data_V2Y
# 
_chem_comp.id                                    V2Y 
_chem_comp.name                                  "~{N}-[[(2~{R},3~{S},4~{R},5~{R})-5-[8-[3-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy]prop-1-ynyl]-6-azanyl-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl]-2-(2-azanyl-2-oxidanylidene-ethyl)benzamide" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C32 H34 N12 O9" 
_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                        730.687 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     V2Y 
_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        8QG2 
_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 
V2Y C1  C4  C 0 1 Y N N N N N 20.533 11.226 13.051 3.723   -4.667 -0.045 C1  V2Y 1  
V2Y C2  C5  C 0 1 Y N N N N N 20.289 12.398 12.364 3.421   -5.163 1.237  C2  V2Y 2  
V2Y C3  C6  C 0 1 Y N N N N N 21.371 13.136 11.882 3.928   -6.426 1.596  C3  V2Y 3  
V2Y C4  C8  C 0 1 Y N N N N N 18.415 11.514 12.844 2.471   -3.215 1.058  C4  V2Y 4  
V2Y N1  N1  N 0 1 Y N N N N N 22.587 12.691 12.180 4.667   -7.086 0.710  N1  V2Y 5  
V2Y N2  N3  N 0 1 Y N N N N N 21.773 10.833 13.309 4.470   -5.402 -0.861 N2  V2Y 6  
V2Y C5  C1* C 0 1 N N R N N N 16.785 8.414  8.980  -4.882  0.756  -0.200 C5  V2Y 7  
V2Y C6  C2  C 0 1 Y N N N N N 22.771 11.575 12.873 4.924   -6.578 -0.481 C6  V2Y 8  
V2Y C7  C2* C 0 1 N N R N N N 16.608 9.567  7.968  -5.010  2.267  0.094  C7  V2Y 9  
V2Y C8  C3* C 0 1 N N S N N N 15.356 10.278 8.520  -3.562  2.717  0.387  C8  V2Y 10 
V2Y C9  C4* C 0 1 N N R N N N 15.348 9.879  9.996  -2.729  1.425  0.235  C9  V2Y 11 
V2Y C10 C5* C 0 1 N N N N N N 14.009 10.052 10.698 -1.608  1.388  1.275  C10 V2Y 12 
V2Y C11 CAB C 0 1 N N N N N N 13.078 6.048  12.192 2.611   5.475  1.328  C11 V2Y 13 
V2Y C12 CAD C 0 1 N N N N N N 13.701 6.125  10.772 3.366   5.820  0.071  C12 V2Y 14 
V2Y C13 CAE C 0 1 Y N N N N N 14.742 4.998  10.550 4.697   5.113  0.074  C13 V2Y 15 
V2Y C14 CAF C 0 1 Y N N N N N 14.452 4.151  9.474  5.841   5.795  0.433  C14 V2Y 16 
V2Y C15 CAG C 0 1 Y N N N N N 15.253 3.052  9.163  7.064   5.148  0.437  C15 V2Y 17 
V2Y C16 CAH C 0 1 Y N N N N N 16.364 2.771  9.948  7.148   3.813  0.082  C16 V2Y 18 
V2Y C17 CAI C 0 1 Y N N N N N 16.627 3.582  11.054 6.011   3.119  -0.279 C17 V2Y 19 
V2Y C18 CAJ C 0 1 Y N N N N N 15.780 4.640  11.427 4.774   3.765  -0.279 C18 V2Y 20 
V2Y C19 CAK C 0 1 N N N N N N 16.281 5.471  12.616 3.551   3.026  -0.658 C19 V2Y 21 
V2Y C20 CAN C 0 1 N N N N N N 16.484 7.613  13.819 2.429   1.029  -1.488 C20 V2Y 22 
V2Y C21 CAO C 0 1 N N R N N N 17.880 7.394  14.378 2.809   -0.374 -1.968 C21 V2Y 23 
