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 
# 
