data_H9D
# 
_chem_comp.id                                    H9D 
_chem_comp.name                                  "(2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-[[2-[[9-[(2~{R},3~{R},4~{S},5~{S})-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]purin-6-yl]amino]ethylamino]methyl]oxolane-3,4-diol" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C22 H29 N11 O7" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-07-21 
_chem_comp.pdbx_modified_date                    2023-11-03 
_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                        559.535 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     H9D 
_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        8PW9 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBE 
# 
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.pdbx_backbone_atom_flag 
_chem_comp_atom.pdbx_n_terminal_atom_flag 
_chem_comp_atom.pdbx_c_terminal_atom_flag 
_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 
H9D N1  N1   N 0 1 Y N N N N N -39.132 40.335 26.666 -10.497 1.979  0.279  N1  H9D 1  
H9D N2  N3   N 0 1 Y N N N N N -40.480 38.485 27.151 -9.035  0.320  0.952  N2  H9D 2  
H9D C1  C4   C 0 1 Y N N N N N -41.015 38.501 25.907 -8.100  0.743  0.108  C1  H9D 3  
H9D C2  C5   C 0 1 Y N N N N N -40.617 39.471 24.988 -8.369  1.855  -0.709 C2  H9D 4  
H9D C3  C6   C 0 1 Y N N N N N -39.623 40.418 25.425 -9.625  2.473  -0.594 C3  H9D 5  
H9D C4  C8   C 0 1 Y N N N N N -42.148 38.174 24.045 -6.358  1.187  -1.169 C4  H9D 6  
H9D C5  C1*  C 0 1 N N R N N N -51.219 32.440 23.397 7.682   1.211  0.147  C5  H9D 7  
H9D C6  C2   C 0 1 Y N N N N N -39.556 39.391 27.516 -10.198 0.932  1.026  C6  H9D 8  
H9D C7  C2*  C 0 1 N N R N N N -51.464 32.365 24.909 8.403   0.388  1.237  C7  H9D 9  
H9D C8  C3*  C 0 1 N N S N N N -51.741 33.816 25.316 9.250   -0.629 0.442  C8  H9D 10 
H9D C9  C4*  C 0 1 N N S N N N -51.235 34.644 24.151 8.941   -0.301 -1.036 C9  H9D 11 
H9D C10 C5*  C 0 1 N N N N N N -51.958 35.935 23.858 10.199  -0.463 -1.892 C10 H9D 12 
H9D C11 CAH  C 0 1 Y N N N N N -47.117 33.278 25.171 3.736   1.575  2.256  C11 H9D 13 
H9D C12 CAJ  C 0 1 Y N N N N N -49.571 31.098 22.096 5.995   -0.155 -1.141 C12 H9D 14 
H9D C13 CAL  C 0 1 N N N N N N -42.863 31.366 23.495 -0.449  -1.285 -0.178 C13 H9D 15 
H9D C14 CAM  C 0 1 N N N N N N -44.083 30.468 23.620 0.527   -0.441 0.644  C14 H9D 16 
H9D C15 CAN  C 0 1 N N N N N N -42.418 33.569 24.383 -2.748  -2.030 -0.327 C15 H9D 17 
H9D C16 CAZ  C 0 1 Y N N N N N -46.333 31.824 23.530 2.911   0.194  0.601  C16 H9D 18 
H9D C17 CBB  C 0 1 Y N N N N N -47.687 31.635 23.073 4.193   0.153  0.026  C17 H9D 19 
H9D C18 CBD  C 0 1 Y N N N N N -48.718 32.312 23.724 5.224   0.875  0.650  C18 H9D 20 
H9D C19 CBF  C 0 1 N N S N N N -44.120 35.072 25.609 -5.125  -2.881 -0.370 C19 H9D 21 