V2Y C22 CAQ C 0 1 N N R N N N 19.164 9.409  14.193 3.136   -2.543 -1.292 C22 V2Y 24 
V2Y C23 CAR C 0 1 N N R N N N 18.243 9.535  15.412 1.780   -2.581 -2.032 C23 V2Y 25 
V2Y C24 CAT C 0 1 N N S N N N 18.241 8.067  15.736 1.560   -1.121 -2.487 C24 V2Y 26 
V2Y C25 CBF C 0 1 N N N N N N 17.026 11.368 12.883 1.710   -2.045 1.377  C25 V2Y 27 
V2Y C26 CBG C 0 1 N N N N N N 15.851 11.200 12.955 1.086   -1.086 1.638  C26 V2Y 28 
V2Y C27 CBH C 0 1 N N N N N N 14.455 10.830 13.112 0.303   0.117  1.966  C27 V2Y 29 
V2Y C28 CBS C 0 1 Y N N N N N 15.920 6.664  7.540  -6.111  -0.542 1.581  C28 V2Y 30 
V2Y C29 CBU C 0 1 Y N N N N N 17.541 5.237  7.610  -8.008  -0.941 0.608  C29 V2Y 31 
V2Y C30 CBV C 0 1 Y N N N N N 17.889 6.304  8.422  -7.222  -0.204 -0.294 C30 V2Y 32 
V2Y C31 CBX C 0 1 Y N N N N N 19.890 5.303  8.924  -8.940  -0.273 -1.820 C31 V2Y 33 
V2Y C32 CBZ C 0 1 Y N N N N N 18.442 4.195  7.490  -9.300  -1.321 0.205  C32 V2Y 34 
V2Y N3  N6  N 0 1 N N N N N N 21.184 14.258 11.140 3.665   -6.966 2.842  N3  V2Y 35 
V2Y N4  N7  N 0 1 Y N N N N N 18.968 12.554 12.226 2.658   -4.238 1.859  N4  V2Y 36 
V2Y N5  N9  N 0 1 Y N N N N N 19.368 10.703 13.384 3.111   -3.442 -0.136 N5  V2Y 37 
V2Y N6  NAA N 0 1 N N N N N N 12.302 7.071  12.543 1.386   5.996  1.543  N6  V2Y 38 
V2Y N7  NAM N 0 1 N N N N N N 16.023 6.780  12.679 3.641   1.761  -1.113 N7  V2Y 39 
V2Y N8  NBR N 0 1 Y N N N N N 16.885 7.151  8.357  -6.030  0.029  0.345  N8  V2Y 40 
V2Y N9  NBT N 0 1 Y N N N N N 16.315 5.466  7.095  -7.272  -1.110 1.733  N9  V2Y 41 
V2Y N10 NBW N 0 1 Y N N N N N 19.061 6.335  9.070  -7.724  0.105  -1.485 N10 V2Y 42 
V2Y N11 NBY N 0 1 Y N N N N N 19.599 4.262  8.165  -9.715  -0.966 -1.007 N11 V2Y 43 
V2Y N12 NCA N 0 1 N N N N N N 18.141 3.143  6.709  -10.119 -2.048 1.050  N12 V2Y 44 
V2Y O1  O2* O 0 1 N N N N N N 17.754 10.423 7.992  -5.528  2.957  -1.045 O1  V2Y 45 
V2Y O2  O3* O 0 1 N N N N N N 15.387 11.676 8.336  -3.141  3.699  -0.562 O2  V2Y 46 
V2Y O3  O4* O 0 1 N N N N N N 15.757 8.511  9.945  -3.667  0.352  0.469  O3  V2Y 47 
V2Y O4  O5* O 0 1 N N N N N N 14.045 9.782  12.113 -0.781  0.246  1.044  O4  V2Y 48 
V2Y O5  OAC O 0 1 N N N N N N 13.352 5.133  12.956 3.104   4.728  2.146  O5  V2Y 49 
V2Y O6  OAL O 0 1 N N N N N N 16.540 4.850  13.650 2.463   3.560  -0.559 O6  V2Y 50 
V2Y O7  OAP O 0 1 N N N N N N 18.437 8.435  13.413 3.284   -1.172 -0.863 O7  V2Y 51 
V2Y O8  OAS O 0 1 N N N N N N 18.954 10.169 16.512 1.851   -3.452 -3.162 O8  V2Y 52 
V2Y O9  OAU O 0 1 N N N N N N 19.445 7.606  16.304 1.488   -1.046 -3.912 O9  V2Y 53 
V2Y H1  H1  H 0 1 N N N N N N 17.739 8.606  9.493  -4.799  0.585  -1.273 H1  V2Y 54 
