data_DY0
# 
_chem_comp.id                                    DY0 
_chem_comp.name                                  "[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2S,3S,4S,5S,6R)-6-[(1R)-1,2-bis(oxidanyl)ethyl]-3,4,5-tris(oxidanyl)oxan-2-yl] hydrogen phosphate" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C17 H27 N5 O16 P2" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2019-09-18 
_chem_comp.pdbx_modified_date                    2025-07-25 
_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                        619.368 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     DY0 
_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        6KWP 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBJ 
_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 
DY0 C18 C1  C 0 1 Y N N N N N 36.475 37.412 52.245 8.812  1.807  -2.076 C18 DY0 1  
DY0 C19 C2  C 0 1 N N R N N N 35.702 42.878 53.984 5.676  -1.906 -0.891 C19 DY0 2  
DY0 C03 C3  C 0 1 N N N N N N 41.226 42.864 51.942 -7.268 -2.048 -0.953 C03 DY0 3  
DY0 C05 C4  C 0 1 N N R N N N 42.503 42.165 52.470 -7.572 -0.629 -1.440 C05 DY0 4  
DY0 C07 C5  C 0 1 N N R N N N 43.439 43.226 53.001 -6.963 0.385  -0.470 C07 DY0 5  
DY0 C09 C6  C 0 1 N N S N N N 44.588 42.558 53.744 -7.267 1.804  -0.957 C09 DY0 6  
DY0 C10 C7  C 0 1 N N S N N N 45.461 43.544 54.411 -6.604 2.812  -0.014 C10 DY0 7  
DY0 C11 C8  C 0 1 N N S N N N 44.703 44.480 55.261 -5.100 2.527  0.045  C11 DY0 8  
DY0 C13 C9  C 0 1 N N S N N N 43.510 45.109 54.543 -4.880 1.080  0.494  C13 DY0 9  
DY0 C14 C10 C 0 1 N N R N N N 36.146 42.012 53.117 5.148  -0.456 -0.815 C14 DY0 10 
DY0 C22 C11 C 0 1 N N S N N N 35.572 44.167 53.191 4.412  -2.779 -0.723 C22 DY0 11 
DY0 C27 C12 C 0 1 Y N N N N N 36.978 39.653 53.449 7.191  1.028  -0.646 C27 DY0 12 
DY0 C28 C13 C 0 1 N N R N N N 36.703 44.077 52.120 3.266  -1.754 -0.567 C28 DY0 13 
DY0 C30 C14 C 0 1 Y N N N N N 37.835 39.018 54.296 7.801  1.727  0.409  C30 DY0 14 
DY0 C31 C15 C 0 1 N N N N N N 37.933 44.938 52.575 2.235  -2.258 0.444  C31 DY0 15 
DY0 C33 C16 C 0 1 Y N N N N N 38.074 37.466 54.156 8.959  2.472  0.129  C33 DY0 16 
DY0 C36 C17 C 0 1 Y N N N N N 37.797 41.150 54.831 6.067  0.711  1.224  C36 DY0 17 
DY0 N15 N1  N 0 1 Y N N N N N 37.394 36.733 53.149 9.421  2.481  -1.117 N15 DY0 18 
DY0 N23 N2  N 0 1 Y N N N N N 36.253 38.876 52.381 7.726  1.096  -1.861 N23 DY0 19 
DY0 N34 N3  N 0 1 N N N N N N 39.001 36.779 55.066 9.604  3.181  1.128  N34 DY0 20 
DY0 N35 N4  N 0 1 Y N N N N N 38.343 39.936 55.146 7.066  1.491  1.522  N35 DY0 21 
DY0 N37 N5  N 0 1 Y N N N N N 36.956 40.971 53.786 6.101  0.397  -0.102 N37 DY0 22 
