data_ZD4
#

_chem_comp.id                                   ZD4
_chem_comp.name                                 "2-chloroadenosine 5'-(trihydrogen diphosphate)"
_chem_comp.type                                 non-polymer
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C10 H14 Cl N5 O10 P2"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2021-04-14
_chem_comp.pdbx_modified_date                   2021-12-03
_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                       461.646
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    ZD4
_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       7MGT
_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
ZD4  "C1'"   C1   C   0  1  N  N  R  38.324  35.925  21.266   1.656   0.875   0.249  "C1'"   ZD4   1  
ZD4  C2      C2   C   0  1  Y  N  N  34.257  35.625  19.843   5.927  -0.463   0.597  C2      ZD4   2  
ZD4  "C2'"   C3   C   0  1  N  N  R  39.670  35.737  21.883   1.797   2.006  -0.802  "C2'"   ZD4   3  
ZD4  "C3'"   C4   C   0  1  N  N  S  40.486  34.994  20.898   0.540   2.865  -0.524  "C3'"   ZD4   4  
ZD4  C4      C5   C   0  1  Y  N  N  36.193  34.929  20.803   3.709  -0.585   0.003  C4      ZD4   5  
ZD4  "C4'"   C6   C   0  1  N  N  R  40.021  35.539  19.575  -0.416   1.908   0.214  "C4'"   ZD4   6  
ZD4  C5      C7   C   0  1  Y  N  N  35.618  33.616  20.954   3.945  -1.843  -0.576  C5      ZD4   7  
ZD4  "C5'"   C8   C   0  1  N  N  N  39.971  34.531  18.483  -1.728   1.781  -0.563  "C5'"   ZD4   8  
ZD4  C6      C9   C   0  1  Y  N  N  34.310  33.449  20.507   5.249  -2.363  -0.527  C6      ZD4   9  
ZD4  C8      C10  C   0  1  Y  N  N  37.719  33.608  21.749   1.842  -1.389  -0.851  C8      ZD4  10  
ZD4  N1      N1   N   0  1  Y  N  N  33.668  34.462  19.953   6.197  -1.643   0.065  N1      ZD4  11  
ZD4  N3      N2   N   0  1  Y  N  N  35.446  35.872  20.274   4.720   0.064   0.573  N3      ZD4  12  
ZD4  N6      N3   N   0  1  N  N  N  33.689  32.164  20.611   5.541  -3.597  -1.081  N6      ZD4  13  
ZD4  N7      N4   N   0  1  Y  N  N  36.641  32.813  21.591   2.764  -2.278  -1.079  N7      ZD4  14  
ZD4  N9      N5   N   0  1  Y  N  N  37.413  34.830  21.317   2.375  -0.325  -0.185  N9      ZD4  15  
ZD4  O1A     O1   O   0  1  N  N  N  39.539  35.317  14.795  -4.049   0.016  -1.688  O1A     ZD4  16  
ZD4  O1B     O2   O   0  1  N  N  N  43.767  33.827  14.859  -6.029  -2.460   1.793  O1B     ZD4  17  
ZD4  "O2'"   O3   O   0  1  N  N  N  40.300  37.023  22.060   2.990   2.761  -0.581  "O2'"   ZD4  18  
ZD4  O2A     O4   O   0  1  N  N  N  39.112  33.143  15.862  -4.998   1.979  -0.417  O2A     ZD4  19  
ZD4  O2B     O5   O   0  1  N  N  N  43.322  35.448  16.550  -7.447  -0.602   0.589  O2B     ZD4  20  
ZD4  "O3'"   O6   O   0  1  N  N  N  41.888  35.231  21.067   0.870   3.981   0.305  "O3'"   ZD4  21  
ZD4  O3A     O7   O   0  1  N  N  N  41.434  33.936  15.821  -4.827  -0.406   0.676  O3A     ZD4  22  
ZD4  O3B     O8   O   0  1  N  N  N  42.417  35.816  14.366  -5.967  -2.177  -0.715  O3B     ZD4  23  
ZD4  "O4'"   O9   O   0  1  N  N  N  38.657  36.085  19.820   0.234   0.628   0.289  "O4'"   ZD4  24  
ZD4  "O5'"   O10  O   0  1  N  N  N  39.723  35.200  17.270  -2.644   0.972   0.178  "O5'"   ZD4  25  
ZD4  PA      P1   P   0  1  N  N  N  39.911  34.382  15.869  -4.128   0.627  -0.342  PA      ZD4  26  
ZD4  PB      P2   P   0  1  N  N  N  42.761  34.786  15.356  -6.065  -1.428   0.558  PB      ZD4  27  
ZD4  CL6     CL1  CL  0  0  N  N  N  33.416  36.992  19.132   7.211   0.422   1.361  CL6     ZD4  28  
ZD4  "H1'"   H1   H   0  1  N  N  N  37.858  36.845  21.650   2.018   1.207   1.222  "H1'"   ZD4  29  
ZD4  "H2'"   H2   H   0  1  N  N  N  39.594  35.186  22.832   1.777   1.601  -1.814  "H2'"   ZD4  30  
ZD4  "H3'"   H3   H   0  1  N  N  N  40.262  33.919  20.956   0.095   3.204  -1.460  "H3'"   ZD4  31  
ZD4  "H4'"   H4   H   0  1  N  N  N  40.688  36.361  19.275  -0.613   2.283   1.219  "H4'"   ZD4  32  
ZD4  "H5'2"  H5   H   0  0  N  N  N  39.165  33.809  18.681  -2.158   2.771  -0.715  "H5'2"  ZD4  33  
