data_P5E # _chem_comp.id P5E _chem_comp.name "[[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-sulfanyl-phosphoryl] phosphono hydrogen phosphate" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C9 H15 N2 O14 P3 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2020-04-15 _chem_comp.pdbx_modified_date 2020-12-04 _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 500.207 _chem_comp.one_letter_code ? _chem_comp.three_letter_code P5E _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 6YMW _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBE # # 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 P5E PA P1 P 0 1 N N S 45.603 61.322 69.959 -1.504 -1.568 0.612 PA P5E 1 P5E O2A O1 O 0 1 N N N 44.606 60.373 70.521 -1.401 -1.250 2.054 O2A P5E 2 P5E O3A O2 O 0 1 N N N 44.793 62.476 69.124 -2.547 -0.560 -0.087 O3A P5E 3 P5E "O5'" O3 O 0 1 N N N 46.393 62.017 71.224 -0.058 -1.408 -0.077 "O5'" P5E 4 P5E PB P2 P 0 1 N N N 43.304 62.966 69.592 -4.109 -0.238 0.132 PB P5E 5 P5E O1B O4 O 0 1 N N N 43.324 64.399 69.910 -4.388 -0.110 1.579 O1B P5E 6 P5E O2B O5 O 0 1 N N N 42.904 62.194 70.784 -4.994 -1.435 -0.481 O2B P5E 7 P5E O3B O6 O 0 1 N N N 42.201 62.665 68.392 -4.482 1.140 -0.612 O3B P5E 8 P5E PG P3 P 0 1 N N N 41.051 61.489 68.561 -5.684 2.201 -0.464 PG P5E 9 P5E O1G O7 O 0 1 N N N 39.917 62.015 69.390 -7.022 1.590 -1.120 O1G P5E 10 P5E O2G O8 O 0 1 N N N 40.535 61.094 67.210 -5.922 2.480 0.970 O2G P5E 11 P5E O3G O9 O 0 1 N N N 41.647 60.337 69.211 -5.291 3.567 -1.220 O3G P5E 12 P5E "C5'" C1 C 0 1 N N N 45.716 62.063 72.419 1.107 -2.092 0.389 "C5'" P5E 13 P5E "C4'" C2 C 0 1 N N R 46.514 62.908 73.486 2.304 -1.717 -0.487 "C4'" P5E 14 P5E "O4'" O10 O 0 1 N N N 47.959 63.251 72.974 2.681 -0.341 -0.261 "O4'" P5E 15 P5E "C1'" C3 C 0 1 N N R 47.994 64.764 72.883 4.048 -0.242 -0.717 "C1'" P5E 16 P5E "C2'" C4 C 0 1 N N R 46.720 65.125 72.789 4.720 -1.546 -0.235 "C2'" P5E 17 P5E "O2'" O11 O 0 1 N N N 46.549 66.404 73.408 5.651 -2.019 -1.210 "O2'" P5E 18 P5E "C3'" C5 C 0 1 N N S 45.926 64.046 73.679 3.547 -2.539 -0.080 "C3'" P5E 19 P5E "O3'" O12 O 0 1 N N N 46.046 64.415 75.085 3.717 -3.656 -0.955 "O3'" P5E 20 P5E N1 N1 N 0 1 N N N 48.752 65.158 71.671 4.701 0.924 -0.117 N1 P5E 21 P5E C6 C6 C 0 1 N N N 48.613 64.449 70.549 4.698 1.078 1.243 C6 P5E 22 P5E C2 C7 C 0 1 N N N 49.590 66.222 71.704 5.305 1.830 -0.908 C2 P5E 23 P5E O2 O13 O 0 1 N N N 49.721 66.845 72.698 5.300 1.671 -2.113 O2 P5E 24 P5E N3 N2 N 0 1 N N N 50.278 66.569 70.602 5.913 2.910 -0.383 N3 P5E 25 P5E C4 C8 C 0 1 N N N 50.137 65.882 69.505 5.928 3.101 0.952 C4 P5E 26 P5E O4 O14 O 0 1 N N N 50.730 66.182 68.557 6.478 4.077 1.427 O4 P5E 27 P5E C5 C9 C 0 1 N N N 49.284 64.786 69.468 5.305 2.150 1.796 C5 P5E 28 P5E S1A S1 S 0 1 N N N 46.590 60.753 68.978 -2.183 -3.563 0.376 S1A P5E 29 P5E H1 H1 H 0 1 N N N 42.743 62.788 71.508 -4.862 -1.577 -1.429 H1 P5E 30 P5E H2 H2 H 0 1 N N N 39.114 61.986 68.883 -6.939 1.382 -2.061 H2 P5E 31 P5E H3 H3 H 0 1 N N N 41.581 59.581 68.639 -5.971 4.252 -1.172 H3 P5E 32 P5E H4 H4 H 0 1 N N N 44.731 62.525 72.257 1.308 -1.804 1.421 H4 P5E 33 