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 ? #