ZD4  "H5'1"  H6   H   0  0  N  N  N  40.932  34.000  18.424  -1.534   1.317  -1.530  "H5'1"  ZD4  34  
ZD4  H8      H7   H   0  1  N  N  N  38.671  33.304  22.158   0.807  -1.480  -1.145  H8      ZD4  35  
ZD4  HN61    H8   H   0  0  N  N  N  32.771  32.204  20.217   4.841  -4.113  -1.511  HN61    ZD4  36  
ZD4  HN62    H9   H   0  0  N  N  N  34.235  31.489  20.115   6.445  -3.945  -1.041  HN62    ZD4  37  
ZD4  H1      H10  H   0  1  N  N  N  44.013  34.057  13.971  -6.748  -3.107   1.786  H1      ZD4  38  
ZD4  "HO2'"  H11  H   0  0  N  N  N  39.805  37.535  22.689   3.123   3.480  -1.213  "HO2'"  ZD4  39  
ZD4  H2      H12  H   0  1  N  N  N  38.486  33.173  15.148  -5.092   2.434   0.431  H2      ZD4  40  
ZD4  H3      H13  H   0  1  N  N  N  43.336  36.388  16.414  -7.579  -0.086   1.396  H3      ZD4  41  
ZD4  H4      H14  H   0  1  N  N  N  42.170  34.883  21.905   1.514   4.586  -0.088  H4      ZD4  42  
#   #
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
ZD4  O3B    PB      DOUB  N  N   1  
ZD4  O1A    PA      DOUB  N  N   2  
ZD4  O1B    PB      SING  N  N   3  
ZD4  PB     O3A     SING  N  N   4  
ZD4  PB     O2B     SING  N  N   5  
ZD4  O3A    PA      SING  N  N   6  
ZD4  O2A    PA      SING  N  N   7  
ZD4  PA     "O5'"   SING  N  N   8  
ZD4  "O5'"  "C5'"   SING  N  N   9  
ZD4  "C5'"  "C4'"   SING  N  N  10  
ZD4  CL6    C2      SING  N  N  11  
ZD4  "C4'"  "O4'"   SING  N  N  12  
ZD4  "C4'"  "C3'"   SING  N  N  13  
ZD4  "O4'"  "C1'"   SING  N  N  14  
ZD4  C2     N1      DOUB  Y  N  15  
ZD4  C2     N3      SING  Y  N  16  
ZD4  N1     C6      SING  Y  N  17  
ZD4  N3     C4      DOUB  Y  N  18  
ZD4  C6     N6      SING  N  N  19  
ZD4  C6     C5      DOUB  Y  N  20  
ZD4  C4     C5      SING  Y  N  21  
ZD4  C4     N9      SING  Y  N  22  
ZD4  "C3'"  "O3'"   SING  N  N  23  
ZD4  "C3'"  "C2'"   SING  N  N  24  
ZD4  C5     N7      SING  Y  N  25  
ZD4  "C1'"  N9      SING  N  N  26  
ZD4  "C1'"  "C2'"   SING  N  N  27  
ZD4  N9     C8      SING  Y  N  28  
ZD4  N7     C8      DOUB  Y  N  29  
ZD4  "C2'"  "O2'"   SING  N  N  30  
ZD4  "C1'"  "H1'"   SING  N  N  31  
ZD4  "C2'"  "H2'"   SING  N  N  32  
ZD4  "C3'"  "H3'"   SING  N  N  33  
ZD4  "C4'"  "H4'"   SING  N  N  34  
ZD4  "C5'"  "H5'2"  SING  N  N  35  
ZD4  "C5'"  "H5'1"  SING  N  N  36  
ZD4  C8     H8      SING  N  N  37  
ZD4  N6     HN61    SING  N  N  38  
ZD4  N6     HN62    SING  N  N  39  
ZD4  O1B    H1      SING  N  N  40  
ZD4  "O2'"  "HO2'"  SING  N  N  41  
ZD4  O2A    H2      SING  N  N  42  
ZD4  O2B    H3      SING  N  N  43  
ZD4  "O3'"  H4      SING  N  N  44  
#   #
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
ZD4  SMILES            ACDLabs               12.01  "O=P(O)(O)OP(=O)(O)OCC1OC(n2cnc3c(N)nc(Cl)nc32)C(O)C1O"  
ZD4  InChI             InChI                 1.03   "InChI=1S/C10H14ClN5O10P2/c11-10-14-7(12)4-8(15-10)16(2-13-4)9-6(18)5(17)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,17-18H,1H2,(H,22,23)(H2,12,14,15)(H2,19,20,21)/t3-,5-,6-,9-/m1/s1"  
ZD4  InChIKey          InChI                 1.03   POWNGKCXGCOKLX-UUOKFMHZSA-N  
ZD4  SMILES_CANONICAL  CACTVS                3.385  "Nc1nc(Cl)nc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O"  
ZD4  SMILES            CACTVS                3.385  "Nc1nc(Cl)nc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O"  
ZD4  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "c1nc2c(nc(nc2n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)O)O)O)Cl)N"  
ZD4  SMILES            "OpenEye OEToolkits"  2.0.7  "c1nc2c(nc(nc2n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)Cl)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
ZD4  "SYSTEMATIC NAME"  ACDLabs               12.01  "2-chloroadenosine 5'-(trihydrogen diphosphate)"  
ZD4  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  2.0.7  "[(2~{R},3~{S},4~{R},5~{R})-5-(6-azanyl-2-chloranyl-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl phosphono 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
ZD4  "Create component"  2021-04-14  RCSB  
ZD4  "Initial release"   2021-12-08  RCSB  
##
