data_Y4I # _chem_comp.id Y4I _chem_comp.name "1-[(2~{R},4~{S},5~{R})-5-[[[(2~{R},6~{S})-2-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-6-(hydroxymethyl)morpholin-4-yl]-oxidanyl-phosphinothioyl]oxymethyl]-4-oxidanyl-oxolan-2-yl]-5-methyl-pyrimidine-2,4-dione" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C19 H26 N5 O10 P S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2023-11-20 _chem_comp.pdbx_modified_date 2023-12-01 _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 547.476 _chem_comp.one_letter_code ? _chem_comp.three_letter_code Y4I _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 8R5V _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.pdbx_n_terminal_atom_flag _chem_comp_atom.pdbx_backbone_atom_flag _chem_comp_atom.pdbx_c_terminal_atom_flag _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 Y4I O11 O1 O 0 1 N N N N N N 6.260 -0.080 18.981 -4.216 -0.184 -1.699 O11 Y4I 1 Y4I O13 O2 O 0 1 N N N N N N 3.276 -5.246 17.475 -8.984 1.484 1.612 O13 Y4I 2 Y4I C20 C1 C 0 1 N N N N N N 3.975 -4.330 17.923 -7.885 1.295 1.121 C20 Y4I 3 Y4I N19 N1 N 0 1 N N N N N N 3.987 -4.095 19.298 -7.123 2.339 0.737 N19 Y4I 4 Y4I C18 C2 C 0 1 N N N N N N 4.708 -3.121 19.960 -5.909 2.128 0.195 C18 Y4I 5 Y4I O12 O3 O 0 1 N N N N N N 4.655 -2.984 21.181 -5.232 3.079 -0.147 O12 Y4I 6 Y4I C21 C3 C 0 1 N N N N N N 4.811 -3.450 17.133 -7.395 -0.023 0.955 C21 Y4I 7 Y4I C22 C4 C 0 1 N N N N N N 5.521 -2.490 17.745 -6.174 -0.205 0.408 C22 Y4I 8 Y4I N17 N2 N 0 1 N N N N N N 5.474 -2.311 19.125 -5.433 0.881 0.026 N17 Y4I 9 Y4I C12 C5 C 0 1 N N R N N N 6.320 -1.266 19.753 -4.108 0.684 -0.567 C12 Y4I 10 Y4I C13 C6 C 0 1 N N N N N N 7.738 -1.848 19.834 -3.174 0.050 0.468 C13 Y4I 11 Y4I N14 N3 N 0 1 N N N N N N 8.775 -0.834 20.009 -1.870 -0.216 -0.156 N14 Y4I 12 Y4I C15 C7 C 0 1 N N N N N N 8.576 0.365 19.205 -2.019 -1.109 -1.314 C15 Y4I 13 Y4I C16 C8 C 0 1 N N S N N N 7.181 0.868 19.525 -2.964 -0.464 -2.331 C16 Y4I 14 Y4I C23 C9 C 0 1 N N N N N N 6.854 2.234 18.993 -3.186 -1.423 -3.502 C23 Y4I 15 Y4I O15 O4 O 0 1 N N N N N N 7.517 3.184 19.837 -3.978 -0.779 -4.502 O15 Y4I 16 Y4I P P1 P 0 1 N N S N N N 10.193 -1.720 20.642 -0.786 -0.854 0.963 P Y4I 17 Y4I SP S1 S 0 1 N N N N N N 11.544 -1.896 19.230 -1.463 -2.453 1.640 SP Y4I 18 Y4I OP1 O5 O 0 1 N N N N N N 9.963 -3.023 21.403 -0.579 0.193 2.167 OP1 Y4I 19 Y4I "O5'" O6 O 0 1 N N N N N N 10.673 -0.602 21.665 0.627 -1.132 0.243 "O5'" Y4I 20 Y4I "C5'" C10 C 0 1 N N N N N N 9.862 -0.183 22.809 1.723 -1.770 0.900 "C5'" Y4I 21 Y4I "C4'" C11 C 0 1 N N R N N N 10.791 0.406 23.848 2.906 -1.876 -0.065 "C4'" Y4I 22 Y4I "C3'" C12 