data_V09 # _chem_comp.id V09 _chem_comp.name "(2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-[3-[6-azanyl-9-(phenylmethyl)purin-8-yl]prop-2-ynoxymethyl]oxolane-3,4-diol" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C25 H24 N10 O4" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2023-09-07 _chem_comp.pdbx_modified_date 2025-03-14 _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 528.523 _chem_comp.one_letter_code ? _chem_comp.three_letter_code V09 _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 8QG6 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBE _chem_comp.pdbx_pcm ? # 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 V09 C1 C2 C 0 1 Y N N N N N 22.478 11.298 13.109 8.083 1.511 0.421 C1 V09 1 V09 C2 C4 C 0 1 Y N N N N N 20.189 11.077 13.128 6.167 0.316 -0.006 C2 V09 2 V09 C3 C5 C 0 1 Y N N N N N 20.074 12.182 12.302 6.125 0.867 -1.299 C3 V09 3 V09 C4 C6 C 0 1 Y N N N N N 21.228 12.830 11.899 7.146 1.760 -1.673 C4 V09 4 V09 N1 N9 N 0 1 Y N N N N N 18.953 10.653 13.340 5.079 -0.516 0.092 N1 V09 5 V09 C5 C1* C 0 1 N N R N N N 15.959 8.414 8.887 -3.945 -0.789 0.107 C5 V09 6 V09 C6 C2* C 0 1 N N R N N N 16.032 9.593 7.893 -4.720 -2.096 -0.171 C6 V09 7 V09 C7 C3* C 0 1 N N S N N N 15.158 10.682 8.565 -3.614 -3.140 -0.440 C7 V09 8 V09 C8 C4* C 0 1 N N R N N N 14.694 10.021 9.866 -2.300 -2.340 -0.293 C8 V09 9 V09 C9 C5* C 0 1 N N N N N N 13.375 10.501 10.433 -1.270 -2.815 -1.320 C9 V09 10 V09 C10 C8 C 0 1 Y N N N N N 18.091 11.452 12.723 4.412 -0.459 -1.107 C10 V09 11 V09 C11 CAA C 0 1 Y N N N N N 17.687 6.082 11.788 2.112 0.973 3.773 C11 V09 12 V09 C12 CAB C 0 1 Y N N N N N 18.999 6.330 12.180 1.581 0.183 2.771 C12 V09 13 V09 C13 CAC C 0 1 Y N N N N N 19.300 7.440 12.960 2.419 -0.557 1.957 C13 V09 14 V09 C14 CAD C 0 1 Y N N N N N 18.276 8.295 13.340 3.787 -0.508 2.147 C14 V09 15 V09 C15 CAE C 0 1 Y N N N N N 16.966 8.047 12.950 4.318 0.282 3.149 C15 V09 16 V09 C16 CAF C 0 1 Y N N N N N 16.666 6.940 12.171 3.481 1.023 3.962 C16 V09 17 V09 C17 CAG C 0 1 N N N N N N 18.559 9.522 14.193 4.700 -1.315 1.260 C17 V09 18 V09 C18 CAR C 0 1 N N N N N N 16.675 11.291 12.739 3.217 -1.183 -1.421 C18 V09 19 V09 C19 CAS C 0 1 N N N N N N 15.471 11.157 12.752 2.238 -1.776 -1.679 C19 V09 20 V09 C20 CAT C 0 1 N N N N N N 14.011 11.039 12.751 1.009 -2.520 -2.002 C20 V09 21 V09 C21 CBC C 0 1 Y N N N N N 15.709 6.217 7.709 -4.471 0.887 -1.704 C21 V09 22 V09 C22 CBE C 0 1 Y N N N N N 17.664 5.337 7.793 -6.007 2.092 -0.760 C22 V09 23 V09 C23 CBF C 0 1 Y N N N N N 17.710 6.568 8.429 -5.629 1.100 0.160 C23 V09 24 V09 C24 CBH C 0 1 Y N N N N N 19.958 6.222 8.865 -7.152 1.939 1.663 C24 V09 25 V09 C25 CBJ C 0 1 Y N N N N N 18.815 4.568 7.716 -7.004 3.005 -0.378 C25 V09 26 V09 N2 N1 N 0 1 Y N N N N N 22.410 12.361 12.322 8.090 2.050 -0.784 N2 V09 27 V09 