data_A1L89
# 
_chem_comp.id                                    A1L89 
_chem_comp.name                                  
;P1-(5'-Adenosyl) P4-(5'-uridyl) tetraphosphate
;
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C19 H27 N7 O21 P4" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         
;[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [[[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl] hydrogen phosphate; Adenosine(5')tetraphosphate uridine; Ap4U
;
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2025-04-22 
_chem_comp.pdbx_modified_date                    2025-08-29 
_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                        813.347 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A1L89 
_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        9ULS 
_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_n_terminal_atom_flag 
_chem_comp_atom.pdbx_backbone_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 
A1L89 C1E  C1  C 0 1 N N R N N N 157.138 156.820 149.834 -6.631 1.449  0.759  C1E  A1L89 1  
A1L89 C1F  C2  C 0 1 N N R N N N 155.865 151.800 160.857 6.670  2.966  -0.735 C1F  A1L89 2  
A1L89 C2A  C3  C 0 1 Y N N N N N 161.291 156.800 151.422 -7.879 5.689  -0.023 C2A  A1L89 3  
A1L89 C2B  C4  C 0 1 N N N N N N 158.240 151.327 161.334 7.472  2.907  1.559  C2B  A1L89 4  
A1L89 C2E  C5  C 0 1 N N R N N N 157.637 156.300 148.471 -7.790 0.908  1.624  C2E  A1L89 5  
A1L89 C2F  C6  C 0 1 N N R N N N 155.957 153.312 161.136 7.998  2.529  -1.405 C2F  A1L89 6  
A1L89 C3E  C7  C 0 1 N N S N N N 156.558 155.265 148.135 -7.268 -0.451 2.144  C3E  A1L89 7  
A1L89 C3F  C8  C 0 1 N N S N N N 155.749 153.872 159.734 7.532  1.377  -2.328 C3F  A1L89 8  
A1L89 C4A  C9  C 0 1 Y N N N N N 159.088 156.172 151.287 -7.497 3.472  -0.492 C4A  A1L89 9  
A1L89 C4B  C10 C 0 1 N N N N N N 159.593 150.136 159.663 7.427  4.779  2.957  C4B  A1L89 10 
A1L89 C4E  C11 C 0 1 N N R N N N 155.300 155.917 148.698 -5.855 -0.569 1.531  C4E  A1L89 11 
A1L89 C4F  C12 C 0 1 N N R N N N 154.693 152.938 159.167 6.189  0.927  -1.722 C4F  A1L89 12 
A1L89 C5A  C13 C 0 1 Y N N N N N 159.295 155.311 152.337 -7.946 3.684  -1.806 C5A  A1L89 13 
A1L89 C5B  C14 C 0 1 N N N N N N 158.445 150.071 158.811 6.862  5.538  1.903  C5B  A1L89 14 
A1L89 C5E  C15 C 0 1 N N N N N N 154.247 154.889 149.056 -5.567 -2.018 1.133  C5E  A1L89 15 
A1L89 C5F  C16 C 0 1 N N N N N N 154.792 152.872 157.657 6.259  -0.554 -1.344 C5F  A1L89 16 
A1L89 C6A  C17 C 0 1 Y N N N N N 160.596 155.228 152.923 -8.366 4.977  -2.164 C6A  A1L89 17 
A1L89 C6B  C18 C 0 1 N N N N N N 157.296 150.611 159.236 6.622  4.938  0.717  C6B  A1L89 18 
A1L89 C8A  C19 C 0 1 Y N N N N N 157.204 155.143 151.734 -7.402 1.592  -1.640 C8A  A1L89 19 
A1L89 N1A  N1  N 0 1 Y N N N N N 161.592 155.997 152.437 -8.308 5.937  -1.246 N1A  A1L89 20 
A1L89 N1B  N2  N 0 1 N N N N N N 157.168 151.226 160.459 6.931  3.616  0.552  N1B  A1L89 21 
A1L89 N3A  N3  N 0 1 Y N N N N N 160.116 156.927 150.835 -7.481 4.494  0.358  N3A  A1L89 22 
A1L89 N3B  N4  N 0 1 N N N N N N 159.408 150.766 160.877 7.717  3.478  2.753  N3B  A1L89 23 
A1L89 N6A  N5  N 0 1 N N N N N N 160.844 154.399 153.946 -8.818 5.246  -3.443 N6A  A1L89 24 
A1L89 N7A  N6  N 0 1 Y N N N N N 158.114 154.675 152.604 -7.863 2.497  -2.454 N7A  A1L89 25 
A1L89 N9A  N7  N 0 1 Y N N N N N 157.802 156.070 150.926 -7.156 2.145  -0.419 N9A  A1L89 26 
