data_F5D # _chem_comp.id F5D _chem_comp.name "5'-O-[(S)-({5-[(2R,3aS,4S,6aR)-2-hydroxyhexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoyl}oxy){[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]adenosine" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C20 H32 N7 O15 P3 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2018-02-28 _chem_comp.pdbx_modified_date 2018-03-29 _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 735.492 _chem_comp.one_letter_code ? _chem_comp.three_letter_code F5D _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 6CK0 _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 F5D C10 C1 C 0 1 Y N N 17.472 0.819 36.830 -7.836 3.725 -0.872 C10 F5D 1 F5D C13 C2 C 0 1 N N R 15.722 2.947 32.129 -4.477 -0.738 0.676 C13 F5D 2 F5D C21 C3 C 0 1 N N N 13.185 -3.441 31.119 2.749 0.965 1.088 C21 F5D 3 F5D C22 C4 C 0 1 N N N 13.814 -4.122 32.356 4.131 0.716 0.480 C22 F5D 4 F5D C24 C5 C 0 1 N N N 15.082 -6.201 33.175 6.538 1.385 0.544 C24 F5D 5 F5D C28 C6 C 0 1 N N R 16.194 -9.839 32.590 9.824 3.360 0.860 C28 F5D 6 F5D C02 C7 C 0 1 Y N N 17.091 0.201 38.035 -8.911 4.629 -0.822 C02 F5D 7 F5D C04 C8 C 0 1 Y N N 15.284 1.605 38.225 -9.690 3.546 1.062 C04 F5D 8 F5D C06 C9 C 0 1 Y N N 16.690 1.845 36.371 -7.761 2.729 0.117 C06 F5D 9 F5D C08 C10 C 0 1 Y N N 18.301 1.563 34.959 -6.065 2.542 -1.280 C08 F5D 10 F5D C11 C11 C 0 1 N N R 16.668 3.354 34.428 -6.134 0.848 0.589 C11 F5D 11 F5D C14 C12 C 0 1 N N N 16.132 1.658 31.378 -3.211 -1.245 -0.018 C14 F5D 12 F5D C19 C13 C 0 1 N N N 12.885 -1.938 31.250 1.740 0.062 0.427 C19 F5D 13 F5D C23 C14 C 0 1 N N N 14.096 -5.629 32.159 5.156 1.633 1.151 C23 F5D 14 F5D C25 C15 C 0 1 N N S 15.025 -7.719 33.457 7.562 2.302 1.215 C25 F5D 15 F5D C27 C16 C 0 1 N N N 15.967 -9.748 34.258 8.968 4.628 1.008 C27 F5D 16 F5D C30 C17 C 0 1 N N R 17.878 -8.446 31.878 9.632 3.099 -1.446 C30 F5D 17 F5D C33 C18 C 0 1 N N S 15.534 -8.683 32.090 8.968 2.105 0.603 C33 F5D 18 F5D C43 C19 C 0 1 N N S 16.625 3.918 32.123 -5.714 -1.516 0.174 C43 F5D 19 F5D C45 C20 C 0 1 N N R 17.510 3.791 33.527 -6.829 -0.448 0.115 C45 F5D 20 F5D N01 N1 N 0 1 N N N 17.878 -0.880 38.547 -9.038 5.630 -1.769 N01 F5D 21 F5D N03 N2 N 0 1 Y N N 16.016 0.600 38.698 -9.803 4.499 0.155 N03 F5D 22 F5D N05 N3 N 0 1 Y N N 15.610 2.212 37.085 -8.700 2.678 1.055 N05 F5D 23 F5D N07 N4 N 0 1 Y N N 17.231 2.289 35.228 -6.634 1.999 -0.167 N07 F5D 24 F5D N09 N5 N 0 1 Y N N 18.459 0.673 35.926 -6.769 3.558 -1.689 N09 F5D 25 F5D N29 N6 N 0 1 N N N 17.692 -9.744 32.118 10.613 3.488 -0.400 N29 