   C8   C  0  1  N  N  N  37.972  -33.524  -35.390   -8.931   0.671  -0.579  C5   8JD  16  
8JD  O5   O2   O  0  1  N  N  N  38.567  -33.875  -36.406   -8.832   0.919  -1.762  O5   8JD  17  
8JD  C6   C9   C  0  1  N  N  N  38.711  -32.814  -34.265   -8.017  -0.346   0.056  C6   8JD  18  
8JD  C7   C10  C  0  1  N  N  N  39.723  -33.747  -33.573   -7.068  -0.910  -1.003  C7   8JD  19  
8JD  N8   N7   N  0  1  N  N  N  39.184  -35.035  -33.157   -6.180  -1.898  -0.386  N8   8JD  20  
8JD  C9   C11  C  0  1  N  N  N  38.704  -35.260  -31.926   -5.253  -2.531  -1.132  C9   8JD  21  
8JD  O9   O3   O  0  1  N  N  N  38.650  -34.388  -31.057   -5.215  -2.353  -2.331  O9   8JD  22  
8JD  C13  C12  C  0  1  N  N  N  35.927  -35.634  -31.235   -2.965  -1.428   0.173  C13  8JD  23  
8JD  C11  C13  C  0  1  N  N  N  36.694  -36.792  -31.880   -2.879  -2.812  -0.475  C11  8JD  24  
8JD  C14  C14  C  0  1  N  N  N  36.447  -36.789  -33.383   -2.379  -2.671  -1.914  C14  8JD  25  
8JD  C12  C15  C  0  1  N  N  N  36.234  -38.126  -31.300   -1.907  -3.687   0.320  C12  8JD  26  
8JD  P1A  P1   P  0  1  N  N  N  38.687  -40.709  -28.380    3.553  -3.139   0.825  P1A  8JD  27  
8JD  O2A  O4   O  0  1  N  N  N  39.824  -41.046  -29.312    3.842  -4.458   0.220  O2A  8JD  28  
8JD  O1A  O5   O  0  1  N  N  N  37.925  -41.856  -27.757    4.030  -3.137   2.363  O1A  8JD  29  
8JD  O3A  O6   O  0  1  N  N  N  37.738  -39.633  -29.140    1.970  -2.851   0.753  O3A  8JD  30  
8JD  O5X  O7   O  0  1  N  N  N  39.294  -39.767  -27.246    4.344  -1.993   0.017  O5X  8JD  31  
8JD  C4X  C16  C  0  1  N  N  R  41.247  -39.124  -25.995    6.180  -0.790  -0.994  C4X  8JD  32  
8JD  O4X  O8   O  0  1  N  N  N  42.117  -38.878  -27.110    6.044   0.404  -0.193  O4X  8JD  33  
8JD  C1X  C17  C  0  1  N  N  R  41.945  -37.530  -27.525    6.900   1.383  -0.821  C1X  8JD  34  
8JD  C2X  C18  C  0  1  N  N  R  40.580  -37.065  -26.998    8.168   0.599  -1.224  C2X  8JD  35  
8JD  O2X  O9   O  0  1  N  N  N  40.491  -35.639  -26.831    8.666   1.063  -2.480  O2X  8JD  36  
8JD  C3X  C19  C  0  1  N  N  S  40.499  -37.822  -25.694    7.684  -0.864  -1.341  C3X  8JD  37  
8JD  C5X  C20  C  0  1  N  N  N  40.313  -40.255  -26.377    5.757  -2.023  -0.193  C5X  8JD  38  
8JD  P2A  P2   P  0  1  N  N  N  36.181  -39.260  -28.876    0.658  -3.730   1.066  P2A  8JD  39  
8JD  O4A  O10  O  0  1  N  N  N  35.327  -40.410  -29.324    0.863  -5.112   0.579  O4A  8JD  40  
8JD  O5A  O11  O  0  1  N  N  N  35.984  -38.669  -27.505    0.396  -3.754   2.655  O5A  8JD  41  
8JD  O6A  O12  O  0  1  N  N  N  36.039  -38.017  -29.893   -0.613  -3.080   0.322  O6A  8JD  42  
8JD  C10  C21  C  0  1  N  N  R  38.198  -36.648  -31.598   -4.264  -3.461  -0.477  C10  8JD  43  
8JD  O10  O13  O  0  1  N  N  N  38.921  -37.684  -32.295   -4.672  -3.719   0.868  O10  8JD  44  
8JD  C3   C22  C  0  1  N  N  N  35.886  -34.632  -36.055  -10.745   2.292  -0.450  C3   8JD  45  
