data_A8P # _chem_comp.id A8P _chem_comp.name "8-n-octylamino-adenosine diphosphate hydroxypyrrolidinediol" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C23 H42 N7 O12 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 1 _chem_comp.pdbx_initial_date 2012-07-10 _chem_comp.pdbx_modified_date 2014-09-05 _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 670.567 _chem_comp.one_letter_code ? _chem_comp.three_letter_code A8P _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 4A1I _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site EBI # 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 A8P C1 C1 C 0 1 N N N 32.351 -4.117 -2.393 11.396 6.712 -2.100 C1 A8P 1 A8P C2 C2 C 0 1 N N N 33.276 -3.111 -1.741 10.820 5.850 -0.975 C2 A8P 2 A8P C3 C3 C 0 1 N N N 33.019 -1.627 -2.049 9.686 4.984 -1.526 C3 A8P 3 A8P C4 C4 C 0 1 N N N 31.569 -1.150 -2.046 9.109 4.122 -0.401 C4 A8P 4 A8P C5 C5 C 0 1 N N N 31.171 -0.094 -0.983 7.975 3.256 -0.951 C5 A8P 5 A8P C6 C6 C 0 1 N N N 29.863 0.577 -1.360 7.399 2.394 0.174 C6 A8P 6 A8P C7 C7 C 0 1 N N N 28.855 0.905 -0.292 6.264 1.528 -0.377 C7 A8P 7 A8P C8 C8 C 0 1 N N N 27.648 0.034 -0.363 5.688 0.666 0.748 C8 A8P 8 A8P N9 N9 N 0 1 N N N 27.711 -1.155 0.047 4.602 -0.163 0.221 N9 A8P 9 A8P C10 C10 C 0 1 Y N N 26.682 -1.963 -0.272 3.926 -1.029 1.057 C10 A8P 10 A8P N11 N11 N 0 1 Y N N 25.514 -1.650 -0.784 4.168 -1.185 2.334 N11 A8P 11 A8P C12 C12 C 0 1 Y N N 24.857 -2.856 -0.922 3.319 -2.113 2.844 C12 A8P 12 A8P C13 C13 C 0 1 Y N N 23.559 -3.175 -1.390 3.119 -2.672 4.116 C13 A8P 13 A8P N14 N14 N 0 1 Y N N 23.205 -4.472 -1.374 2.166 -3.587 4.264 N14 A8P 14 A8P C15 C15 C 0 1 Y N N 24.091 -5.353 -0.933 1.421 -3.968 3.243 C15 A8P 15 A8P N16 N16 N 0 1 Y N N 25.323 -5.179 -0.470 1.573 -3.472 2.033 N16 A8P 16 A8P C17 C17 C 0 1 Y N N 25.650 -3.896 -0.492 2.500 -2.551 1.790 C17 A8P 17 A8P N18 N18 N 0 1 Y N N 26.838 -3.323 -0.082 2.899 -1.849 0.677 N18 A8P 18 A8P C19 C19 C 0 1 N N R 27.986 -4.050 0.489 2.331 -1.960 -0.669 C19 A8P 19 A8P C20 C20 C 0 1 N N R 29.377 -3.818 -0.112 2.734 -3.305 -1.313 C20 A8P 20 A8P C21 C21 C 0 1 N N S 30.082 -3.101 1.055 1.480 -3.731 -2.109 C21 A8P 21 A8P C22 C22 C 0 1 N N R 29.406 -3.671 2.285 0.468 -2.593 -1.852 C22 A8P 22 A8P O23 O23 O 0 1 N N N 28.043 -3.793 1.874 0.889 -2.000 -0.604 O23 A8P 23 A8P C24 C24 C 0 1 N N N 29.447 -2.838 3.530 -0.948 -3.159 -1.722 C24 A8P 24 A8P O25 O25 O 0 1 N N N 28.901 -1.547 3.256 -1.881 -2.083 -1.601 O25 A8P 25 A8P P26 P26 P 0 1 N N N 29.143 -0.346 4.241 -3.467 -2.312 -1.446 P26 A8P 26 A8P O27 O27 O 0 1 N N N 30.545 0.138 4.207 -4.045 -2.990 -2.787 O27 A8P 27 A8P O28 O28 O 0 1 N N N 28.083 0.728 4.005 -3.727 -3.202 -0.292 O28 A8P 28 A8P O29 O29 O 0 1 N N N 28.738 -1.042 5.613 -4.193 -0.896 -1.205 O29 A8P 29 A8P P30 P30 P 0 1 N N