data_5ZL # _chem_comp.id 5ZL _chem_comp.name "[[(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-(2-oxidanyl-4-phosphonooxy-pyrimidin-1-yl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C9 H17 N2 O18 P4" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 1 _chem_comp.pdbx_initial_date 2021-09-07 _chem_comp.pdbx_modified_date 2021-09-10 _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 565.129 _chem_comp.one_letter_code ? _chem_comp.three_letter_code ? _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 7DPT _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ # # 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 5ZL C21 C1 C 0 1 N N S 118.226 131.633 145.028 -1.679 -3.406 -0.244 C21 5ZL 1 5ZL C22 C2 C 0 1 N N R 118.225 133.053 145.322 -2.988 -2.770 0.274 C22 5ZL 2 5ZL C24 C3 C 0 1 N N R 116.880 133.345 145.804 -2.520 -1.494 1.009 C24 5ZL 3 5ZL C26 C4 C 0 1 Y N N 116.133 135.575 146.286 -4.537 -0.301 1.575 C26 5ZL 4 5ZL C28 C5 C 0 1 Y N N 117.565 135.649 148.735 -4.162 1.497 -0.377 C28 5ZL 5 5ZL C23 C6 C 0 1 N N R 117.306 131.013 145.999 -0.575 -2.440 0.240 C23 5ZL 6 5ZL C25 C7 C 0 1 N N N 118.062 130.420 147.124 0.527 -2.320 -0.815 C25 5ZL 7 5ZL C27 C8 C 0 1 Y N N 117.616 134.486 147.921 -3.259 0.470 -0.180 C27 5ZL 8 5ZL C29 C9 C 0 1 Y N N 116.803 136.760 148.322 -5.272 1.576 0.462 C29 5ZL 9 5ZL N19 N1 N 1 1 Y N N 116.877 134.457 146.672 -3.474 -0.403 0.794 N19 5ZL 10 5ZL N20 N2 N 0 1 Y N N 116.085 136.729 147.088 -5.424 0.667 1.418 N20 5ZL 11 5ZL O04 O1 O 0 1 N N N 116.414 132.095 146.519 -1.245 -1.172 0.414 O04 5ZL 12 5ZL O05 O2 O 0 1 N N N 117.658 131.419 143.717 -1.494 -4.704 0.326 O05 5ZL 13 5ZL O06 O3 O 0 1 N N N 118.546 133.860 144.138 -3.651 -3.654 1.179 O06 5ZL 14 5ZL O07 O4 O 0 1 N N N 118.589 131.480 147.880 1.592 -1.516 -0.302 O07 5ZL 15 5ZL O08 O5 O 0 1 N N N 115.437 135.542 145.097 -4.725 -1.216 2.556 O08 5ZL 16 5ZL O09 O6 O 0 1 N N N 120.608 129.793 148.388 3.954 -0.367 -0.216 O09 5ZL 17 5ZL O10 O7 O 0 1 N N N 120.772 132.257 148.999 3.550 -2.440 -1.598 O10 5ZL 18 5ZL O11 O8 O 0 1 N N N 119.370 131.064 150.236 2.531 -0.284 -2.426 O11 5ZL 19 5ZL O12 O9 O 0 1 N N N 116.693 137.923 149.053 -6.183 2.567 0.305 O12 5ZL 20 5ZL O13 O10 O 0 1 N N N 121.946 128.136 150.066 5.885 1.155 0.717 O13 5ZL 21 5ZL O14 O11 O 0 1 N N N 120.315 127.238 148.343 5.823 0.447 -1.706 O14 5ZL 22 5ZL O15 O12 O 0 1 N N N 119.455 128.318 150.070 6.394 -1.323 0.001 O15 5ZL 23 5ZL O16 O13 O 0 1 N N N 123.470 129.501 151.596 7.352 2.817 -0.489 O16 5ZL 24 5ZL O17 O14 O 0 1 N N N 122.220 127.909 152.651 6.689 3.370 1.882 O17 5ZL 25 5ZL O18 O15 O 0 1 N N N 121.292 129.808 151.916 8.417 1.460 1.353 O18 5ZL 26 5ZL O31 O16 O 0 1 N N N 117.780 137.680 151.366 -8.327 3.487 -0.908 O31 5ZL 27 5ZL O32 O17 O 0 1 N N N 119.164 138.385 149.680 -6.828 1.778 -2.005 O32 5ZL 28 5ZL O33 O18 O 0 1 N N N 117.595 139.801 150.562 -8.255 0.994 -0.077 O33 5ZL 29 5ZL P01 P1 P 0 1 N N N 119.833 131.173 148.888 2.921 -1.179 -1.146 P01 5ZL 30 5ZL P02 P2 P 0 1 N N N 120.604 128.348 149.217 5.521 -0.012 -0.331 P02 5ZL 31 5ZL P03 P3 P 0 1 N N N 122.218 128.812 151.530 7.092 2.214 0.837 P03 5ZL 32 5ZL P30 P4 P 0 1 N N N 117.797 138.427 150.145 -7.386 2.197 -0.700 P30 5ZL 33 5ZL H1 H1 H 0 1 N N N 119.236 131.204 145.108 -1.687 -3.464 -1.332 H1 5ZL 34 5ZL H2 H2 H 0 1 N N N 118.954 133.266 146.117 -3.643 -2.512 -0.559 H2 5ZL 35 5ZL H3 H3 H 0 1 N N N 116.215 133.531 144.947 -2.403 -1.692 2.075 H3 5ZL 36 5ZL H4 H4 H 0 1 N N N 118.109 135.682 