8JD  C2   C23  C  0  1  N  N  N  35.075  -33.902  -37.091  -11.694   2.856   0.609  C2   8JD  46  
8JD  H1   H1   H  0  1  N  N  N  43.341  -35.022  -33.761    8.763   7.348   2.143  H1   8JD  47  
8JD  H2   H2   H  0  1  N  N  N  42.923  -36.593  -33.602    8.355   5.983   3.033  H2   8JD  48  
8JD  H3   H3   H  0  1  N  N  N  45.114  -34.127  -29.801    8.340   6.168  -2.242  H3   8JD  49  
8JD  H4   H4   H  0  1  N  N  N  40.401  -38.650  -29.670    6.967   1.462   2.042  H4   8JD  50  
8JD  H5   H5   H  0  1  N  N  N  32.899  -34.216  -40.991  -14.282   6.530   0.338  H5   8JD  51  
8JD  H6   H6   H  0  1  N  N  N  34.253  -35.223  -40.376  -15.457   5.245  -0.030  H6   8JD  52  
8JD  H7   H7   H  0  1  N  N  N  32.554  -35.739  -40.103  -15.444   6.004   1.579  H7   8JD  53  
8JD  H8   H8   H  0  1  N  N  N  33.875  -33.246  -38.990  -13.193   5.057   2.008  H8   8JD  54  
8JD  H9   H9   H  0  1  N  N  N  32.176  -33.762  -38.717  -14.368   3.771   1.641  H9   8JD  55  
8JD  H10  H10  H  0  1  N  N  N  41.127  -37.625  -23.849    8.794  -1.414  -2.943  H10  8JD  56  
8JD  H11  H11  H  0  1  N  N  N  36.221  -33.331  -34.404   -9.936   1.105   1.114  H11  8JD  57  
8JD  H12  H12  H  0  1  N  N  N  39.249  -31.950  -34.681   -7.437   0.131   0.846  H12  8JD  58  
8JD  H13  H13  H  0  1  N  N  N  37.979  -32.467  -33.521   -8.612  -1.155   0.479  H13  8JD  59  
8JD  H14  H14  H  0  1  N  N  N  40.551  -33.933  -34.273   -7.647  -1.387  -1.794  H14  8JD  60  
8JD  H15  H15  H  0  1  N  N  N  40.107  -33.233  -32.680   -6.473  -0.101  -1.426  H15  8JD  61  
8JD  H16  H16  H  0  1  N  N  N  39.172  -35.784  -33.819   -6.258  -2.097   0.561  H16  8JD  62  
8JD  H17  H17  H  0  1  N  N  N  36.105  -35.635  -30.149   -3.321  -1.528   1.198  H17  8JD  63  
8JD  H18  H18  H  0  1  N  N  N  36.274  -34.682  -31.662   -1.978  -0.965   0.175  H18  8JD  64  
8JD  H19  H19  H  0  1  N  N  N  34.851  -35.753  -31.430   -3.657  -0.804  -0.393  H19  8JD  65  
8JD  H20  H20  H  0  1  N  N  N  35.369  -36.892  -33.578   -3.028  -1.985  -2.459  H20  8JD  66  
8JD  H21  H21  H  0  1  N  N  N  36.808  -35.843  -33.812   -1.361  -2.281  -1.908  H21  8JD  67  
8JD  H22  H22  H  0  1  N  N  N  36.985  -37.630  -33.845   -2.391  -3.646  -2.400  H22  8JD  68  
8JD  H23  H23  H  0  1  N  N  N  35.286  -38.420  -31.775   -2.263  -3.787   1.345  H23  8JD  69  
8JD  H24  H24  H  0  1  N  N  N  36.998  -38.891  -31.501   -1.845  -4.672  -0.141  H24  8JD  70  
8JD  H25  H25  H  0  1  N  N  N  38.290  -42.680  -28.057    3.870  -2.302   2.823  H25  8JD  71  
8JD  H26  H26  H  0  1  N  N  N  41.830  -39.417  -25.110    5.585  -0.706  -1.903  H26  8JD  72  
8JD  H27  H27  H  0  1  N  N  N  42.722  -36.900  -27.067    6.414   1.801  -1.702  H27  8JD  73  
8JD  H28  H28  H  0  1  N  N  N  39.792  -37.422  -27.677    8.934   0.689  -0.454  H28  8JD  74  
8JD  H29  H29  H  0  1  N  N  N  39.629  -35.411  -26.504    9.462   0.604  -2.782  H29  8JD  75  