DY0 O04 O1  O 0 1 N N N N N N 41.602 43.787 50.923 -7.735 -2.993 -1.918 O04 DY0 23 
DY0 O06 O2  O 0 1 N N N N N N 43.127 41.505 51.422 -8.987 -0.440 -1.502 O06 DY0 24 
DY0 O08 O3  O 0 1 N N N N N N 42.662 44.120 53.869 -5.548 0.196  -0.409 O08 DY0 25 
DY0 O12 O4  O 0 1 N N N N N N 34.336 42.461 54.517 6.288  -2.150 -2.158 O12 DY0 26 
DY0 O16 O5  O 0 1 N N N N N N 39.421 44.949 56.195 0.317  -1.469 2.986  O16 DY0 27 
DY0 O17 O6  O 0 1 N N N N N N 41.266 47.736 56.119 -2.952 0.258  3.017  O17 DY0 28 
DY0 O20 O7  O 0 1 N N N N N N 38.072 46.598 55.350 -0.728 -2.910 1.196  O20 DY0 29 
DY0 O21 O8  O 0 1 N N N N N N 42.384 47.926 54.157 -3.490 -1.579 1.370  O21 DY0 30 
DY0 O24 O9  O 0 1 N N N N N N 40.382 46.296 54.175 -1.248 -0.441 1.140  O24 DY0 31 
DY0 O25 O10 O 0 1 N N N N N N 42.729 45.734 55.479 -3.481 0.789  0.497  O25 DY0 32 
DY0 O26 O11 O 0 1 N N N N N N 34.344 44.229 52.581 4.207  -3.591 -1.881 O26 DY0 33 
DY0 O29 O12 O 0 1 N N N N N N 37.044 42.835 52.048 3.909  -0.553 -0.077 O29 DY0 34 
DY0 O32 O13 O 0 1 N N N N N N 38.391 44.466 53.835 1.129  -1.354 0.488  O32 DY0 35 
DY0 O38 O14 O 0 1 N N N N N N 45.384 41.807 52.801 -8.681 2.014  -0.964 O38 DY0 36 
DY0 O39 O15 O 0 1 N N N N N N 46.418 42.816 55.256 -6.820 4.137  -0.502 O39 DY0 37 
DY0 O40 O16 O 0 1 N N N N N N 44.220 43.763 56.436 -4.527 2.718  -1.250 O40 DY0 38 
DY0 P01 P1  P 0 1 N N N N N N 39.070 45.586 54.913 -0.145 -1.573 1.447  P01 DY0 39 
DY0 P02 P2  P 0 1 N N N N N N 41.692 46.933 54.983 -2.808 -0.272 1.503  P02 DY0 40 
DY0 H1  H1  H 0 1 N N N N N N 35.957 36.854 51.479 9.219  1.845  -3.076 H1  DY0 41 
DY0 H2  H2  H 0 1 N N N N N N 36.392 43.033 54.827 6.382  -2.098 -0.083 H2  DY0 42 
DY0 H3  H3  H 0 1 N N N N N N 40.730 43.401 52.764 -6.193 -2.164 -0.821 H3  DY0 43 
DY0 H4  H4  H 0 1 N N N N N N 40.537 42.113 51.527 -7.772 -2.221 -0.002 H4  DY0 44 
DY0 H5  H5  H 0 1 N N N N N N 42.229 41.472 53.279 -7.143 -0.486 -2.432 H5  DY0 45 
DY0 H6  H6  H 0 1 N N N N N N 43.848 43.798 52.155 -7.392 0.241  0.522  H6  DY0 46 
DY0 H7  H7  H 0 1 N N N N N N 44.169 41.877 54.499 -6.874 1.935  -1.965 H7  DY0 47 
DY0 H8  H8  H 0 1 N N N N N N 46.011 44.114 53.648 -7.034 2.716  0.983  H8  DY0 48 
DY0 H9  H9  H 0 1 N N N N N N 45.374 45.289 55.585 -4.628 3.205  0.756  H9  DY0 49 
DY0 H10 H10 H 0 1 N N N N N N 43.887 45.831 53.804 -5.281 0.946  1.498  H10 DY0 50 
DY0 H11 H11 H 0 1 N N N N N N 35.328 41.532 52.560 4.965  -0.066 -1.816 H11 DY0 51 
DY0 H12 H12 H 0 1 N N N N N N 35.756 45.032 53.846 4.492  -3.400 0.169  H12 DY0 52 
DY0 H13 H13 H 0 1 N N N N N N 36.324 44.476 51.167 2.791  -1.567 -1.530 H13 DY0 53 