149.668 -4.011 2.222 -1.163 H4 5ZL 37 5ZL H5 H5 H 0 1 N N N 116.701 130.239 145.504 -0.159 -2.783 1.187 H5 5ZL 38 5ZL H6 H6 H 0 1 N N N 117.392 129.810 147.748 0.906 -3.313 -1.059 H6 5ZL 39 5ZL H7 H7 H 0 1 N N N 118.878 129.791 146.739 0.121 -1.855 -1.713 H7 5ZL 40 5ZL H8 H8 H 0 1 N N N 118.199 133.631 148.229 -2.388 0.379 -0.812 H8 5ZL 41 5ZL H9 H9 H 0 1 N N N 117.657 130.490 143.520 -2.192 -5.334 0.104 H9 5ZL 42 5ZL H10 H10 H 0 1 N N N 118.536 134.781 144.370 -3.914 -4.497 0.784 H10 5ZL 43 5ZL H11 H11 H 0 1 N N N 119.805 131.714 150.774 2.113 0.559 -2.203 H11 5ZL 44 5ZL H12 H12 H 0 1 N N N 118.883 127.607 149.807 6.246 -1.680 0.887 H12 5ZL 45 5ZL H13 H13 H 0 1 N N N 123.034 128.003 153.132 7.372 4.044 2.005 H13 5ZL 46 5ZL H14 H14 H 0 1 N N N 121.755 130.617 152.100 8.319 1.040 2.219 H14 5ZL 47 5ZL H15 H15 H 0 1 N N N 118.654 137.356 151.552 -9.074 3.337 -1.503 H15 5ZL 48 5ZL H16 H16 H 0 1 N N N 118.394 140.296 150.422 -8.653 1.199 0.780 H16 5ZL 49 5ZL H17 H17 H 0 1 N N N 114.984 136.368 144.971 -4.320 -0.975 3.401 H17 5ZL 50 # # 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 5ZL O05 C21 SING N N 1 5ZL O06 C22 SING N N 2 5ZL C21 C22 SING N N 3 5ZL C21 C23 SING N N 4 5ZL O08 C26 SING N N 5 5ZL C22 C24 SING N N 6 5ZL C24 O04 SING N N 7 5ZL C24 N19 SING N N 8 5ZL C23 O04 SING N N 9 5ZL C23 C25 SING N N 10 5ZL C26 N19 SING Y N 11 5ZL C26 N20 DOUB Y N 12 5ZL N19 C27 DOUB Y N 13 5ZL N20 C29 SING Y N 14 5ZL C25 O07 SING N N 15 5ZL O07 P01 SING N N 16 5ZL C27 C28 SING Y N 17 5ZL C29 C28 DOUB Y N 18 5ZL C29 O12 SING N N 19 5ZL O14 P02 DOUB N N 20 5ZL O09 P01 SING N N 21 5ZL O09 P02 SING N N 22 5ZL P01 O10 DOUB N N 23 5ZL P01 O11 SING N N 24 5ZL O12 P30 SING N N 25 5ZL P02 O13 SING N N 26 5ZL P02 O15 SING N N 27 5ZL O32 P30 DOUB N N 28 5ZL O13 P03 SING N N 29 5ZL P30 O33 SING N N 30 5ZL P30 O31 SING N N 31 5ZL P03 O16 DOUB N N 32 5ZL P03 O18 SING N N 33 5ZL P03 O17 SING N N 34 5ZL C21 H1 SING N N 35 5ZL C22 H2 SING N N 36 5ZL C24 H3 SING N N 37 5ZL C28 H4 SING N N 38 5ZL C23 H5 SING N N 39 5ZL C25 H6 SING N N 40 5ZL C25 H7 SING N N 41 5ZL C27 H8 SING N N 42 5ZL O05 H9 SING N N 43 5ZL O06 H10 SING N N 44 5ZL O11 H11 SING N N 45 5ZL O15 H12 SING N N 46 5ZL O17 H13 SING N N 47 5ZL O18 H14 SING N N 48 5ZL O31 H15 SING N N 49 5ZL O33 H16 SING N N 50 5ZL O08 H17 SING N N 51 # # 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 5ZL InChI InChI 1.03 "InChI=1S/C9H16N2O18P4/c12-6-4(3-25-32(21,22)29-33(23,24)28-31(18,19)20)26-8(7(6)13)11-2-1-5(10-9(11)14)27-30(15,16)17/h1-2,4,6-8,12-13H,3H2,(H6,15,16,17,18,19,20,21,22,23,24)/p+1/t4-,6-,7-,8-/m1/s1" 5ZL InChIKey InChI 1.03 RYGLMDXZXSWNKW-XVFCMESISA-O 5ZL SMILES_CANONICAL CACTVS 3.385 "O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[n+]2ccc(O[P](O)(O)=O)nc2O" 5ZL SMILES CACTVS 3.385 "O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[n+]2ccc(O[P](O)(O)=O)nc2O" 5ZL SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1c[n+](c(nc1OP(=O)(O)O)O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O" 5ZL SMILES "OpenEye OEToolkits" 2.0.7 "c1c[n+](c(nc1OP(=O)(O)O)O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O" # _pdbx_chem_comp_identifier.comp_id 5ZL _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})-3,4-bis(oxidanyl)-5-(2-oxidanyl-4-phosphonooxy-pyrimidin-1-ium-1-yl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono 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 5ZL "Create component" 2021-09-07 PDBJ 5ZL "Initial release" 2021-09-15 RCSB ##