C 0 1 N N S N N N 11.870 1.388 23.361 4.107 -2.577 0.618 "C3'" Y4I 23 Y4I "O3'" O7 O 0 1 N N N N N N 11.979 2.434 24.301 4.006 -3.997 0.495 "O3'" Y4I 24 Y4I "C2'" C13 C 0 1 N N N N N N 13.148 0.578 23.399 5.306 -2.035 -0.198 "C2'" Y4I 25 Y4I "C1'" C14 C 0 1 N N R N N N 12.908 -0.402 24.533 4.769 -0.743 -0.845 "C1'" Y4I 26 Y4I "O4'" O8 O 0 1 N N N N N N 11.503 -0.669 24.552 3.419 -0.565 -0.386 "O4'" Y4I 27 Y4I N1 N4 N 0 1 N N N N N N 13.605 -1.741 24.356 5.592 0.398 -0.437 N1 Y4I 28 Y4I C6 C15 C 0 1 N N N N N N 13.097 -2.681 23.517 6.322 1.076 -1.375 C6 Y4I 29 Y4I C5 C16 C 0 1 N N N N N N 13.672 -3.886 23.346 7.081 2.128 -0.999 C5 Y4I 30 Y4I C5M C17 C 0 1 N N N N N N 13.138 -4.980 22.428 7.891 2.888 -2.017 C5M Y4I 31 Y4I C4 C18 C 0 1 N N N N N N 14.915 -4.125 24.037 7.103 2.509 0.365 C4 Y4I 32 Y4I O4 O9 O 0 1 N N N N N N 15.547 -5.176 23.990 7.779 3.454 0.728 O4 Y4I 33 Y4I N3 N5 N 0 1 N N N N N N 15.363 -3.156 24.891 6.370 1.814 1.258 N3 Y4I 34 Y4I C2 C19 C 0 1 N N N N N N 14.776 -1.939 25.076 5.619 0.773 0.855 C2 Y4I 35 Y4I O2 O10 O 0 1 N N N N N N 15.295 -1.128 25.783 4.958 0.159 1.670 O2 Y4I 36 Y4I H1 H1 H 0 1 N N N N N N 3.416 -4.692 19.861 -7.450 3.244 0.851 H1 Y4I 37 Y4I H2 H2 H 0 1 N N N N N N 4.862 -3.565 16.060 -7.989 -0.871 1.261 H2 Y4I 38 Y4I H22 H3 H 0 1 N N N N N N 6.146 -1.839 17.151 -5.783 -1.202 0.273 H22 Y4I 39 Y4I H12 H4 H 0 1 N N N N N N 5.961 -1.073 20.775 -3.704 1.645 -0.883 H12 Y4I 40 Y4I H131 H5 H 0 0 N N N N N N 7.782 -2.541 20.687 -3.044 0.734 1.307 H131 Y4I 41 Y4I H132 H6 H 0 0 N N N N N N 7.942 -2.398 18.904 -3.606 -0.885 0.823 H132 Y4I 42 Y4I H151 H7 H 0 0 N N N N N N 9.325 1.127 19.467 -1.045 -1.272 -1.775 H151 Y4I 43 Y4I H152 H8 H 0 0 N N N N N N 8.657 0.123 18.135 -2.431 -2.064 -0.987 H152 Y4I 44 Y4I H16 H9 H 0 1 N N N N N N 7.071 0.891 20.619 -2.526 0.464 -2.698 H16 Y4I 45 Y4I H231 H10 H 0 0 N N N N N N 5.767 2.399 19.020 -2.224 -1.706 -3.928 H231 Y4I 46 Y4I H232 H11 H 0 0 N N N N N N 7.214 2.332 17.958 -3.704 -2.315 -3.148 H232 Y4I 47 Y4I HO15 H12 H 0 0 N N N N N N 7.333 4.064 19.530 -4.159 -1.330 -5.276 HO15 Y4I 48 Y4I HOP1 H13 H 0 0 N N N N N N 10.527 -3.701 21.049 -0.228 1.050 1.887 HOP1 Y4I 49 Y4I "H5'2" H14 H 0 0 N N N N N N 9.130 0.574 22.491 2.016 -1.183 1.771 "H5'2" Y4I 50 Y4I "H5'1" H15 H 0 0 N N N N N N 9.333 -1.051 23.230 1.424 -2.768 1.219 "H5'1" Y4I 51 Y4I "H4'" H16 H 0 1 N N N N N N 10.170 0.941 24.582 2.613 -2.406 -0.971 "H4'" Y4I 52 Y4I "H3'" H17 H 0 1 N N N N N N 11.650 1.744 22.344 4.185 -2.283 1.665 "H3'" Y4I 53 Y4I "HO3'" H18 H 0 0 N N N N N N 12.643 3.050 24.014 4.735 -4.480 0.907 "HO3'" Y4I 54 Y4I "H2'2" H19 