A1L89 O1A  O1  O 0 1 N N N N N N 152.977 152.276 149.659 -3.722 -4.539 1.236  O1A  A1L89 27 
A1L89 O1B  O2  O 0 1 N N N N N N 154.546 153.361 153.809 -0.849 -5.416 0.595  O1B  A1L89 28 
A1L89 O1D  O3  O 0 1 N N N N N N 155.123 150.702 155.569 5.076  -3.444 -1.483 O1D  A1L89 29 
A1L89 O1G  O4  O 0 1 N N N N N N 153.231 150.537 153.129 2.501  -4.996 -0.859 O1G  A1L89 30 
A1L89 O2A  O5  O 0 1 N N N N N N 154.801 151.849 151.361 -4.321 -4.007 -1.158 O2A  A1L89 31 
A1L89 O2B  O6  O 0 1 N N N N N N 152.680 155.047 153.859 -0.794 -4.859 -1.866 O2B  A1L89 32 
A1L89 O2D  O7  O 0 1 N N N N N N 153.931 149.625 157.524 5.534  -2.815 0.918  O2D  A1L89 33 
A1L89 O2E  O8  O 0 1 N N N N N N 157.684 157.355 147.508 -8.058 1.794  2.713  O2E  A1L89 34 
A1L89 O2F  O9  O 0 1 N N N N N N 154.923 153.726 162.030 8.560  3.599  -2.167 O2F  A1L89 35 
A1L89 O2G  O10 O 0 1 N N N N N N 150.807 150.494 153.781 2.317  -4.502 1.610  O2G  A1L89 36 
A1L89 O3A  O11 O 0 1 N N N N N N 152.996 153.572 151.837 -2.006 -3.295 -0.136 O3A  A1L89 37 
A1L89 O3B  O12 O 0 1 N N N N N N 152.168 152.593 154.092 0.616  -3.489 -0.120 O3B  A1L89 38 
A1L89 O3E  O13 O 0 1 N N N N N N 156.411 155.079 146.723 -7.196 -0.447 3.571  O3E  A1L89 39 
A1L89 O3F  O14 O 0 1 N N N N N N 155.262 155.216 159.753 7.344  1.852  -3.663 O3F  A1L89 40 
A1L89 O3G  O15 O 0 1 N N N N N N 152.595 150.493 155.560 3.114  -2.669 -0.098 O3G  A1L89 41 
A1L89 O4B  O16 O 0 1 N N N N N N 160.697 149.677 159.377 7.648  5.296  4.037  O4B  A1L89 42 
A1L89 O4E  O17 O 0 1 N N N N N N 155.749 156.584 149.884 -5.889 0.276  0.360  O4E  A1L89 43 
A1L89 O4F  O18 O 0 1 N N N N N N 155.013 151.653 159.741 5.964  1.721  -0.545 O4F  A1L89 44 
A1L89 O5E  O19 O 0 1 N N N N N N 154.755 154.035 150.100 -4.217 -2.128 0.677  O5E  A1L89 45 
A1L89 O5F  O20 O 0 1 N N N N N N 153.688 152.113 157.131 4.976  -0.992 -0.892 O5F  A1L89 46 
A1L89 PA   P1  P 0 1 N N N N N N 153.880 152.861 150.719 -3.570 -3.515 0.178  PA   A1L89 47 
A1L89 PB   P2  P 0 1 N N N N N N 153.122 153.672 153.420 -0.760 -4.290 -0.361 PB   A1L89 48 
A1L89 PD   P3  P 0 1 N N N N N N 153.896 150.690 156.454 4.684  -2.501 -0.412 PD   A1L89 49 
A1L89 PG   P4  P 0 1 N N N N N N 152.189 151.005 154.110 2.145  -3.937 0.112  PG   A1L89 50 
A1L89 O2B1 O21 O 0 0 N N N N N N 158.170 151.864 162.433 7.739  1.733  1.390  O2B1 A1L89 51 
A1L89 H1   H1  H 0 1 N N N N N N 157.363 157.893 149.919 -5.998 2.117  1.343  H1   A1L89 52 
A1L89 H2   H2  H 0 1 N N N N N N 155.467 151.282 161.742 6.109  3.629  -1.392 H2   A1L89 53 
A1L89 H3   H3  H 0 1 N N N N N N 162.092 157.413 151.037 -7.848 6.499  0.692  H3   A1L89 54 
A1L89 H4   H4  H 0 1 N N N N N N 158.614 155.808 148.587 -8.685 0.767  1.019  H4   A1L89 55 
A1L89 H5   H5  H 0 1 N N N N N N 156.957 153.572 161.512 8.709  2.169  -0.661 H5   A1L89 56 
A1L89 H6   H6  H 0 1 N N N N N N 156.764 154.317 148.653 -7.905 -1.263 1.795  H6   A1L89 57 
A1L89 H7   H7  H 0 1 N N N N N N 156.679 153.789 159.153 8.253  0.560  -2.313 H7   A1L89 58 
A1L89 H8   H8  H 0 1 N N N N N N 154.893 156.634 147.969 -5.104 -0.213 2.236  H8   A1L89 59 
A1L89 H9   H9  H 0 1 N N N N N N 153.689 153.272 159.469 5.385  1.091  -2.439 H9   A1L89 60 
A1L89 H10  H10 H 0 1 N N N N N N 158.504 149.595 157.843 6.623  6.581  2.048  H10  A1L89 61 
A1L89 H11  H11 H 0 1 N N N N N N 153.339 155.400 149.408 -5.713 -2.668 1.997  H11  A1L89 62 
A1L89 H12  H12 H 0 1 N N N N N N 154.007 154.284 148.169 -6.246 -2.318 0.335  H12  A1L89 63 