N3 N3 N 0 1 Y N N N N N 21.398 10.657 13.518 7.155 0.663 0.812 N3 V09 28 V09 N4 N6 N 0 1 N N N N N N 21.163 13.895 11.103 7.158 2.334 -2.932 N4 V09 29 V09 N5 N7 N 0 1 Y N N N N N 18.779 12.386 12.065 5.038 0.359 -1.920 N5 V09 30 V09 N6 NBB N 0 1 Y N N N N N 16.481 7.087 8.361 -4.655 0.359 -0.461 N6 V09 31 V09 N7 NBD N 0 1 Y N N N N N 16.424 5.150 7.362 -5.265 1.904 -1.878 N7 V09 32 V09 N8 NBG N 0 1 Y N N N N N 18.874 6.980 8.953 -6.222 1.061 1.349 N8 V09 33 V09 N9 NBI N 0 1 Y N N N N N 19.943 5.043 8.261 -7.540 2.888 0.832 N9 V09 34 V09 N10 NBK N 0 1 N N N N N N 18.796 3.382 7.111 -7.418 4.004 -1.242 N10 V09 35 V09 O1 O2* O 0 1 N N N N N N 17.365 9.982 7.640 -5.495 -2.471 0.970 O1 V09 36 V09 O2 O3* O 0 1 N N N N N N 15.962 11.822 8.863 -3.671 -4.191 0.526 O2 V09 37 V09 O3 O4* O 0 1 N N N N N N 14.772 8.612 9.622 -2.672 -0.969 -0.551 O3 V09 38 V09 O4 O5* O 0 1 N N N N N N 13.237 10.236 11.830 -0.027 -2.146 -1.092 O4 V09 39 V09 H1 H1 H 0 1 N N N N N N 23.448 10.944 13.427 8.873 1.771 1.111 H1 V09 40 V09 H2 H2 H 0 1 N N N N N N 16.739 8.689 9.612 -3.802 -0.654 1.179 H2 V09 41 V09 H3 H3 H 0 1 N N N N N N 15.543 9.287 6.957 -5.359 -1.982 -1.047 H3 V09 42 V09 H4 H4 H 0 1 N N N N N N 14.298 10.933 7.927 -3.706 -3.543 -1.449 H4 V09 43 V09 H5 H5 H 0 1 N N N N N N 15.458 10.263 10.619 -1.904 -2.444 0.717 H5 V09 44 V09 H6 H6 H 0 1 N N N N N N 13.299 11.587 10.273 -1.127 -3.891 -1.221 H6 V09 45 V09 H7 H7 H 0 1 N N N N N N 12.558 9.994 9.898 -1.626 -2.587 -2.325 H7 V09 46 V09 H8 H8 H 0 1 N N N N N N 17.462 5.217 11.182 1.459 1.555 4.406 H8 V09 47 V09 H9 H9 H 0 1 N N N N N N 19.787 5.657 11.877 0.512 0.144 2.623 H9 V09 48 V09 H10 H10 H 0 1 N N N N N N 20.317 7.634 13.266 2.004 -1.175 1.175 H10 V09 49 V09 H11 H11 H 0 1 N N N N N N 16.178 8.719 13.255 5.387 0.320 3.297 H11 V09 50 V09 H12 H12 H 0 1 N N N N N N 15.648 6.748 11.865 3.896 1.640 4.746 H12 V09 51 V09 H13 H13 H 0 1 N N N N N N 17.653 9.790 14.756 4.183 -2.216 0.931 H13 V09 52 V09 H14 H14 H 0 1 N N N N N N 19.374 9.296 14.896 5.595 -1.592 1.817 H14 V09 53 V09 H15 H15 H 0 1 N N N N N N 13.636 12.066 12.629 0.700 -2.286 -3.021 H15 V09 54 V09 H16 H16 H 0 1 N N N N N N 13.748 10.669 13.753 1.199 -3.590 -1.917 H16 V09 55 V09 H17 H17 H 0 1 N N N N N N 14.660 6.358 7.495 -3.767 0.519 -2.436 H17 V09 56 V09 H18 H18 H 0 1 N N N N N N 20.881 6.576 9.299 -7.614 1.879 2.638 H18 V09 57 V09 H19 H19 H 0 1 N N N N N N 22.087 14.227 10.914 6.458 2.122 -3.569 H19 V09 58 V09 H20 H20 H 0 1 N N N N N N 20.718 13.642 10.244 7.868 2.949 -3.178 H20 V09 59 V09 H21 H21 H 0 1 N N N N N N 19.708 2.973 7.150 -7.018 4.080 -2.123 H21 V09 60 V09 H22 H22 H 0 1 N N N N N N 18.142 2.783 7.572 -8.107 4.629 -0.967 H22 V09 61 V09 H23 H23 H 0 1 N N N N N N 17.832 9.264 7.230 -5.956 -3.315 0.872 H23 V09 62 V09 H24 H24 H 0 1 N N N N N N 15.426 12.489 9.275 -4.500 -4.688 0.518 H24 V09 63 # 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 V09 N10 C25 SING N N 1 V09 N7 C21 DOUB Y N 2 V09 N7 C22 SING Y N 3 V09 O1 C6 SING N N 4 V09 C21 N6 SING Y N 5 V09 C25 C22 DOUB Y N 6 V09 C25 N9 SING Y N 7 V09 C22 C23 SING Y N 8 V09 C6 C7 SING N N 9 V09 C6 C5 SING N N 10 V09 N9 C24 DOUB Y N 11 V09 N6 C23 SING Y N 12 V09 N6 C5 SING N N 13 V09 C23 N8 DOUB Y N 14 V09 C7 O2 SING N N 15 V09 C7 C8 SING N N 16 V09 C24 N8 SING Y N 17 V09 C5 O3 SING N N 18 V09 O3 C8 SING N N 19 V09 C8 C9 SING N N 20 V09 C9 O4 SING N N 21 V09 N4 C4 SING N N 22 V09 C11 C16 DOUB Y N 23 V09 C11 C12 SING Y N 24 V09 O4 C20 SING N N 25 V09 C4 C3 DOUB Y N 26 V09 C4 N2 SING Y N 27 V09 N5 C3 SING Y N 28 V09 N5 C10 DOUB Y N 29 V09 C16 C15 SING Y N 30 V09 C12 C13 DOUB Y N 31 V09 C3 C2 SING Y N 32 V09 N2 C1 DOUB Y N 33 V09 C10 C18 SING N N 34 V09 C10 N1 SING Y N 35 V09 C18 C19 TRIP N N 36 V09 C20 C19 SING N N 37 V09 C15 C14 DOUB Y N 38 V09 C13 C14 SING Y N 39 V09 C1 N3 SING Y N 40 V09 C2 N1 SING Y N 41 V09 C2 N3 DOUB Y N 42 V09 C14 C17 SING N N 43 V09 N1 C17 SING N N 44 V09 C1 H1 SING N N 45 V09 C5 H2 SING N N 46 V09 C6 H3 SING N N 47 V09 C7 H4 SING N N 48 V09 C8 H5 SING N N 49 V09 C9 H6 SING N N 50 V09 C9 H7 SING N N 51 V09 C11 H8 SING N N 52 V09 C12 H9 SING N N 53 V09 C13 H10 SING N N 54 V09 C15 H11 SING N N 55 V09 C16 H12 SING N N 56 V09 C17 H13 SING N N 57 V09 C17 H14 SING N N 58 V09 C20 H15 SING N N 59 V09 C20 H16 SING N N 60 V09 C21 H17 SING N N 61 V09 C24 H18 SING N N 62 V09 N4 H19 SING N N 63 V09 N4 H20 SING N N 64 V09 N10 H21 SING N N 65 V09 N10 H22 SING N N 66 V09 O1 H23 SING N N 67 V09 O2 H24 SING N N 68 # 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 V09 InChI InChI 1.06 "InChI=1S/C25H24N10O4/c26-21-17-23(30-11-28-21)35(13-32-17)25-20(37)19(36)15(39-25)10-38-8-4-7-16-33-18-22(27)29-12-31-24(18)34(16)9-14-5-2-1-3-6-14/h1-3,5-6,11-13,15,19-20,25,36-37H,8-10H2,(H2,26,28,30)(H2,27,29,31)/t15-,19-,20-,25-/m1/s1" V09 InChIKey InChI 1.06 XLLUWHJOLMVTMI-NQAQNOALSA-N V09 SMILES_CANONICAL CACTVS 3.385 "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](COCC#Cc4nc5c(N)ncnc5n4Cc6ccccc6)[C@@H](O)[C@H]3O" V09 SMILES CACTVS 3.385 "Nc1ncnc2n(cnc12)[CH]3O[CH](COCC#Cc4nc5c(N)ncnc5n4Cc6ccccc6)[CH](O)[CH]3O" V09 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1ccc(cc1)Cn2c(nc3c2ncnc3N)C#CCOC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O" V09 SMILES "OpenEye OEToolkits" 2.0.7 "c1ccc(cc1)Cn2c(nc3c2ncnc3N)C#CCOCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O" # _pdbx_chem_comp_identifier.comp_id V09 _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-[3-[6-azanyl-9-(phenylmethyl)purin-8-yl]prop-2-ynoxymethyl]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 V09 "Create component" 2023-09-07 PDBE V09 "Initial release" 2025-03-19 RCSB #