DY0 H14 H14 H 0 1 N N N N N N 38.740 44.849 51.833 1.885  -3.246 0.146  H14 DY0 54 
DY0 H15 H15 H 0 1 N N N N N N 37.632 45.992 52.664 2.694  -2.318 1.431  H15 DY0 55 
DY0 H16 H16 H 0 1 N N N N N N 38.001 42.087 55.329 5.322  0.364  1.925  H16 DY0 56 
DY0 H17 H17 H 0 1 N N N N N N 39.033 35.806 54.837 9.257  3.167  2.034  H17 DY0 57 
DY0 H18 H18 H 0 1 N N N N N N 39.915 37.174 54.972 10.402 3.692  0.922  H18 DY0 58 
DY0 H19 H19 H 0 1 N N N N N N 40.827 44.224 50.589 -7.575 -3.915 -1.674 H19 DY0 59 
DY0 H20 H20 H 0 1 N N N N N N 43.911 41.074 51.741 -9.436 -0.552 -0.653 H20 DY0 60 
DY0 H21 H21 H 0 1 N N N N N N 34.031 43.104 55.146 6.612  -3.054 -2.271 H21 DY0 61 
DY0 H22 H22 H 0 1 N N N N N N 38.926 45.355 56.897 0.709  -0.618 3.222  H22 DY0 62 
DY0 H23 H23 H 0 1 N N N N N N 41.550 48.634 55.997 -2.528 1.112  3.177  H23 DY0 63 
DY0 H24 H24 H 0 1 N N N N N N 33.664 44.283 53.242 4.927  -4.212 -2.058 H24 DY0 64 
DY0 H25 H25 H 0 1 N N N N N N 46.104 41.387 53.257 -8.946 2.895  -1.262 H25 DY0 65 
DY0 H26 H26 H 0 1 N N N N N N 46.989 43.436 55.694 -6.427 4.828  0.048  H26 DY0 66 
DY0 H27 H27 H 0 1 N N N N N N 43.730 44.358 56.991 -3.575 2.554  -1.287 H27 DY0 67 
# 
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 
DY0 O04 C03 SING N N 1  
DY0 O06 C05 SING N N 2  
DY0 C03 C05 SING N N 3  
DY0 O29 C28 SING N N 4  
DY0 O29 C14 SING N N 5  
DY0 C28 C31 SING N N 6  
DY0 C28 C22 SING N N 7  
DY0 C18 N23 DOUB Y N 8  
DY0 C18 N15 SING Y N 9  
DY0 N23 C27 SING Y N 10 
DY0 C05 C07 SING N N 11 
DY0 C31 O32 SING N N 12 
DY0 O26 C22 SING N N 13 
DY0 O38 C09 SING N N 14 
DY0 C07 C09 SING N N 15 
DY0 C07 O08 SING N N 16 
DY0 C14 N37 SING N N 17 
DY0 C14 C19 SING N N 18 
DY0 N15 C33 DOUB Y N 19 
DY0 C22 C19 SING N N 20 
DY0 C27 N37 SING Y N 21 
DY0 C27 C30 DOUB Y N 22 
DY0 C09 C10 SING N N 23 
DY0 N37 C36 SING Y N 24 
DY0 O32 P01 SING N N 25 
DY0 O08 C13 SING N N 26 
DY0 C19 O12 SING N N 27 
DY0 C33 C30 SING Y N 28 
DY0 C33 N34 SING N N 29 
DY0 O21 P02 DOUB N N 30 
DY0 O24 P01 SING N N 31 
DY0 O24 P02 SING N N 32 
DY0 C30 N35 SING Y N 33 
DY0 C10 O39 SING N N 34 
DY0 C10 C11 SING N N 35 
DY0 C13 C11 SING N N 36 
DY0 C13 O25 SING N N 37 
DY0 C36 N35 DOUB Y N 38 
DY0 P01 O20 DOUB N N 39 
DY0 P01 O16 SING N N 40 
DY0 P02 O25 SING N N 41 
DY0 P02 O17 SING N N 42 
DY0 C11 O40 SING N N 43 
DY0 C18 H1  SING N N 44 
DY0 C19 H2  SING N N 45 
DY0 C03 H3  SING N N 46 
DY0 C03 H4  SING N N 47 
DY0 C05 H5  SING N N 48 
DY0 C07 H6  SING N N 49 
DY0 C09 H7  SING N N 50 
DY0 C10 H8  SING N N 51 
DY0 C11 H9  SING N N 52 
DY0 C13 H10 SING N N 53 
DY0 C14 H11 SING N N 54 
DY0 C22 H12 SING N N 55 