A1L89 H13  H13 H 0 1 N N N N N N 155.737 152.387 157.373 6.556  -1.138 -2.216 H13  A1L89 64 
A1L89 H14  H14 H 0 1 N N N N N N 154.765 153.891 157.244 6.992  -0.692 -0.549 H14  A1L89 65 
A1L89 H15  H15 H 0 1 N N N N N N 156.432 150.561 158.590 6.191  5.501  -0.097 H15  A1L89 66 
A1L89 H16  H16 H 0 1 N N N N N N 156.170 154.837 151.681 -7.236 0.556  -1.896 H16  A1L89 67 
A1L89 H17  H17 H 0 1 N N N N N N 160.202 150.819 161.483 8.104  2.951  3.470  H17  A1L89 68 
A1L89 H18  H18 H 0 1 N N N N N N 161.803 154.481 154.217 -8.848 4.539  -4.106 H18  A1L89 69 
A1L89 H19  H19 H 0 1 N N N N N N 160.258 154.640 154.720 -9.105 6.143  -3.678 H19  A1L89 70 
A1L89 H20  H20 H 0 1 N N N N N N 154.650 150.994 150.976 -4.263 -3.384 -1.895 H20  A1L89 71 
A1L89 H21  H21 H 0 1 N N N N N N 153.394 155.480 154.312 -0.739 -4.175 -2.547 H21  A1L89 72 
A1L89 H22  H22 H 0 1 N N N N N N 154.740 149.132 157.455 5.328  -2.234 1.663  H22  A1L89 73 
A1L89 H23  H23 H 0 1 N N N N N N 158.362 157.975 147.749 -8.778 1.502  3.289  H23  A1L89 74 
A1L89 H24  H24 H 0 1 N N N N N N 155.084 153.360 162.892 9.392  3.374  -2.606 H24  A1L89 75 
A1L89 H25  H25 H 0 1 N N N N N N 150.845 149.958 152.998 2.100  -3.860 2.299  H25  A1L89 76 
A1L89 H26  H26 H 0 1 N N N N N N 155.735 154.432 146.557 -8.048 -0.314 4.008  H26  A1L89 77 
A1L89 H27  H27 H 0 1 N N N N N N 155.930 155.790 160.109 8.147  2.202  -4.073 H27  A1L89 78 
# 
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 
A1L89 O3E C3E  SING N N 1  
A1L89 O2E C2E  SING N N 2  
A1L89 C3E C2E  SING N N 3  
A1L89 C3E C4E  SING N N 4  
A1L89 C2E C1E  SING N N 5  
A1L89 C4E C5E  SING N N 6  
A1L89 C4E O4E  SING N N 7  
A1L89 C5E O5E  SING N N 8  
A1L89 O1A PA   DOUB N N 9  
A1L89 C1E O4E  SING N N 10 
A1L89 C1E N9A  SING N N 11 
A1L89 O5E PA   SING N N 12 
A1L89 PA  O2A  SING N N 13 
A1L89 PA  O3A  SING N N 14 
A1L89 N3A C4A  DOUB Y N 15 
A1L89 N3A C2A  SING Y N 16 
A1L89 N9A C4A  SING Y N 17 
A1L89 N9A C8A  SING Y N 18 
A1L89 C4A C5A  SING Y N 19 
A1L89 C2A N1A  DOUB Y N 20 
A1L89 C8A N7A  DOUB Y N 21 
A1L89 O3A PB   SING N N 22 
A1L89 C5A N7A  SING Y N 23 
A1L89 C5A C6A  DOUB Y N 24 
A1L89 N1A C6A  SING Y N 25 
A1L89 C6A N6A  SING N N 26 
A1L89 O1G PG   DOUB N N 27 
A1L89 PB  O1B  DOUB N N 28 
A1L89 PB  O2B  SING N N 29 
A1L89 PB  O3B  SING N N 30 
A1L89 O2G PG   SING N N 31 
A1L89 O3B PG   SING N N 32 
A1L89 PG  O3G  SING N N 33 
A1L89 O3G PD   SING N N 34 
A1L89 O1D PD   DOUB N N 35 
A1L89 PD  O5F  SING N N 36 
A1L89 PD  O2D  SING N N 37 
A1L89 O5F C5F  SING N N 38 
A1L89 C5F C4F  SING N N 39 
A1L89 C5B C6B  DOUB N N 40 
A1L89 C5B C4B  SING N N 41 
A1L89 C4F C3F  SING N N 42 
A1L89 C4F O4F  SING N N 43 
A1L89 C6B N1B  SING N N 44 
A1L89 O4B C4B  DOUB N N 45 
A1L89 C4B N3B  SING N N 46 
A1L89 C3F O3F  SING N N 47 
A1L89 C3F C2F  SING N N 48 
A1L89 O4F C1F  SING N N 49 
A1L89 N1B C1F  SING N N 50 
A1L89 N1B C2B  SING N N 51 
A1L89 C1F C2F  SING N N 52 
A1L89 N3B C2B  SING N N 53 
A1L89 C2F O2F  SING N N 54 
A1L89 C2B O2B1 DOUB N N 55 
A1L89 C1E H1   SING N N 56 
A1L89 C1F H2   SING N N 57 
A1L89 C2A H3   SING N N 58 
A1L89 C2E H4   SING N N 59 
A1L89 C2F H5   SING N N 60 
A1L89 C3E H6   SING N N 61 
A1L89 C3F H7   SING N N 62 
A1L89 C4E H8   SING N N 63 
A1L89 C4F H9   SING N N 64 
A1L89 C5B H10  SING N N 65 
A1L89 C5E H11  SING N N 66 
A1L89 C5E H12  SING N N 67 
A1L89 C5F H13  SING N N 68 
A1L89 C5F H14  SING N N 69 
A1L89 C6B H15  SING N N 70 
A1L89 C8A H16  SING N N 71 
A1L89 N3B H17  SING N N 72 