V2Y H2  H2  H 0 1 N N N N N N 23.782 11.261 13.089 5.529   -7.149 -1.170 H2  V2Y 55 
V2Y H3  H3  H 0 1 N N N N N N 16.411 9.168  6.962  -5.647  2.434  0.963  H3  V2Y 56 
V2Y H4  H4  H 0 1 N N N N N N 14.468 9.848  8.034  -3.480  3.107  1.402  H4  V2Y 57 
V2Y H5  H5  H 0 1 N N N N N N 16.104 10.478 10.526 -2.315  1.357  -0.771 H5  V2Y 58 
V2Y H6  H6  H 0 1 N N N N N N 13.675 11.090 10.553 -1.007  2.294  1.194  H6  V2Y 59 
V2Y H7  H7  H 0 1 N N N N N N 13.285 9.366  10.234 -2.040  1.327  2.274  H7  V2Y 60 
V2Y H8  H8  H 0 1 N N N N N N 14.197 7.099  10.651 2.789   5.504  -0.798 H8  V2Y 61 
V2Y H9  H9  H 0 1 N N N N N N 12.901 6.026  10.024 3.527   6.897  0.028  H9  V2Y 62 
V2Y H10 H10 H 0 1 N N N N N N 13.582 4.354  8.867  5.783   6.837  0.711  H10 V2Y 63 
V2Y H11 H11 H 0 1 N N N N N N 15.011 2.424  8.318  7.957   5.686  0.718  H11 V2Y 64 
V2Y H12 H12 H 0 1 N N N N N N 17.012 1.941  9.708  8.105   3.313  0.087  H12 V2Y 65 
V2Y H13 H13 H 0 1 N N N N N N 17.512 3.390  11.643 6.078   2.078  -0.556 H13 V2Y 66 
V2Y H14 H14 H 0 1 N N N N N N 16.429 8.662  13.494 1.917   1.561  -2.290 H14 V2Y 67 
V2Y H15 H15 H 0 1 N N N N N N 15.777 7.447  14.645 1.770   0.951  -0.624 H15 V2Y 68 
V2Y H16 H16 H 0 1 N N N N N N 18.281 6.378  14.251 3.567   -0.315 -2.749 H16 V2Y 69 
V2Y H17 H17 H 0 1 N N N N N N 20.141 9.012  14.506 3.945   -2.819 -1.968 H17 V2Y 70 
V2Y H18 H18 H 0 1 N N N N N N 17.252 9.955  15.185 0.984   -2.894 -1.356 H18 V2Y 71 
V2Y H19 H19 H 0 1 N N N N N N 17.411 7.872  16.432 0.656   -0.712 -2.036 H19 V2Y 72 
V2Y H20 H20 H 0 1 N N N N N N 13.830 11.724 12.969 -0.090  0.030  2.979  H20 V2Y 73 
V2Y H21 H21 H 0 1 N N N N N N 14.302 10.435 14.127 0.944   0.997  1.900  H21 V2Y 74 
V2Y H22 H22 H 0 1 N N N N N N 14.992 7.158  7.291  -5.326  -0.528 2.322  H22 V2Y 75 
V2Y H23 H23 H 0 1 N N N N N N 20.836 5.318  9.446  -9.317  -0.005 -2.796 H23 V2Y 76 
V2Y H24 H24 H 0 1 N N N N N N 22.072 14.643 10.888 4.021   -7.837 3.078  H24 V2Y 77 
V2Y H25 H25 H 0 1 N N N N N N 20.673 14.028 10.311 3.125   -6.474 3.480  H25 V2Y 78 
V2Y H26 H26 H 0 1 N N N N N N 11.917 7.113  13.465 0.900   5.774  2.352  H26 V2Y 79 
V2Y H27 H27 H 0 1 N N N N N N 12.104 7.798  11.885 0.992   6.593  0.888  H27 V2Y 80 
V2Y H28 H28 H 0 1 N N N N N N 15.506 7.210  11.939 4.509   1.335  -1.192 H28 V2Y 81 
V2Y H29 H29 H 0 1 N N N N N N 18.891 2.483  6.735  -9.804  -2.301 1.932  H29 V2Y 82 
V2Y H30 H30 H 0 1 N N N N N N 17.304 2.709  7.042  -11.009 -2.304 0.761  H30 V2Y 83 
V2Y H31 H31 H 0 1 N N N N N N 18.506 9.956  7.647  -5.574  3.917  -0.937 H31 V2Y 84 
V2Y H32 H32 H 0 1 N N N N N N 14.595 12.060 8.693  -3.669  4.509  -0.552 H32 V2Y 85 
V2Y H33 H33 H 0 1 N N N N N N 18.376 10.243 17.262 1.026   -3.514 -3.664 H33 V2Y 86 