8JD  H30  H30  H  0  1  N  N  N  39.453  -38.031  -25.426    8.210  -1.498  -0.627  H30  8JD  76  
8JD  H31  H31  H  0  1  N  N  N  39.851  -40.670  -25.469    6.267  -2.023   0.770  H31  8JD  77  
8JD  H32  H32  H  0  1  N  N  N  40.884  -41.043  -26.890    6.023  -2.924  -0.746  H32  8JD  78  
8JD  H33  H33  H  0  1  N  N  N  35.288  -39.134  -27.056    0.253  -2.881   3.043  H33  8JD  79  
8JD  H34  H34  H  0  1  N  N  N  38.338  -36.800  -30.518   -4.225  -4.398  -1.031  H34  8JD  80  
8JD  H35  H35  H  0  1  N  N  N  38.567  -38.533  -32.057   -4.729  -2.927   1.420  H35  8JD  81  
8JD  H36  H36  H  0  1  N  N  N  35.197  -35.216  -35.427  -10.150   3.101  -0.873  H36  8JD  82  
8JD  H37  H37  H  0  1  N  N  N  36.575  -35.314  -36.575  -11.325   1.815  -1.241  H37  8JD  83  
8JD  H38  H38  H  0  1  N  N  N  35.686  -33.727  -37.989  -11.115   3.332   1.400  H38  8JD  84  
8JD  H39  H39  H  0  1  N  N  N  34.733  -32.938  -36.687  -12.290   2.047   1.032  H39  8JD  85  
#   #
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
8JD  C1M  CP   SING  N  N   1  
8JD  CP   S1   SING  N  N   2  
8JD  S1   C2   SING  N  N   3  
8JD  C2   C3   SING  N  N   4  
8JD  O5   C5   DOUB  N  N   5  
8JD  C3   N4   SING  N  N   6  
8JD  C5   N4   SING  N  N   7  
8JD  C5   C6   SING  N  N   8  
8JD  C6   C7   SING  N  N   9  
8JD  C7   N8   SING  N  N  10  
8JD  C14  C11  SING  N  N  11  
8JD  N6A  C6A  SING  N  N  12  
8JD  N8   C9   SING  N  N  13  
8JD  O10  C10  SING  N  N  14  
8JD  C6A  N1A  DOUB  Y  N  15  
8JD  C6A  C5A  SING  Y  N  16  
8JD  C9   C10  SING  N  N  17  
8JD  C9   O9   DOUB  N  N  18  
8JD  C11  C10  SING  N  N  19  
8JD  C11  C12  SING  N  N  20  
8JD  C11  C13  SING  N  N  21  
8JD  N1A  C2A  SING  Y  N  22  
8JD  C12  O6A  SING  N  N  23  
8JD  N7A  C5A  SING  Y  N  24  
8JD  N7A  C8A  DOUB  Y  N  25  
8JD  C5A  C4A  DOUB  Y  N  26  
8JD  C2A  N3A  DOUB  Y  N  27  
8JD  C8A  N9A  SING  Y  N  28  
8JD  O6A  P2A  SING  N  N  29  
8JD  C4A  N3A  SING  Y  N  30  
8JD  C4A  N9A  SING  Y  N  31  
8JD  O4A  P2A  DOUB  N  N  32  
8JD  O2A  P1A  DOUB  N  N  33  
8JD  O3A  P2A  SING  N  N  34  
8JD  O3A  P1A  SING  N  N  35  
8JD  N9A  C1X  SING  N  N  36  
8JD  P2A  O5A  SING  N  N  37  
8JD  P1A  O1A  SING  N  N  38  
8JD  P1A  O5X  SING  N  N  39  
8JD  C1X  O4X  SING  N  N  40  
8JD  C1X  C2X  SING  N  N  41  
8JD  O5X  C5X  SING  N  N  42  
8JD  O4X  C4X  SING  N  N  43  
8JD  C2X  O2X  SING  N  N  44  
8JD  C2X  C3X  SING  N  N  45  
8JD  C5X  C4X  SING  N  N  46  
8JD  C4X  C3X  SING  N  N  47  
8JD  C3X  O3X  SING  N  N  48  
8JD  N6A  H1   SING  N  N  49  
8JD  N6A  H2   SING  N  N  50  
8JD  C2A  H3   SING  N  N  51  
8JD  C8A  H4   SING  N  N  52  
8JD  C1M  H5   SING  N  N  53  
8JD  C1M  H6   SING  N  N  54  
8JD  C1M  H7   SING  N  N  55  
8JD  CP   H8   SING  N  N  56  
8JD  CP   H9   SING  N  N  57  
8JD  O3X  H10  SING  N  N  58  
8JD  N4   H11  SING  N  N  59  
8JD  C6   H12  SING  N  N  60  
8JD  C6   H13  SING  N  N  61  
8JD  C7   H14  SING  N  N  62  