F5D 26 F5D N32 N7 N 0 1 N N N 16.527 -7.993 31.203 8.862 1.977 -0.863 N32 F5D 27 F5D O12 O1 O 0 1 N N N 15.472 2.660 33.645 -4.732 0.636 0.313 O12 F5D 28 F5D O15 O2 O 0 1 N N N 15.101 0.685 31.465 -2.068 -0.597 0.542 O15 F5D 29 F5D O17 O3 O 0 1 N N N 14.509 0.833 29.033 -0.472 -0.675 -1.412 O17 F5D 30 F5D O18 O4 O 0 1 N N N 13.258 -1.017 30.222 0.452 0.106 0.803 O18 F5D 31 F5D O20 O5 O 0 1 N N N 12.302 -1.602 32.227 2.091 -0.703 -0.441 O20 F5D 32 F5D O31 O6 O 0 1 N N N 18.999 -8.155 31.121 10.312 2.670 -2.628 O31 F5D 33 F5D O34 O7 O 0 1 N N N 12.688 1.698 30.602 -0.174 -2.414 0.392 O34 F5D 34 F5D O36 O8 O 0 1 N N N 13.470 4.187 31.133 1.250 -3.215 -1.532 O36 F5D 35 F5D O37 O9 O 0 1 N N N 12.924 3.610 28.786 2.349 -3.067 0.736 O37 F5D 36 F5D O38 O10 O 0 1 N N N 11.095 3.946 30.549 0.572 -4.928 0.194 O38 F5D 37 F5D O40 O11 O 0 1 N N N 8.904 5.111 30.263 2.601 -6.371 -0.219 O40 F5D 38 F5D O41 O12 O 0 1 N N N 9.181 2.876 29.213 0.519 -7.520 0.627 O41 F5D 39 F5D O42 O13 O 0 1 N N N 10.260 4.851 28.210 0.673 -6.601 -1.831 O42 F5D 40 F5D O44 O14 O 0 1 N N N 15.962 5.188 32.184 -6.061 -2.552 1.095 O44 F5D 41 F5D O46 O15 O 0 1 N N N 17.999 5.086 33.910 -7.899 -0.793 0.997 O46 F5D 42 F5D P16 P1 P 0 1 N N S 13.886 0.547 30.322 -0.563 -0.890 0.049 P16 F5D 43 F5D P35 P2 P 0 1 N N N 12.588 3.344 30.236 1.005 -3.402 -0.084 P35 F5D 44 F5D P39 P3 P 0 1 N N N 9.841 4.205 29.506 1.124 -6.355 -0.305 P39 F5D 45 F5D S26 S1 S 0 1 N N N 15.994 -8.112 34.469 7.235 4.066 0.810 S26 F5D 46 F5D H1 H1 H 0 1 N N N 14.772 3.296 31.698 -4.380 -0.835 1.758 H1 F5D 47 F5D H2 H2 H 0 1 N N N 13.878 -3.573 30.275 2.780 0.755 2.157 H2 F5D 48 F5D H3 H3 H 0 1 N N N 12.237 -3.954 30.899 2.465 2.005 0.930 H3 F5D 49 F5D H4 H4 H 0 1 N N N 14.765 -3.618 32.584 4.416 -0.324 0.639 H4 F5D 50 F5D H5 H5 H 0 1 N N N 13.124 -4.006 33.205 4.101 0.926 -0.589 H5 F5D 51 F5D H6 H6 H 0 1 N N N 16.095 -5.972 32.814 6.823 0.345 0.702 H6 F5D 52 F5D H7 H7 H 0 1 N N N 14.907 -5.683 34.130 6.508 1.595 -0.525 H7 F5D 53 F5D H8 H8 H 0 1 N N N 15.740 -10.771 32.223 10.467 3.221 1.729 H8 F5D 54 F5D H9 H9 H 0 1 N N N 14.413 1.933 38.773 -10.437 3.477 1.839 H9 F5D 55 F5D H10 H10 H 0 1 N N N 18.940 1.676 34.095 -5.161 2.185 -1.751 H10 F5D 56 F5D H11 H11 H 0 1 N N N 16.262 4.152 35.066 -6.295 0.996 1.656 H11 F5D 57 F5D H12 H12 H 0 1 N N N 16.316 1.898 30.320 -3.125 -2.322 0.126 H12 F5D 58 F5D H13 H13 H 0 1 N N N 17.051 1.253 31.827 -3.268 -1.025 -1.084 H13 F5D 59 F5D H14 H14 H 0 1 N N N 13.146 -6.176 32.250 4.871 2.674 0.993 H14 F5D 60 F5D H15 H15 H 0 1 N N N 14.510 -5.777 