P5E H5 H5 H 0 1 N N N 45.583 61.039 72.797 0.942 -3.168 0.338 H5 P5E 34 P5E H6 H6 H 0 1 N N N 46.601 62.313 74.407 2.069 -1.880 -1.539 H6 P5E 35 P5E H7 H7 H 0 1 N N N 48.481 65.174 73.780 4.081 -0.177 -1.804 H7 P5E 36 P5E H8 H8 H 0 1 N N N 46.329 65.110 71.761 5.218 -1.388 0.722 H8 P5E 37 P5E H9 H9 H 0 1 N N N 45.639 66.668 73.344 6.103 -2.836 -0.958 H9 P5E 38 P5E H10 H10 H 0 1 N N N 44.870 64.047 73.369 3.462 -2.872 0.954 H10 P5E 39 P5E H11 H11 H 0 1 N N N 45.580 63.783 75.620 4.484 -4.207 -0.745 H11 P5E 40 P5E H12 H12 H 0 1 N N N 47.949 63.597 70.528 4.211 0.347 1.870 H12 P5E 41 P5E H13 H13 H 0 1 N N N 50.897 67.354 70.625 6.344 3.553 -0.968 H13 P5E 42 P5E H14 H14 H 0 1 N N N 49.172 64.214 68.558 5.306 2.286 2.867 H14 P5E 43 P5E H15 H15 H 0 1 N N N 46.230 59.505 68.926 -2.228 -3.711 -0.960 H15 P5E 44 # # 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 P5E O2G PG DOUB N N 1 P5E O3B PG SING N N 2 P5E O3B PB SING N N 3 P5E O4 C4 DOUB N N 4 P5E PG O3G SING N N 5 P5E PG O1G SING N N 6 P5E S1A PA SING N N 7 P5E O3A PB SING N N 8 P5E O3A PA SING N N 9 P5E C5 C4 SING N N 10 P5E C5 C6 DOUB N N 11 P5E C4 N3 SING N N 12 P5E PB O1B DOUB N N 13 P5E PB O2B SING N N 14 P5E PA O2A DOUB N N 15 P5E PA "O5'" SING N N 16 P5E C6 N1 SING N N 17 P5E N3 C2 SING N N 18 P5E "O5'" "C5'" SING N N 19 P5E N1 C2 SING N N 20 P5E N1 "C1'" SING N N 21 P5E C2 O2 DOUB N N 22 P5E "C5'" "C4'" SING N N 23 P5E "C2'" "C1'" SING N N 24 P5E "C2'" "O2'" SING N N 25 P5E "C2'" "C3'" SING N N 26 P5E "C1'" "O4'" SING N N 27 P5E "O4'" "C4'" SING N N 28 P5E "C4'" "C3'" SING N N 29 P5E "C3'" "O3'" SING N N 30 P5E O2B H1 SING N N 31 P5E O1G H2 SING N N 32 P5E O3G H3 SING N N 33 P5E "C5'" H4 SING N N 34 P5E "C5'" H5 SING N N 35 P5E "C4'" H6 SING N N 36 P5E "C1'" H7 SING N N 37 P5E "C2'" H8 SING N N 38 P5E "O2'" H9 SING N N 39 P5E "C3'" H10 SING N N 40 P5E "O3'" H11 SING N N 41 P5E C6 H12 SING N N 42 P5E N3 H13 SING N N 43 P5E C5 H14 SING N N 44 P5E S1A H15 SING N N 45 # # 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 P5E InChI InChI 1.03 "InChI=1S/C9H15N2O14P3S/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(23-8)3-22-28(21,29)25-27(19,20)24-26(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H,21,29)(H,10,12,15)(H2,16,17,18)/t4-,6-,7-,8-,28+/m1/s1" P5E InChIKey InChI 1.03 BWPNYQWDXHLOGU-KWWYXVLOSA-N P5E SMILES_CANONICAL CACTVS 3.385 "O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P@@](S)(=O)O[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O" P5E SMILES CACTVS 3.385 "O[CH]1[CH](O)[CH](O[CH]1CO[P](S)(=O)O[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O" P5E SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)(OP(=O)(O)OP(=O)(O)O)S)O)O" P5E SMILES "OpenEye OEToolkits" 2.0.7 "C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(OP(=O)(O)OP(=O)(O)O)S)O)O" # _pdbx_chem_comp_identifier.comp_id P5E _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-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-sulfanyl-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 P5E "Create component" 2020-04-15 PDBE P5E "Initial release" 2020-12-09 RCSB ##