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 #