H9D C20 CBH  C 0 1 N N R N N N -43.946 36.240 25.192 -6.455  -2.096 -0.339 C20 H9D 22 
H9D C21 CBJ  C 0 1 N N R N N N -42.629 34.412 25.593 -4.121  -1.947 0.343  C21 H9D 23 
H9D C22 CBL  C 0 1 N N R N N N -42.581 36.644 25.887 -6.098  -0.781 0.389  C22 H9D 24 
H9D N3  N6   N 0 1 N N N N N N -39.100 41.496 24.545 -9.948  3.572  -1.372 N3  H9D 25 
H9D N4  N7   N 0 1 Y N N N N N -41.337 39.237 23.847 -7.265  2.072  -1.463 N4  H9D 26 
H9D N5  N9   N 0 1 Y N N N N N -41.968 37.726 25.291 -6.825  0.344  -0.205 N5  H9D 27 
H9D N6  NAP  N 0 1 Y N N N N N -46.084 32.638 24.564 2.736   0.913  1.705  N6  H9D 28 
H9D N7  NAR  N 0 1 Y N N N N N -48.384 33.130 24.780 4.953   1.565  1.753  N7  H9D 29 
H9D N8  NAT  N 0 1 Y N N N N N -48.265 30.897 22.066 4.731   -0.453 -1.060 N8  H9D 30 
H9D N9  NAU  N 0 1 N N N N N N -42.799 32.224 24.735 -1.782  -1.229 0.437  N9  H9D 31 
H9D N10 NAV  N 0 1 N N N N N N -45.196 31.099 22.836 1.857   -0.497 0.030  N10 H9D 32 
H9D N11 NBN  N 0 1 Y N N N N N -49.895 31.967 23.096 6.347   0.662  -0.108 N11 H9D 33 
H9D O1  O2*  O 0 1 N N N N N N -52.476 31.415 25.248 9.244   1.232  2.027  O1  H9D 34 
H9D O2  O3*  O 0 1 N N N N N N -53.140 34.012 25.471 10.641  -0.445 0.715  O2  H9D 35 
H9D O3  O4*  O 0 1 N N N N N N -51.394 33.780 23.000 8.514   1.079  -1.026 O3  H9D 36 
H9D O4  O5*  O 0 1 N N N N N N -53.052 35.703 22.978 9.881   -0.197 -3.260 O4  H9D 37 
H9D O5  OAD  O 0 1 N N N N N N -44.580 35.076 27.046 -5.254  -4.113 0.341  O5  H9D 38 
H9D O6  OAF  O 0 1 N N N N N N -44.946 37.259 25.706 -7.447  -2.820 0.392  O6  H9D 39 
H9D O7  OAX  O 0 1 N N N N N N -41.777 35.429 25.623 -4.677  -0.623 0.190  O7  H9D 40 
H9D H1  H81  H 0 1 N N N N N N -42.828 37.756 23.317 -5.379  1.129  -1.622 H1  H9D 41 
H9D H2  H1*1 H 0 0 N N N N N N -51.960 31.800 22.896 7.610   2.257  0.445  H2  H9D 42 
H9D H3  H21  H 0 1 N N N N N N -39.147 39.357 28.515 -10.936 0.563  1.722  H3  H9D 43 
H9D H4  H2*1 H 0 0 N N N N N N -50.519 32.062 25.383 7.679   -0.126 1.869  H4  H9D 44 
H9D H5  H3*1 H 0 0 N N N N N N -51.188 34.066 26.234 8.947   -1.649 0.680  H5  H9D 45 
H9D H6  H4*1 H 0 0 N N N N N N -50.168 34.861 24.307 8.142   -0.943 -1.408 H6  H9D 46 
H9D H7  H5*2 H 0 0 N N N N N N -51.259 36.643 23.389 10.962  0.237  -1.553 H7  H9D 47 
H9D H8  H5*1 H 0 0 N N N N N N -52.335 36.361 24.800 10.573  -1.483 -1.798 H8  H9D 48 
H9D H9  HAH1 H 0 0 N N N N N N -46.904 33.933 26.003 3.549   2.151  3.151  H9  H9D 49 
H9D H10 HAJ1 H 0 0 N N N N N N -50.281 30.639 21.424 6.666   -0.504 -1.911 H10 H9D 50 
H9D H11 HAL2 H 0 0 N N N N N N -41.953 30.753 23.415 -0.501  -0.894 -1.194 H11 H9D 51 
H9D H12 HAL1 H 0 0 N N N N N N -42.956 32.003 22.603 -0.104  -2.318 -0.204 H12 H9D 52 
H9D H13 HAM2 H 0 0 N N N N N N -43.857 29.471 23.214 0.182   0.592  0.670  H13 H9D 53 