DY0 C28 H13 SING N N 56 
DY0 C31 H14 SING N N 57 
DY0 C31 H15 SING N N 58 
DY0 C36 H16 SING N N 59 
DY0 N34 H17 SING N N 60 
DY0 N34 H18 SING N N 61 
DY0 O04 H19 SING N N 62 
DY0 O06 H20 SING N N 63 
DY0 O12 H21 SING N N 64 
DY0 O16 H22 SING N N 65 
DY0 O17 H23 SING N N 66 
DY0 O26 H24 SING N N 67 
DY0 O38 H25 SING N N 68 
DY0 O39 H26 SING N N 69 
DY0 O40 H27 SING N N 70 
# 
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 
DY0 InChI            InChI                1.03  "InChI=1S/C17H27N5O16P2/c18-14-7-15(20-3-19-14)22(4-21-7)16-11(28)8(25)6(35-16)2-34-39(30,31)38-40(32,33)37-17-12(29)9(26)10(27)13(36-17)5(24)1-23/h3-6,8-13,16-17,23-29H,1-2H2,(H,30,31)(H,32,33)(H2,18,19,20)/t5-,6-,8-,9+,10+,11-,12+,13-,16-,17+/m1/s1" 
DY0 InChIKey         InChI                1.03  KMSFWBYFWSKGGR-FQBROAFUSA-N                                                                                                                                                                                                                                 
DY0 SMILES_CANONICAL CACTVS               3.385 "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[C@@H]4O[C@H]([C@H](O)CO)[C@@H](O)[C@H](O)[C@@H]4O)[C@@H](O)[C@H]3O"                                                                                                                                 
DY0 SMILES           CACTVS               3.385 "Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[CH]4O[CH]([CH](O)CO)[CH](O)[CH](O)[CH]4O)[CH](O)[CH]3O"                                                                                                                                                
DY0 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)O[C@H]4[C@H]([C@H]([C@@H]([C@H](O4)[C@@H](CO)O)O)O)O)O)O)N"                                                                                                                              
DY0 SMILES           "OpenEye OEToolkits" 2.0.7 "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OC4C(C(C(C(O4)C(CO)O)O)O)O)O)O)N"                                                                                                                                                                          
# 
_pdbx_chem_comp_identifier.comp_id           DY0 
_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~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{S},3~{S},4~{S},5~{S},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-3,4,5-tris(oxidanyl)oxan-2-yl] hydrogen phosphate" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
DY0 "Create component" 2019-09-18 PDBJ 
DY0 "Initial release"  2025-07-30 RCSB 
# 