8JD  C7   H15  SING  N  N  63  
8JD  N8   H16  SING  N  N  64  
8JD  C13  H17  SING  N  N  65  
8JD  C13  H18  SING  N  N  66  
8JD  C13  H19  SING  N  N  67  
8JD  C14  H20  SING  N  N  68  
8JD  C14  H21  SING  N  N  69  
8JD  C14  H22  SING  N  N  70  
8JD  C12  H23  SING  N  N  71  
8JD  C12  H24  SING  N  N  72  
8JD  O1A  H25  SING  N  N  73  
8JD  C4X  H26  SING  N  N  74  
8JD  C1X  H27  SING  N  N  75  
8JD  C2X  H28  SING  N  N  76  
8JD  O2X  H29  SING  N  N  77  
8JD  C3X  H30  SING  N  N  78  
8JD  C5X  H31  SING  N  N  79  
8JD  C5X  H32  SING  N  N  80  
8JD  O5A  H33  SING  N  N  81  
8JD  C10  H34  SING  N  N  82  
8JD  O10  H35  SING  N  N  83  
8JD  C3   H36  SING  N  N  84  
8JD  C3   H37  SING  N  N  85  
8JD  C2   H38  SING  N  N  86  
8JD  C2   H39  SING  N  N  87  
#   #
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
8JD  SMILES            ACDLabs               12.01  "Nc2ncnc3n(C1OC(C(O)C1O)COP(O)(=O)OP(O)(=O)OCC(C)(C(C(NCCC(NCCSCC)=O)=O)O)C)cnc23"  
8JD  InChI             InChI                 1.03   "InChI=1S/C23H39N7O13P2S/c1-4-46-8-7-25-14(31)5-6-26-21(35)18(34)23(2,3)10-41-45(38,39)43-44(36,37)40-9-13-16(32)17(33)22(42-13)30-12-29-15-19(24)27-11-28-20(15)30/h11-13,16-18,22,32-34H,4-10H2,1-3H3,(H,25,31)(H,26,35)(H,36,37)(H,38,39)(H2,24,27,28)/t13-,16-,17-,18+,22-/m1/s1"  
8JD  InChIKey          InChI                 1.03   ZYQGAGMIMDQCKA-ZSJPKINUSA-N  
8JD  SMILES_CANONICAL  CACTVS                3.385  "CCSCCNC(=O)CCNC(=O)[C@H](O)C(C)(C)CO[P](O)(=O)O[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23"  
8JD  SMILES            CACTVS                3.385  "CCSCCNC(=O)CCNC(=O)[CH](O)C(C)(C)CO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23"  
8JD  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.6  "CCSCCNC(=O)CCNC(=O)[C@@H](C(C)(C)COP(=O)(O)OP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O)O"  
8JD  SMILES            "OpenEye OEToolkits"  2.0.6  "CCSCCNC(=O)CCNC(=O)C(C(C)(C)COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)O)O"  
#   #
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
8JD  "SYSTEMATIC NAME"  ACDLabs               12.01  "[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (3R)-4-[(3-{[2-(ethylsulfanyl)ethyl]amino}-3-oxopropyl)amino]-3-hydroxy-2,2-dimethyl-4-oxobutyl dihydrogen diphosphate (non-preferred name)"  
8JD  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  2.0.6  "[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(3~{R})-4-[[3-(2-ethylsulfanylethylamino)-3-oxidanylidene-propyl]amino]-2,2-dimethyl-3-oxidanyl-4-oxidanylidene-butyl] 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
8JD  "Create component"    2017-02-09  RCSB  
8JD  "Other modification"  2018-02-27  RCSB  
8JD  "Initial release"     2018-03-14  RCSB  
8JD  "Modify synonyms"     2021-03-01  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     8JD
_pdbx_chem_comp_synonyms.name        "Ethyl Coenzyme A"
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