31.151 5.186 1.424 2.221 H15 F5D 61 F5D H16 H16 H 0 1 N N N 14.003 -8.023 33.728 7.578 2.145 2.293 H16 F5D 62 F5D H18 H18 H 0 1 N N N 15.003 -10.182 34.562 9.112 5.069 1.995 H18 F5D 63 F5D H19 H19 H 0 1 N N N 16.781 -10.243 34.807 9.222 5.349 0.231 H19 F5D 64 F5D H20 H20 H 0 1 N N N 17.945 -7.903 32.832 8.970 3.934 -1.672 H20 F5D 65 F5D H21 H21 H 0 1 N N N 14.631 -8.948 31.520 9.452 1.224 1.026 H21 F5D 66 F5D H23 H23 H 0 1 N N N 17.317 3.865 31.270 -5.528 -1.930 -0.817 H23 F5D 67 F5D H24 H24 H 0 1 N N N 18.342 3.096 33.341 -7.195 -0.335 -0.905 H24 F5D 68 F5D H25 H25 H 0 1 N N N 17.476 -1.210 39.401 -8.381 5.714 -2.477 H25 F5D 69 F5D H26 H26 H 0 1 N N N 17.898 -1.624 37.879 -9.785 6.248 -1.724 H26 F5D 70 F5D H27 H27 H 0 1 N N N 18.311 -10.064 32.835 10.928 4.437 -0.535 H27 F5D 71 F5D H29 H29 H 0 1 N N N 16.417 -6.999 31.228 7.898 2.008 -1.159 H29 F5D 72 F5D H31 H31 H 0 1 N N N 19.061 -7.216 30.995 10.866 3.352 -3.032 H31 F5D 73 F5D H32 H32 H 0 1 N N N 13.621 4.253 28.735 2.262 -3.169 1.693 H32 F5D 74 F5D H33 H33 H 0 1 N N N 8.299 2.875 29.567 0.810 -8.410 0.383 H33 F5D 75 F5D H34 H34 H 0 1 N N N 9.847 5.703 28.132 -0.285 -6.603 -1.963 H34 F5D 76 F5D H35 H35 H 0 1 N N N 15.071 5.096 31.867 -6.831 -3.072 0.829 H35 F5D 77 F5D H36 H36 H 0 1 N N N 18.610 5.401 33.254 -8.371 -1.600 0.747 H36 F5D 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 F5D C10 C02 DOUB Y N 1 F5D C10 C06 SING Y N 2 F5D C10 N09 SING Y N 3 F5D C13 C14 SING N N 4 F5D C13 C43 SING N N 5 F5D C13 O12 SING N N 6 F5D C21 C22 SING N N 7 F5D C21 C19 SING N N 8 F5D C22 C23 SING N N 9 F5D C24 C23 SING N N 10 F5D C24 C25 SING N N 11 F5D C28 C27 SING N N 12 F5D C28 C33 SING N N 13 F5D C28 N29 SING N N 14 F5D C02 N01 SING N N 15 F5D C02 N03 SING Y N 16 F5D C04 N03 DOUB Y N 17 F5D C04 N05 SING Y N 18 F5D C06 N05 DOUB Y N 19 F5D C06 N07 SING Y N 20 F5D C08 N07 SING Y N 21 F5D C08 N09 DOUB Y N 22 F5D C11 C45 SING N N 23 F5D C11 N07 SING N N 24 F5D C11 O12 SING N N 25 F5D C14 O15 SING N N 26 F5D C19 O18 SING N N 27 F5D C19 O20 DOUB N N 28 F5D C25 S26 SING N N 29 F5D C27 S26 SING N N 30 F5D C30 N29 SING N N 31 F5D C30 N32 SING N N 32 F5D C30 O31 SING N N 33 F5D C33 N32 SING N N 34 F5D C43 C45 SING N N 35 F5D C43 O44 SING N N 36 F5D C45 O46 SING N N 37 F5D O15 P16 SING N N 38 F5D O17 P16 DOUB N N 39 F5D O18 P16 SING N N 40 F5D O34 P16 SING N N 41 F5D O34 P35 SING N N 42 F5D O36 P35 DOUB N N 43 F5D O37 P35 SING N N 44 F5D O38 P35 SING N N 45 F5D O38 P39 SING N N 46 F5D O40 P39 DOUB N N 47 F5D O41 P39 SING N N 48 F5D O42 P39 SING N N 49 F5D C13 