H9D H14 HAM1 H 0 0 N N N N N N -44.374 30.377 24.677 0.580   -0.832 1.660  H14 H9D 54 
H9D H15 HAN2 H 0 0 N N N N N N -41.360 33.596 24.084 -2.419  -3.068 -0.353 H15 H9D 55 
H9D H16 HAN1 H 0 0 N N N N N N -43.043 33.934 23.555 -2.816  -1.644 -1.344 H16 H9D 56 
H9D H17 HBF1 H 0 0 N N N N N N -44.789 34.454 24.992 -4.812  -3.062 -1.399 H17 H9D 57 
H9D H18 HBH1 H 0 0 N N N N N N -43.839 36.329 24.101 -6.800  -1.889 -1.352 H18 H9D 58 
H9D H19 HBJ1 H 0 0 N N N N N N -42.538 33.782 26.490 -4.044  -2.208 1.398  H19 H9D 59 
H9D H20 HBL1 H 0 0 N N N N N N -42.742 36.787 26.966 -6.328  -0.861 1.452  H20 H9D 60 
H9D H21 H62  H 0 1 N N N N N N -38.417 42.031 25.042 -10.818 3.990  -1.284 H21 H9D 61 
H9D H22 H61  H 0 1 N N N N N N -38.679 41.089 23.734 -9.303  3.923  -2.006 H22 H9D 62 
H9D H23 HAU1 H 0 0 N N N N N N -43.697 32.238 25.175 -1.748  -1.526 1.401  H23 H9D 63 
H9D H25 HAV1 H 0 0 N N N N N N -44.769 31.763 22.222 1.997   -1.018 -0.775 H25 H9D 64 
H9D H26 H2*2 H 0 0 N N N N N N -52.211 30.551 24.955 9.721   0.767  2.727  H26 H9D 65 
H9D H27 H3*2 H 0 0 N N N N N N -53.454 33.492 26.201 11.219  -1.058 0.241  H27 H9D 66 
H9D H28 H5*3 H 0 0 N N N N N N -53.497 36.524 22.803 10.634  -0.281 -3.862 H28 H9D 67 
H9D H29 HAD1 H 0 0 N N N N N N -44.706 34.182 27.341 -5.916  -4.713 -0.030 H29 H9D 68 
H9D H30 HAF1 H 0 0 N N N N N N -44.743 38.113 25.343 -7.665  -3.681 0.011  H30 H9D 69 
# 
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 
H9D C11 N6  DOUB Y N 1  
H9D C11 N7  SING Y N 2  
H9D C12 N8  DOUB Y N 3  
H9D C12 N11 SING Y N 4  
H9D C13 C14 SING N N 5  
H9D C13 N9  SING N N 6  
H9D C14 N10 SING N N 7  
H9D C15 N9  SING N N 8  
H9D C15 C21 SING N N 9  
H9D C16 N6  SING Y N 10 
H9D C16 N10 SING N N 11 
H9D C16 C17 DOUB Y N 12 
H9D N7  C18 DOUB Y N 13 
H9D N8  C17 SING Y N 14 
H9D O5  C19 SING N N 15 
H9D O6  C20 SING N N 16 
H9D O7  C21 SING N N 17 
H9D O7  C22 SING N N 18 
H9D C17 C18 SING Y N 19 
H9D C18 N11 SING Y N 20 
H9D C19 C20 SING N N 21 
H9D C19 C21 SING N N 22 
H9D C20 C22 SING N N 23 
H9D C22 N5  SING N N 24 
H9D N11 C5  SING N N 25 
H9D C10 O4  SING N N 26 
H9D C10 C9  SING N N 27 
H9D C9  O3  SING N N 28 
H9D C9  C8  SING N N 29 
H9D O3  C5  SING N N 30 
H9D C8  O2  SING N N 31 
H9D C8  C7  SING N N 32 
H9D C7  O1  SING N N 33 
H9D C7  C5  SING N N 34 
H9D N1  C6  DOUB Y N 35 
H9D N1  C3  SING Y N 36 
H9D C6  N2  SING Y N 37 
H9D N2  C1  DOUB Y N 38 
H9D C1  C2  SING Y N 39 
H9D C1  N5  SING Y N 40 
H9D C2  C3  DOUB Y N 41 
H9D C2  N4  SING Y N 42 
H9D C3  N3  SING N N 43 
H9D N4  C4  DOUB Y N 44 
H9D C4  N5  SING Y N 45 
H9D C4  H1  SING N N 46 
H9D C5  H2  SING N N 47 
H9D C6  H3  SING N N 48 
H9D C7  H4  SING N N 49 
H9D C8  H5  SING N N 50 
H9D C9  H6  SING N N 51 
H9D C10 H7  SING N N 52 
H9D C10 H8  SING N N 53 