V2Y H34 H34 H 0 1 N N N N N N 19.601 8.057  17.125 0.723   -1.499 -4.292 H34 V2Y 87 
# 
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 
V2Y N12 C32 SING N N 1  
V2Y N9  C28 DOUB Y N 2  
V2Y N9  C29 SING Y N 3  
V2Y C32 C29 DOUB Y N 4  
V2Y C32 N11 SING Y N 5  
V2Y C28 N8  SING Y N 6  
V2Y C29 C30 SING Y N 7  
V2Y C7  O1  SING N N 8  
V2Y C7  C8  SING N N 9  
V2Y C7  C5  SING N N 10 
V2Y N11 C31 DOUB Y N 11 
V2Y O2  C8  SING N N 12 
V2Y N8  C30 SING Y N 13 
V2Y N8  C5  SING N N 14 
V2Y C30 N10 DOUB Y N 15 
V2Y C8  C9  SING N N 16 
V2Y C31 N10 SING Y N 17 
V2Y C5  O3  SING N N 18 
V2Y C15 C14 DOUB Y N 19 
V2Y C15 C16 SING Y N 20 
V2Y C14 C13 SING Y N 21 
V2Y O3  C9  SING N N 22 
V2Y C16 C17 DOUB Y N 23 
V2Y C9  C10 SING N N 24 
V2Y C13 C12 SING N N 25 
V2Y C13 C18 DOUB Y N 26 
V2Y C10 O4  SING N N 27 
V2Y C12 C11 SING N N 28 
V2Y C17 C18 SING Y N 29 
V2Y N3  C3  SING N N 30 
V2Y C18 C19 SING N N 31 
V2Y C3  N1  DOUB Y N 32 
V2Y C3  C2  SING Y N 33 
V2Y O4  C27 SING N N 34 
V2Y N1  C6  SING Y N 35 
V2Y C11 N6  SING N N 36 
V2Y C11 O5  DOUB N N 37 
V2Y N4  C2  SING Y N 38 
V2Y N4  C4  DOUB Y N 39 
V2Y C2  C1  DOUB Y N 40 
V2Y C19 N7  SING N N 41 
V2Y C19 O6  DOUB N N 42 
V2Y N7  C20 SING N N 43 
V2Y C4  C25 SING N N 44 
V2Y C4  N5  SING Y N 45 
V2Y C6  N2  DOUB Y N 46 
V2Y C25 C26 TRIP N N 47 
V2Y C26 C27 SING N N 48 
V2Y C1  N2  SING Y N 49 
V2Y C1  N5  SING Y N 50 
V2Y N5  C22 SING N N 51 
V2Y O7  C22 SING N N 52 
V2Y O7  C21 SING N N 53 
V2Y C20 C21 SING N N 54 
V2Y C22 C23 SING N N 55 
V2Y C21 C24 SING N N 56 
V2Y C23 C24 SING N N 57 
V2Y C23 O8  SING N N 58 
V2Y C24 O9  SING N N 59 
V2Y C5  H1  SING N N 60 
V2Y C6  H2  SING N N 61 
V2Y C7  H3  SING N N 62 
V2Y C8  H4  SING N N 63 
V2Y C9  H5  SING N N 64 
V2Y C10 H6  SING N N 65 
V2Y C10 H7  SING N N 66 
V2Y C12 H8  SING N N 67 
V2Y C12 H9  SING N N 68 
V2Y C14 H10 SING N N 69 
V2Y C15 H11 SING N N 70 
V2Y C16 H12 SING N N 71 
V2Y C17 H13 SING N N 72 
V2Y C20 H14 SING N N 73 
V2Y C20 H15 SING N N 74 
V2Y C21 H16 SING N N 75 
V2Y C22 H17 SING N N 76 
V2Y C23 H18 SING N N 77 
V2Y C24 H19 SING N N 78 
V2Y C27 H20 SING N N 79 
V2Y C27 H21 SING N N 80 
V2Y C28 H22 SING N N 81 
V2Y C31 H23 SING N N 82 
V2Y N3  H24 SING N N 83 
V2Y N3  H25 SING N N 84 
V2Y N6  H26 SING N N 85 
V2Y N6  H27 SING N N 86 
V2Y N7  H28 SING N N 87 
V2Y N12 H29 SING N N 88 
V2Y N12 H30 SING N N 89 
V2Y O1  H31 SING N N 90 
V2Y O2  H32 SING N N 91 
V2Y O8  H33 SING N N 92 
V2Y O9  H34 SING N N 93 
# 
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 