N 29.417 -1.128 7.052 -5.616 -0.458 -0.593 P30 A8P 30 A8P O31 O31 O 0 1 N N N 28.535 -1.853 8.003 -6.779 -0.769 -1.662 O31 A8P 31 A8P O32 O32 O 0 1 N N N 30.824 -1.714 6.892 -5.873 -1.218 0.651 O32 A8P 32 A8P O33 O33 O 0 1 N N N 29.515 0.402 7.435 -5.597 1.118 -0.264 O33 A8P 33 A8P C34 C34 C 0 1 N N N 28.654 0.967 8.450 -6.677 1.791 0.386 C34 A8P 34 A8P C35 C35 C 0 1 N N R 28.821 2.460 8.435 -6.334 3.274 0.543 C35 A8P 35 A8P C36 C36 C 0 1 N N R 27.844 3.199 9.351 -7.431 3.997 1.354 C36 A8P 36 A8P C37 C37 C 0 1 N N S 26.700 3.563 8.408 -7.564 5.386 0.697 C37 A8P 37 A8P C38 C38 C 0 1 N N N 27.501 4.053 7.205 -6.537 5.386 -0.455 C38 A8P 38 A8P N39 N39 N 1 1 N N N 28.557 3.021 7.097 -6.340 3.949 -0.780 N39 A8P 39 A8P O40 O40 O 0 1 N N N 25.852 4.598 8.899 -7.251 6.413 1.640 O40 A8P 40 A8P O41 O41 O 0 1 N N N 28.414 4.407 9.914 -7.032 4.130 2.720 O41 A8P 41 A8P O42 O42 O 0 1 N N N 31.470 -3.377 1.143 1.781 -3.828 -3.503 O42 A8P 42 A8P O43 O43 O 0 1 N N N 30.041 -5.038 -0.450 3.848 -3.126 -2.191 O43 A8P 43 A8P N44 N44 N 0 1 N N N 22.670 -2.266 -1.848 3.897 -2.278 5.193 N44 A8P 44 A8P H1 H1 H 0 1 N N N 32.643 -5.134 -2.091 12.205 7.329 -1.708 H1 A8P 45 A8P H1A H1A H 0 1 N N N 31.316 -3.923 -2.075 11.782 6.068 -2.890 H1A A8P 46 A8P H2 H2 H 0 1 N N N 33.196 -3.243 -0.652 11.603 5.209 -0.571 H2 A8P 47 A8P H3 H3 H 0 1 N N N 33.563 -1.035 -1.298 8.902 5.625 -1.930 H3 A8P 48 A8P H3A H3A H 0 1 N N N 33.432 -1.421 -3.047 10.071 4.340 -2.316 H3A A8P 49 A8P H4 H4 H 0 1 N N N 31.361 -0.717 -3.036 9.893 3.481 0.003 H4 A8P 50 A8P H4A H4A H 0 1 N N N 30.931 -2.032 -1.890 8.724 4.766 0.389 H4A A8P 51 A8P H5 H5 H 0 1 N N N 31.055 -0.589 -0.007 7.192 3.897 -1.355 H5 A8P 52 A8P H5A H5A H 0 1 N N N 31.962 0.668 -0.916 8.361 2.612 -1.742 H5A A8P 53 A8P H6 H6 H 0 1 N N N 30.122 1.525 -1.855 8.182 1.753 0.578 H6 A8P 54 A8P H6A H6A H 0 1 N N N 29.360 -0.087 -2.079 7.013 3.038 0.964 H6A A8P 55 A8P H7 H7 H 0 1 N N N 29.328 0.774 0.692 5.481 2.169 -0.781 H7 A8P 56 A8P H7A H7A H 0 1 N N N 28.542 1.953 -0.412 6.650 0.884 -1.167 H7A A8P 57 A8P H81 H81 H 0 1 N N N 26.861 0.532 0.222 6.471 0.025 1.152 H81 A8P 58 A8P H15 H15 H 0 1 N N N 23.757 -6.380 -0.954 0.658 -4.715 3.407 H15 A8P 59 A8P H19 H19 H 0 1 N N N 27.775 -5.122 0.361 2.660 -1.127 -1.289 H19 A8P 60 A8P H20 H20 H 0 1 N N N 29.306 -3.144 -0.978 2.967 -4.042 -0.544 H20 A8P 61 A8P H21 H21 H 0 1 N N N 29.892 -2.019 0.991 1.095 -4.680 -1.736 H21 A8P 62 A8P H22 H22 H 0 1 N N N 29.829 -4.664 2.499 0.510 -1.859 -2.656 H22 A8P 63 A8P H24 H24 H 0 1 N N N 28.855 -3.327 4.318 -1.186 -3.749 -2.607 H24 A8P 64 A8P H24A H24A H 0 0 N N N 30.489 -2.732 3.866 -1.006 -3.792 -0.837 H24A A8P 65 A8P HO27 HO27 H 0 0 N N N 30.554 1.073 4.037 -3.910 -2.461 -3.585 HO27 A8P 66 A8P HO31 HO31 H 0 0 N N N 29.005 -2.591 8.372 -6.675 -0.303 -2.503 HO31 A8P 67 A8P H34 H34 H 0 1 N N N 27.607 0.708 8.235 -7.582 1.689 -0.213 H34 A8P 68 A8P H34A H34A H 0 0 N N N 28.934 0.572 9.437 -6.840 1.350 1.369 H34A A8P 69 A8P H35 H35 H 0 1 N N N 29.848 2.710 8.740 -5.364 3.390 1.027 H35 A8P 70 A8P H36 H36 H 0 1 N N N 27.483 2.524 10.141 -8.373 3.453 1.286 H36 A8P 71 A8P H37 H37 H 0 1 N N N 26.128 2.662 8.141 -8.572 5.526 0.308 H37 A8P 72 A8P H38 H38 H 0 1 N N N 26.880 4.086 6.298 -6.934 5.919 -1.319 H38 A8P 73 A8P H38A H38A H 0 0 N N N 27.932 5.048 7.390 -5.599 5.836 -0.129 H38A A8P 74 A8P H39A H39A H 0 0 N N N 29.393 3.434 6.736 -5.458 3.812 -1.250 H39A A8P 75 A8P HO40 HO40 H 0 0 N N N 25.166 4.773 8.266 -7.318 7.309 1.283 HO40 A8P 76 A8P HO41 HO41 H 0 0 N N N 27.773 4.829 10.473 -7.682 4.577 3.278 HO41 A8P 77 A8P HO42 HO42 H 0 0 N N N 31.841 -2.906 1.880 2.457 -4.487 -3.714 HO42 A8P 78 A8P HO43 HO43 H 0 0 N N N 30.895 -4.843 -0.817 4.143 -3.940 -2.622 HO43 A8P 79 A8P HN44 HN44 H 0 0 N N N 21.829 -2.731 -2.123 4.589 -1.609 5.073 HN44 A8P 80 A8P HN4A HN4A H 0 0 N N N 22.465 -1.607 -1.125 3.749 -2.671 6.067 HN4A A8P 81 A8P H9 H9 H 0 1 N N N 28.543 -1.561 -0.331 4.357 -0.104 -0.716 H9 A8P 82 A8P H82 H82 H 0 1 N N N 27.347 -0.009 -1.420 5.302 1.310 1.538 H82 A8P 83 A8P H1B H1B H 0 1 N N N 32.422 -4.025 -3.487 10.613 7.353 -2.504 H1B A8P 84 A8P H2A H2A H 0 1 N N N 34.301 -3.345 -2.064 10.434 6.495 -0.185 H2A A8P 85 A8P H39B H39B H 0 0 N N N 28.252 2.293 6.483 -7.101 3.608 -1.347 H39B A8P 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 A8P C1 C2 SING N N 1 A8P C1 H1 SING N N 2 A8P C1 H1A SING N N 3 A8P C3 C2 SING N N 4 A8P C2 H2 SING N N 5 A8P C3 C4 SING N N 6 A8P C3 H3 SING N N 7 A8P C3 H3A SING N N 8 A8P C4 C5 SING N N 9 A8P C4 H4 SING N N 10 A8P C4 H4A SING N N 11 A8P C6 C5 SING N N 12 A8P C5 H5 SING N N 13 A8P C5 H5A SING N N 14 A8P C6 C7 SING N N 15 A8P C6 H6 SING N N 16 A8P C6 H6A SING N N 17 A8P C8 C7 SING N N 18 A8P C7 H7 SING N N 19 A8P C7 H7A SING N N 20 A8P C8 N9 SING N N 21 A8P C8 H81 SING N N 22 A8P C10 N9 SING N N 23 A8P N11 C10 DOUB Y N 24 A8P C10 N18 SING Y N 25 A8P C12 N11 SING Y N 26 A8P C13 C12 DOUB Y N 27 A8P C12 C17 SING Y N 28 A8P N44 C13 SING N N 29 A8P C13 N14 SING Y N 30 A8P N14 C15 DOUB Y N 31 A8P C15 N16 SING Y N 32 A8P C15 H15 SING N N 33 A8P C17 N16 DOUB Y N 34 A8P C17 N18 SING Y N 35 A8P N18 C19 SING N N 36 A8P C20 C19 SING N N 37 A8P C19 O23 SING N N 38 A8P C19 H19 SING N N 39 A8P O43 C20 SING N N 40 A8P C20 C21 SING N N 41 A8P C20 H20 SING N N 42 A8P C21 O42 SING N N 43 A8P C21 C22 SING N N 44 A8P C21 H21 SING N N 45 A8P O23 C22 SING N N 46 A8P C22 C24 SING N N 47 A8P C22 H22 SING N N 48 A8P O25 C24 SING N N 49 A8P C24 H24 SING N N 50 A8P C24 H24A SING N N 51 A8P O25 P26 SING N N 52 A8P O28 P26 DOUB N N 53 A8P O27 P26 SING N N 54 A8P P26 O29 