A1L89 N6A H18  SING N N 73 
A1L89 N6A H19  SING N N 74 
A1L89 O2A H20  SING N N 75 
A1L89 O2B H21  SING N N 76 
A1L89 O2D H22  SING N N 77 
A1L89 O2E H23  SING N N 78 
A1L89 O2F H24  SING N N 79 
A1L89 O2G H25  SING N N 80 
A1L89 O3E H26  SING N N 81 
A1L89 O3F H27  SING N N 82 
# 
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 
A1L89 InChI            InChI                1.06  "InChI=1S/C19H27N7O21P4/c20-15-10-16(22-5-21-15)26(6-23-10)18-14(31)12(29)8(44-18)4-42-49(35,36)46-51(39,40)47-50(37,38)45-48(33,34)41-3-7-11(28)13(30)17(43-7)25-2-1-9(27)24-19(25)32/h1-2,5-8,11-14,17-18,28-31H,3-4H2,(H,33,34)(H,35,36)(H,37,38)(H,39,40)(H2,20,21,22)(H,24,27,32)/t7-,8-,11-,12-,13-,14-,17-,18-/m1/s1" 
A1L89 InChIKey         InChI                1.06  ADWZBTIGCZHWBW-KPKSGTNCSA-N                                                                                                                                                                                                                                                                                                  
A1L89 SMILES_CANONICAL CACTVS               3.385 "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(=O)O[P](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)N5C=CC(=O)NC5=O)[C@@H](O)[C@H]3O"                                                                                                                                                                                
A1L89 SMILES           CACTVS               3.385 "Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)N5C=CC(=O)NC5=O)[CH](O)[CH]3O"                                                                                                                                                                                           
A1L89 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)OP(=O)(O)OP(=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)N5C=CC(=O)NC5=O)O)O)O)O)N"                                                                                                                                                                               
A1L89 SMILES           "OpenEye OEToolkits" 2.0.7 "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)N5C=CC(=O)NC5=O)O)O)O)O)N"                                                                                                                                                                                                                   
# 
_pdbx_chem_comp_identifier.comp_id           A1L89 
_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~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl] 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 
A1L89 "Create component" 2025-04-22 PDBJ 
A1L89 "Initial release"  2025-09-03 RCSB 
# 
loop_
_pdbx_chem_comp_synonyms.ordinal 
_pdbx_chem_comp_synonyms.comp_id 
_pdbx_chem_comp_synonyms.name 
_pdbx_chem_comp_synonyms.provenance 
_pdbx_chem_comp_synonyms.type 
1 A1L89 "[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [[[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl] hydrogen phosphate" PDB     ? 
2 A1L89 
;Adenosine(5')tetraphosphate uridine
;
PUBCHEM ? 
3 A1L89 Ap4U                                                                                                                                                                                                                                                                                     PUBCHEM ? 
# 