H1 SING N N 50 F5D C21 H2 SING N N 51 F5D C21 H3 SING N N 52 F5D C22 H4 SING N N 53 F5D C22 H5 SING N N 54 F5D C24 H6 SING N N 55 F5D C24 H7 SING N N 56 F5D C28 H8 SING N N 57 F5D C04 H9 SING N N 58 F5D C08 H10 SING N N 59 F5D C11 H11 SING N N 60 F5D C14 H12 SING N N 61 F5D C14 H13 SING N N 62 F5D C23 H14 SING N N 63 F5D C23 H15 SING N N 64 F5D C25 H16 SING N N 65 F5D C27 H18 SING N N 66 F5D C27 H19 SING N N 67 F5D C30 H20 SING N N 68 F5D C33 H21 SING N N 69 F5D C43 H23 SING N N 70 F5D C45 H24 SING N N 71 F5D N01 H25 SING N N 72 F5D N01 H26 SING N N 73 F5D N29 H27 SING N N 74 F5D N32 H29 SING N N 75 F5D O31 H31 SING N N 76 F5D O37 H32 SING N N 77 F5D O41 H33 SING N N 78 F5D O42 H34 SING N N 79 F5D O44 H35 SING N N 80 F5D O46 H36 SING N N 81 F5D C33 C25 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 F5D SMILES ACDLabs 12.01 "c12c(N)ncnc1n(cn2)C5C(C(C(COP(=O)(OC(CCCCC3SCC4C3NC(N4)O)=O)OP(=O)(O)OP(=O)(O)O)O5)O)O" F5D InChI InChI 1.03 ;InChI=1S/C20H32N7O15P3S/c21-17-14-18(23-7-22-17)27(8-24-14)19-16(30)15(29)10(39-19)5-38-45(37,42-44(35,36)41-43(32,33)34)40-12(28)4-2-1-3-11-13-9(6-46-11)25-20(31)26-13/h7-11,13,15-16,19-20,25-26,29-31H,1-6H2,(H,35,36)(H2,21,22,23)(H2,32,33,34)/t9-,10+,11-,13?,15+,16+,19+,20+,45-/m0/s1 ; F5D InChIKey InChI 1.03 KMVPKOZRCVFEFI-NSWRTZSASA-N F5D SMILES_CANONICAL CACTVS 3.385 "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](=O)(OC(=O)CCCC[C@@H]4SC[C@@H]5N[C@@H](O)N[C@H]45)O[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O" F5D SMILES CACTVS 3.385 "Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](=O)(OC(=O)CCCC[CH]4SC[CH]5N[CH](O)N[CH]45)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O" F5D SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(OC(=O)CCCCC4C5[C@H](CS4)N[C@H](N5)O)OP(=O)(O)OP(=O)(O)O)O)O)N" F5D SMILES "OpenEye OEToolkits" 2.0.6 "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(OC(=O)CCCCC4C5C(CS4)NC(N5)O)OP(=O)(O)OP(=O)(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 F5D "SYSTEMATIC NAME" ACDLabs 12.01 "5'-O-[(S)-({5-[(2R,3aS,4S,6aR)-2-hydroxyhexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoyl}oxy){[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]adenosine" F5D "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-[oxidanyl(phosphonooxy)phosphoryl]oxy-phosphoryl] 5-[(2~{R},6~{a}~{R})-2-oxidanyl-2,3,3~{a},4,6,6~{a}-hexahydro-1~{H}-thieno[3,4-d]imidazol-4-yl]pentanoate" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site F5D "Create component" 2018-02-28 RCSB F5D "Initial release" 2018-04-04 RCSB #