data_AP5 # _chem_comp.id AP5 _chem_comp.name "BIS(ADENOSINE)-5'-PENTAPHOSPHATE" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C20 H29 N10 O22 P5" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 1999-07-08 _chem_comp.pdbx_modified_date 2011-06-04 _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 916.367 _chem_comp.one_letter_code ? _chem_comp.three_letter_code AP5 _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 1AKE _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB # 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.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 AP5 PA PA P 0 1 N N S 22.201 6.089 19.452 -0.998 0.944 5.000 PA AP5 1 AP5 O1A O1A O 0 1 N N N 22.416 6.745 18.144 0.236 1.740 5.175 O1A AP5 2 AP5 O2A O2A O 0 1 N N N 21.476 6.864 20.478 -2.217 1.922 4.613 O2A AP5 3 AP5 O3A O3A O 0 1 N N N 21.770 4.549 19.290 -0.780 -0.132 3.823 O3A AP5 4 AP5 PB PB P 0 1 N N S 20.344 3.896 18.917 -0.443 0.700 2.487 PB AP5 5 AP5 O1B O1B O 0 1 N N N 20.857 2.643 18.377 0.783 1.500 2.701 O1B AP5 6 AP5 O2B O2B O 0 1 N N N 19.561 4.700 17.951 -1.671 1.682 2.143 O2B AP5 7 AP5 O3B O3B O 0 1 N N N 19.580 3.556 20.304 -0.212 -0.319 1.262 O3B AP5 8 AP5 PG PG P 0 1 N N N 17.985 3.557 20.606 0.118 0.577 -0.033 PG AP5 9 AP5 O1G O1G O 0 1 N N N 17.476 4.926 20.866 -1.018 1.482 -0.310 O1G AP5 10 AP5 O2G O2G O 0 1 N N N 17.289 2.760 19.558 1.443 1.449 0.242 O2G AP5 11 AP5 O3G O3G O 0 1 N N N 18.082 2.680 21.967 0.362 -0.383 -1.301 O3G AP5 12 AP5 PD PD P 0 1 N N S 16.945 2.326 23.101 0.686 0.574 -2.554 PD AP5 13 AP5 O1D O1D O 0 1 N N N 16.975 0.838 23.248 -0.460 1.479 -2.793 O1D AP5 14 AP5 O2D O2D O 0 1 N N N 17.317 3.050 24.336 2.001 1.446 -2.237 O2D AP5 15 AP5 O3D O3D O 0 1 N N N 15.397 2.495 22.602 0.942 -0.325 -3.865 O3D AP5 16 AP5 PE PE P 0 1 N N S 14.541 3.700 21.938 1.258 0.691 -5.073 PE AP5 17 AP5 O1E O1E O 0 1 N N N 14.837 5.089 22.338 0.103 1.594 -5.273 O1E AP5 18 AP5 O2E O2E O 0 1 N N N 14.021 3.514 20.557 2.564 1.562 -4.713 O2E AP5 19 AP5 O5F AO5* O 0 1 N N N 23.694 5.984 20.010 -1.340 0.176 6.373 O5F AP5 20 AP5 C5F AC5* C 0 1 N N N 23.863 5.533 21.343 -1.522 1.180 7.373 C5F AP5 21 AP5 C4F AC4* C 0 1 N N R 24.868 6.417 22.062 -1.852 0.513 8.710 C4F AP5 22 AP5 O4F AO4* O 0 1 N N N 26.197 6.203 21.583 -0.764 -0.337 9.130 O4F AP5 23 AP5 C3F AC3* C 0 1 N N S 24.677 7.945 21.924 -1.977 1.574 9.827 C3F AP5 24 AP5 O3F AO3* O 0 1 N N N 25.346 8.532 23.016 -3.349 1.898 10.058 O3F AP5 25 AP5 C2F AC2* C 0 1 N N R 25.443 8.295 20.628 -1.364 0.886 11.069 C2F AP5 26 AP5 O2F AO2* O 0 1 N N N 26.145 9.548 20.716 -2.339 0.767 12.107 O2F AP5 27 AP5 C1F AC1* C 0 1 N N R 26.421 7.150 20.562 -0.939 -0.506 10.554 C1F AP5 28 AP5 N9A AN9 N 0 1 Y N N 27.112 6.824 