H9D C11 H9  SING N N 54 
H9D C12 H10 SING N N 55 
H9D C13 H11 SING N N 56 
H9D C13 H12 SING N N 57 
H9D C14 H13 SING N N 58 
H9D C14 H14 SING N N 59 
H9D C15 H15 SING N N 60 
H9D C15 H16 SING N N 61 
H9D C19 H17 SING N N 62 
H9D C20 H18 SING N N 63 
H9D C21 H19 SING N N 64 
H9D C22 H20 SING N N 65 
H9D N3  H21 SING N N 66 
H9D N3  H22 SING N N 67 
H9D N9  H23 SING N N 68 
H9D N10 H25 SING N N 69 
H9D O1  H26 SING N N 70 
H9D O2  H27 SING N N 71 
H9D O4  H28 SING N N 72 
H9D O5  H29 SING N N 73 
H9D O6  H30 SING N N 74 
# 
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 
H9D InChI            InChI                1.06  "InChI=1S/C22H29N11O7/c23-17-11-19(28-5-26-17)32(7-30-11)21-15(37)13(35)9(39-21)3-24-1-2-25-18-12-20(29-6-27-18)33(8-31-12)22-16(38)14(36)10(4-34)40-22/h5-10,13-16,21-22,24,34-38H,1-4H2,(H2,23,26,28)(H,25,27,29)" 
H9D InChIKey         InChI                1.06  KXVQIOSAWUIUMH-UHFFFAOYSA-N                                                                                                                                                                                          
H9D SMILES_CANONICAL CACTVS               3.385 "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CNCCNc4ncnc5n(cnc45)[C@@H]6O[C@@H](CO)[C@@H](O)[C@H]6O)[C@@H](O)[C@H]3O"                                                                                                              
H9D SMILES           CACTVS               3.385 "Nc1ncnc2n(cnc12)[CH]3O[CH](CNCCNc4ncnc5n(cnc45)[CH]6O[CH](CO)[CH](O)[CH]6O)[CH](O)[CH]3O"                                                                                                                           
H9D SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CNCCNc4c5c(ncn4)n(cn5)[C@H]6[C@@H]([C@@H]([C@@H](O6)CO)O)O)O)O)N"                                                                                                    
H9D SMILES           "OpenEye OEToolkits" 2.0.7 "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CNCCNc4c5c(ncn4)n(cn5)C6C(C(C(O6)CO)O)O)O)O)N"                                                                                                                                         
# 
_pdbx_chem_comp_identifier.comp_id           H9D 
_pdbx_chem_comp_identifier.type              "SYSTEMATIC NAME" 
_pdbx_chem_comp_identifier.program           "OpenEye OEToolkits" 
_pdbx_chem_comp_identifier.program_version   2.0.7 
_pdbx_chem_comp_identifier.identifier        "(2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-[[2-[[9-[(2~{R},3~{R},4~{S},5~{S})-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]purin-6-yl]amino]ethylamino]methyl]oxolane-3,4-diol" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
H9D "Create component" 2023-07-21 PDBE 
H9D "Initial release"  2023-11-08 RCSB 
# 
