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 #