19.345 0.319 -0.919 11.178 N9A AP5 29 AP5 C8A AC8 C 0 1 Y N N 26.489 6.695 18.135 1.574 -0.648 10.719 C8A AP5 30 AP5 N7A AN7 N 0 1 Y N N 27.295 6.275 17.223 2.461 -1.166 11.518 N7A AP5 31 AP5 C5A AC5 C 0 1 Y N N 28.529 6.124 17.797 1.834 -1.796 12.540 C5A AP5 32 AP5 C6A AC6 C 0 1 Y N N 29.735 5.649 17.285 2.262 -2.520 13.665 C6A AP5 33 AP5 N6A AN6 N 0 1 N N N 29.771 5.190 16.024 3.610 -2.701 13.920 N6A AP5 34 AP5 N1A AN1 N 0 1 Y N N 30.793 5.669 18.130 1.342 -3.022 14.483 N1A AP5 35 AP5 C2A AC2 C 0 1 Y N N 30.595 6.010 19.414 0.054 -2.854 14.248 C2A AP5 36 AP5 N3A AN3 N 0 1 Y N N 29.508 6.464 20.023 -0.392 -2.188 13.204 N3A AP5 37 AP5 C4A AC4 C 0 1 Y N N 28.440 6.487 19.168 0.452 -1.650 12.331 C4A AP5 38 AP5 O5J BO5* O 0 1 N N N 13.178 3.399 22.744 1.526 -0.144 -6.422 O5J AP5 39 AP5 C5J BC5* C 0 1 N N N 13.096 3.370 24.177 1.799 0.808 -7.451 C5J AP5 40 AP5 C4J BC4* C 0 1 N N R 11.797 2.648 24.646 2.063 0.075 -8.768 C4J AP5 41 AP5 O4J BO4* O 0 1 N N N 10.642 3.052 23.872 0.897 -0.670 -9.155 O4J AP5 42 AP5 C3J BC3* C 0 1 N N S 11.850 1.118 24.442 2.352 1.095 -9.887 C3J AP5 43 AP5 O3J BO3* O 0 1 N N N 12.535 0.450 25.490 3.654 0.888 -10.437 O3J AP5 44 AP5 C2J BC2* C 0 1 N N R 10.402 0.698 24.318 1.260 0.805 -10.951 C2J AP5 45 AP5 O2J BO2* O 0 1 N N N 9.706 0.889 25.519 1.805 0.871 -12.270 O2J AP5 46 AP5 C1J BC1* C 0 1 N N R 10.066 1.830 23.414 0.840 -0.644 -10.598 C1J AP5 47 AP5 N9B BN9 N 0 1 Y N N 9.747 1.616 22.023 -0.520 -0.918 -11.065 N9B AP5 48 AP5 C8B BC8 C 0 1 Y N N 10.182 2.374 20.967 -1.675 -0.641 -10.395 C8B AP5 49 AP5 N7B BN7 N 0 1 Y N N 9.821 1.888 19.815 -2.700 -1.016 -11.102 N7B AP5 50 AP5 C5B BC5 C 0 1 Y N N 9.099 0.730 20.087 -2.271 -1.556 -12.268 C5B AP5 51 AP5 C6B BC6 C 0 1 Y N N 8.487 -0.225 19.272 -2.905 -2.115 -13.391 C6B AP5 52 AP5 N6B BN6 N 0 1 N N N 8.669 -0.222 17.956 -4.285 -2.198 -13.457 N6B AP5 53 AP5 N1B BN1 N 0 1 Y N N 7.799 -1.199 19.879 -2.148 -2.563 -14.388 N1B AP5 54 AP5 C2B BC2 C 0 1 Y N N 7.763 -1.199 21.208 -0.831 -2.488 -14.333 C2B AP5 55 AP5 N3B BN3 N 0 1 Y N N 8.373 -0.426 22.108 -0.194 -1.973 -13.303 N3B AP5 56 AP5 C4B BC4 C 0 1 Y N N 9.034 0.571 21.499 -0.867 -1.495 -12.261 C4B AP5 57 AP5 HOA2 2HOA H 0 0 N N N 21.337 6.442 21.318 -3.000 1.364 4.509 HOA2 AP5 58 AP5 HOB2 2HOB H 0 0 N N N 18.720 4.315 17.731 -2.448 1.122 2.011 HOB2 AP5 59 AP5 HOG2 2HOG H 0 0 N N N 16.355 2.760 19.734 2.159 0.823 0.418 HOG2 AP5 60 AP5 HOD2 2HOD H 0 0 N N N 16.660 2.845 24.991 2.723 0.820 -2.088 HOD2 AP5 61 AP5 HOE2 2HOE H 0 0 N N N 13.519 4.220 20.167 3.292 0.937 -4.591 HOE2 AP5 62 AP5 H51A AH51 H 0 0 N N N 22.893 5.469 21.890 -2.341 1.838 7.083 H51A AP5 63 AP5 H52A AH52 H 0 0 N N N 24.144 4.455 21.388 -0.606 1.762 7.474 H52A AP5 64 AP5 H4F AH4* H 0 