V2Y InChI            InChI                1.06  "InChI=1S/C32H34N12O9/c33-18(45)8-14-4-1-2-5-15(14)30(50)36-9-16-22(46)25(49)32(52-16)44-19(42-21-27(35)38-12-40-29(21)44)6-3-7-51-10-17-23(47)24(48)31(53-17)43-13-41-20-26(34)37-11-39-28(20)43/h1-2,4-5,11-13,16-17,22-25,31-32,46-49H,7-10H2,(H2,33,45)(H,36,50)(H2,34,37,39)(H2,35,38,40)/t16-,17-,22-,23-,24-,25-,31-,32-/m1/s1" 
V2Y InChIKey         InChI                1.06  IDURCHWLBBOOLD-SXRMHTKDSA-N                                                                                                                                                                                                                                                                                                            
V2Y SMILES_CANONICAL CACTVS               3.385 "NC(=O)Cc1ccccc1C(=O)NC[C@H]2O[C@H]([C@H](O)[C@@H]2O)n3c(nc4c(N)ncnc34)C#CCOC[C@H]5O[C@H]([C@H](O)[C@@H]5O)n6cnc7c(N)ncnc67"                                                                                                                                                                                                           
V2Y SMILES           CACTVS               3.385 "NC(=O)Cc1ccccc1C(=O)NC[CH]2O[CH]([CH](O)[CH]2O)n3c(nc4c(N)ncnc34)C#CCOC[CH]5O[CH]([CH](O)[CH]5O)n6cnc7c(N)ncnc67"                                                                                                                                                                                                                     
V2Y SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1ccc(c(c1)CC(=O)N)C(=O)NC[C@@H]2[C@H]([C@H]([C@@H](O2)n3c(nc4c3ncnc4N)C#CCOC[C@@H]5[C@H]([C@H]([C@@H](O5)n6cnc7c6ncnc7N)O)O)O)O"                                                                                                                                                                                                     
V2Y SMILES           "OpenEye OEToolkits" 2.0.7 "c1ccc(c(c1)CC(=O)N)C(=O)NCC2C(C(C(O2)n3c(nc4c3ncnc4N)C#CCOCC5C(C(C(O5)n6cnc7c6ncnc7N)O)O)O)O"                                                                                                                                                                                                                                         
# 
_pdbx_chem_comp_identifier.comp_id           V2Y 
_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        "~{N}-[[(2~{R},3~{S},4~{R},5~{R})-5-[8-[3-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy]prop-1-ynyl]-6-azanyl-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl]-2-(2-azanyl-2-oxidanylidene-ethyl)benzamide" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
V2Y "Create component" 2023-09-07 PDBE 
V2Y "Initial release"  2025-03-19 RCSB 
# 