SING N N 55 A8P O27 HO27 SING N N 56 A8P O29 P30 SING N N 57 A8P O32 P30 DOUB N N 58 A8P P30 O33 SING N N 59 A8P P30 O31 SING N N 60 A8P O31 HO31 SING N N 61 A8P O33 C34 SING N N 62 A8P C35 C34 SING N N 63 A8P C34 H34 SING N N 64 A8P C34 H34A SING N N 65 A8P N39 C35 SING N N 66 A8P C35 C36 SING N N 67 A8P C35 H35 SING N N 68 A8P C37 C36 SING N N 69 A8P C36 O41 SING N N 70 A8P C36 H36 SING N N 71 A8P C38 C37 SING N N 72 A8P C37 O40 SING N N 73 A8P C37 H37 SING N N 74 A8P N39 C38 SING N N 75 A8P C38 H38 SING N N 76 A8P C38 H38A SING N N 77 A8P N39 H39A SING N N 78 A8P O40 HO40 SING N N 79 A8P O41 HO41 SING N N 80 A8P O42 HO42 SING N N 81 A8P O43 HO43 SING N N 82 A8P N44 HN44 SING N N 83 A8P N44 HN4A SING N N 84 A8P N9 H9 SING N N 85 A8P C8 H82 SING N N 86 A8P C1 H1B SING N N 87 A8P C2 H2A SING N N 88 A8P N39 H39B SING N N 89 # 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 A8P SMILES ACDLabs 12.01 "O=P(OCC1[NH2+]CC(O)C1O)(O)OP(=O)(O)OCC4OC(n3c(nc2c(ncnc23)N)NCCCCCCCC)C(O)C4O" A8P InChI InChI 1.03 ;InChI=1S/C23H41N7O12P2/c1-2-3-4-5-6-7-8-25-23-29-16-20(24)27-12-28-21(16)30(23)22-19(34)18(33)15(41-22)11-40-44(37,38)42-43(35,36)39-10-13-17(32)14(31)9-26-13/h12-15,17-19,22,26,31-34H,2-11H2,1H3,(H,25,29)(H,35,36)(H,37,38)(H2,24,27,28)/p+1/t13-,14+,15-,17-,18-,19-,22-/m1/s1 ; A8P InChIKey InChI 1.03 HQJQCBXMIIQUTE-WBZRXDBSSA-O A8P SMILES_CANONICAL CACTVS 3.385 "CCCCCCCCNc1nc2c(N)ncnc2n1[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)OC[C@H]4[NH2+]C[C@H](O)[C@@H]4O)[C@@H](O)[C@H]3O" A8P SMILES CACTVS 3.385 "CCCCCCCCNc1nc2c(N)ncnc2n1[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]4[NH2+]C[CH](O)[CH]4O)[CH](O)[CH]3O" A8P SMILES_CANONICAL "OpenEye OEToolkits" 1.9.2 "CCCCCCCCNc1nc2c(ncnc2n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OC[C@@H]4[C@H]([C@H](C[NH2+]4)O)O)O)O)N" A8P SMILES "OpenEye OEToolkits" 1.9.2 "CCCCCCCCNc1nc2c(ncnc2n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C[NH2+]4)O)O)O)O)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 A8P "SYSTEMATIC NAME" ACDLabs 12.01 "5'-O-[(S)-{[(R)-{[(2R,3R,4S)-3,4-dihydroxypyrrolidinium-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-8-(octylamino)adenosine" A8P "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.9.2 "[[(2R,3S,4R,5R)-5-[6-azanyl-8-(octylamino)purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3R,4S)-3,4-bis(oxidanyl)pyrrolidin-1-ium-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 A8P "Create component" 2012-07-10 EBI A8P "Modify formula" 2012-07-11 EBI A8P "Other modification" 2012-07-11 EBI A8P "Other modification" 2012-08-06 EBI A8P "Modify formula" 2012-08-06 EBI A8P "Modify charge" 2012-08-06 EBI A8P "Modify formal charge" 2012-08-06 EBI A8P "Initial release" 2012-12-14 RCSB A8P "Modify descriptor" 2014-09-05 RCSB #