1 N N N 24.696 6.114 23.121 -2.774 -0.061 8.629 H4F AP5 65 AP5 H3F AH3* H 0 1 N N N 23.613 8.280 21.898 -1.412 2.469 9.567 H3F AP5 66 AP5 HO3A AHO3 H 0 0 N N N 25.228 9.470 22.931 -3.364 2.562 10.762 HO3A AP5 67 AP5 H2F AH2* H 0 1 N N N 24.778 8.414 19.740 -0.496 1.441 11.424 H2F AP5 68 AP5 HO2A AHO2 H 0 0 N N N 26.615 9.763 19.919 -2.607 1.666 12.343 HO2A AP5 69 AP5 H1F AH1* H 0 1 N N N 27.422 7.575 20.805 -1.720 -1.239 10.755 H1F AP5 70 AP5 H8A AH8 H 0 1 N N N 25.430 6.910 17.914 1.798 -0.086 9.824 H8A AP5 71 AP5 H61A AH61 H 0 0 N N N 30.653 4.842 15.649 3.893 -3.200 14.703 H61A AP5 72 AP5 H62A AH62 H 0 0 N N N 29.411 5.913 15.400 4.272 -2.333 13.314 H62A AP5 73 AP5 H2A AH2 H 0 1 N N N 31.469 5.898 20.077 -0.659 -3.279 14.938 H2A AP5 74 AP5 H51B BH51 H 0 0 N N N 14.006 2.915 24.632 0.941 1.470 -7.570 H51B AP5 75 AP5 H52B BH52 H 0 0 N N N 13.179 4.392 24.614 2.676 1.395 -7.180 H52B AP5 76 AP5 H4J BH4* H 0 1 N N N 11.718 2.924 25.723 2.912 -0.598 -8.653 H4J AP5 77 AP5 H3J BH3* H 0 1 N N N 12.435 0.839 23.534 2.255 2.112 -9.509 H3J AP5 78 AP5 HO3B BHO3 H 0 0 N N N 12.567 -0.491 25.364 3.751 1.514 -11.169 HO3B AP5 79 AP5 H2J BH2* H 0 1 N N N 10.191 -0.355 24.021 0.420 1.491 -10.844 H2J AP5 80 AP5 HO2B BHO2 H 0 0 N N N 8.796 0.625 25.441 2.046 1.795 -12.427 HO2B AP5 81 AP5 H1J BH1* H 0 1 N N N 8.964 1.972 23.508 1.542 -1.361 -11.023 H1J AP5 82 AP5 H8B BH8 H 0 1 N N N 10.775 3.301 21.038 -1.729 -0.178 -9.421 H8B AP5 83 AP5 H61B BH61 H 0 0 N N N 8.222 -0.919 17.360 -4.710 -2.586 -14.238 H61B AP5 84 AP5 H62B BH62 H 0 0 N N N 9.672 -0.248 17.775 -4.826 -1.868 -12.723 H62B AP5 85 AP5 H2B BH2 H 0 1 N N N 7.112 -1.977 21.640 -0.254 -2.864 -15.165 H2B AP5 86 # 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 AP5 PA O1A DOUB N N 1 AP5 PA O2A SING N N 2 AP5 PA O3A SING N N 3 AP5 PA O5F SING N N 4 AP5 O2A HOA2 SING N N 5 AP5 O3A PB SING N N 6 AP5 PB O1B DOUB N N 7 AP5 PB O2B SING N N 8 AP5 PB O3B SING N N 9 AP5 O2B HOB2 SING N N 10 AP5 O3B PG SING N N 11 AP5 PG O1G DOUB N N 12 AP5 PG O2G SING N N 13 AP5 PG O3G SING N N 14 AP5 O2G HOG2 SING N N 15 AP5 O3G PD SING N N 16 AP5 PD O1D DOUB N N 17 AP5 PD O2D SING N N 18 AP5 PD O3D SING N N 19 AP5 O2D HOD2 SING N N 20 AP5 O3D PE SING N N 21 AP5 PE O1E DOUB N N 22 AP5 PE O2E SING N N 23 AP5 PE O5J SING N N 24 AP5 O2E HOE2 SING N N 25 AP5 O5F C5F SING N N 26 AP5 C5F C4F SING N N 27 AP5 C5F H51A SING N N 28 AP5 C5F H52A SING N N 29 AP5 C4F O4F SING N N 30 AP5 C4F C3F SING N N 31 AP5 C4F H4F SING N N 32 AP5 O4F C1F SING N N 33 AP5 C3F O3F SING N N 34 AP5 C3F C2F SING N N 35 AP5 C3F H3F SING N N 36 AP5 O3F HO3A SING N N 37 AP5 C2F O2F SING N N 38 AP5 C2F C1F SING N N 39 AP5 C2F H2F SING N N 40 AP5 O2F HO2A SING N N 41 AP5 C1F N9A SING N N 42 AP5 C1F H1F SING N N 43 AP5 N9A C8A SING Y N 44 AP5 N9A C4A SING Y N 45 AP5 C8A N7A DOUB Y N 46 AP5 C8A H8A SING N N 47 AP5 N7A C5A SING Y N 48 AP5 C5A C6A SING Y N 49 AP5 C5A C4A DOUB Y N 50 AP5 C6A N6A SING N N 51 AP5 C6A N1A DOUB Y N 52 AP5 N6A H61A SING N N 53 AP5 N6A H62A SING N N 54 AP5 N1A C2A SING Y N 55 AP5 C2A N3A DOUB Y N 56 AP5 C2A H2A SING N N 57 AP5 N3A C4A SING Y N 58 AP5 O5J C5J SING N N 59 AP5 C5J C4J SING N N 60 AP5 C5J H51B SING N N 61 AP5 C5J H52B SING N N 62 AP5 C4J O4J SING N N 63 AP5 C4J C3J SING N N 64 AP5 C4J H4J SING N N 65 AP5 O4J C1J SING N N 66 AP5 C3J O3J SING N N 67 AP5 C3J C2J SING N N 68 AP5 C3J H3J SING N N 69 AP5 O3J HO3B SING N N 70 AP5 C2J O2J SING N N 71 AP5 C2J C1J SING N N 72 AP5 C2J H2J SING N N 73 AP5 O2J HO2B SING N N 74 AP5 C1J N9B SING N N 75 AP5 C1J H1J SING N N 76 AP5 N9B C8B SING Y N 77 AP5 N9B C4B SING Y N 78 AP5 C8B N7B DOUB Y N 79 AP5 C8B H8B SING N N 80 AP5 N7B C5B SING Y N 81 AP5 C5B C6B SING Y N 82 AP5 C5B C4B DOUB Y N 83 AP5 C6B N6B SING N N 84 AP5 C6B N1B DOUB Y N 85 AP5 N6B H61B SING N N 86 AP5 N6B H62B SING N N 87 AP5 N1B C2B SING Y N 88 AP5 C2B N3B DOUB Y N 89 AP5 C2B H2B SING N N 90 AP5 N3B C4B SING Y N 91 # 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 AP5 SMILES_CANONICAL CACTVS 3.341 "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[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)n5cnc6c(N)ncnc56)[C@@H](O)[C@H]3O" AP5 SMILES CACTVS 3.341 "Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(=O)O[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)[CH](O)[CH]3O" AP5 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@](=O)(O)OP(=O)(O)O[P@@](=O)(O)O[P@@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)O)O)N" AP5 SMILES "OpenEye OEToolkits" 1.5.0 "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)N" AP5 InChI InChI 1.03 ;InChI=1S/C20H29N10O22P5/c21-15-9-17(25-3-23-15)29(5-27-9)19-13(33)11(31)7(47-19)1-45-53(35,36)49-55(39,40)51-57(43,44)52-56(41,42)50-54(37,38)46-2-8-12(32)14(34)20(48-8)30-6-28-10-16(22)24-4-26-18(10)30/h3-8,11-14,19-20,31-34H,1-2H2,(H,35,36)(H,37,38)(H,39,40)(H,41,42)(H,43,44)(H2,21,23,25)(H2,22,24,26)/t7-,8-,11-,12-,13-,14-,19-,20-/m1/s1 ; AP5 InChIKey InChI 1.03 OIMACDRJUANHTJ-XPWFQUROSA-N # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version _pdbx_chem_comp_identifier.identifier AP5 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[[[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-hydroxy-phosphoryl]oxy-hydroxy-phosphoryl]oxy-hydroxy-phosphoryl] [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl 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 AP5 "Create component" 1999-07-08 RCSB AP5 "Modify descriptor" 2011-06-04 RCSB #