H 0 0 N N N N N N 13.307 0.049 22.448 6.145 -1.811 0.461 "H2'2" Y4I 55 Y4I "H2'1" H20 H 0 0 N N N N N N 14.015 1.221 23.611 5.603 -2.752 -0.962 "H2'1" Y4I 56 Y4I "H1'" H21 H 0 1 N N N N N N 13.228 0.053 25.482 4.781 -0.840 -1.931 "H1'" Y4I 57 Y4I H6 H22 H 0 1 N N N N N N 12.197 -2.453 22.966 6.293 0.771 -2.410 H6 Y4I 58 Y4I H5M3 H23 H 0 0 N N N N N N 12.190 -4.651 21.977 7.292 3.702 -2.425 H5M3 Y4I 59 Y4I H5M1 H24 H 0 0 N N N N N N 13.871 -5.182 21.633 8.782 3.296 -1.541 H5M1 Y4I 60 Y4I H5M2 H25 H 0 0 N N N N N N 12.968 -5.897 23.011 8.186 2.215 -2.822 H5M2 Y4I 61 Y4I H3 H26 H 0 1 N N N N N N 16.186 -3.355 25.422 6.380 2.069 2.194 H3 Y4I 62 # 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 Y4I OP1 P SING N N 1 Y4I SP P DOUB N N 2 Y4I "O5'" P SING N N 3 Y4I P N14 SING N N 4 Y4I "C5'" "O5'" SING N N 5 Y4I "C4'" "C5'" SING N N 6 Y4I "C4'" "O4'" SING N N 7 Y4I "C3'" "C4'" SING N N 8 Y4I "O4'" "C1'" SING N N 9 Y4I "O3'" "C3'" SING N N 10 Y4I "C2'" "C3'" SING N N 11 Y4I "C1'" "C2'" SING N N 12 Y4I N1 "C1'" SING N N 13 Y4I N1 C2 SING N N 14 Y4I C6 N1 SING N N 15 Y4I O2 C2 DOUB N N 16 Y4I C2 N3 SING N N 17 Y4I N3 C4 SING N N 18 Y4I O4 C4 DOUB N N 19 Y4I C4 C5 SING N N 20 Y4I C5M C5 SING N N 21 Y4I C5 C6 DOUB N N 22 Y4I O11 C12 SING N N 23 Y4I O11 C16 SING N N 24 Y4I C13 C12 SING N N 25 Y4I C12 N17 SING N N 26 Y4I O12 C18 DOUB N N 27 Y4I N14 C13 SING N N 28 Y4I C20 O13 DOUB N N 29 Y4I C15 N14 SING N N 30 Y4I C16 C15 SING N N 31 Y4I O15 C23 SING N N 32 Y4I C23 C16 SING N N 33 Y4I N17 C18 SING N N 34 Y4I N17 C22 SING N N 35 Y4I C18 N19 SING N N 36 Y4I N19 C20 SING N N 37 Y4I C21 C20 SING N N 38 Y4I C22 C21 DOUB N N 39 Y4I N19 H1 SING N N 40 Y4I C21 H2 SING N N 41 Y4I C22 H22 SING N N 42 Y4I C12 H12 SING N N 43 Y4I C13 H131 SING N N 44 Y4I C13 H132 SING N N 45 Y4I C15 H151 SING N N 46 Y4I C15 H152 SING N N 47 Y4I C16 H16 SING N N 48 Y4I C23 H231 SING N N 49 Y4I C23 H232 SING N N 50 Y4I O15 HO15 SING N N 51 Y4I OP1 HOP1 SING N N 52 Y4I "C5'" "H5'2" SING N N 53 Y4I "C5'" "H5'1" SING N N 54 Y4I "C4'" "H4'" SING N N 55 Y4I "C3'" "H3'" SING N N 56 Y4I "O3'" "HO3'" SING N N 57 Y4I "C2'" "H2'2" SING N N 58 Y4I "C2'" "H2'1" SING N N 59 Y4I "C1'" "H1'" SING N N 60 Y4I C6 H6 SING N N 61 Y4I C5M H5M3 SING N N 62 Y4I C5M H5M1 SING N N 63 Y4I C5M H5M2 SING N N 64 Y4I N3 H3 SING N N 65 # 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 Y4I InChI InChI 1.06 "InChI=1S/C19H26N5O10PS/c1-10-5-24(19(30)21-17(10)28)15-4-12(26)13(34-15)9-32-35(31,36)22-6-11(8-25)33-16(7-22)23-3-2-14(27)20-18(23)29/h2-3,5,11-13,15-16,25-26H,4,6-9H2,1H3,(H,31,36)(H,20,27,29)(H,21,28,30)/t11-,12-,13+,15+,16+,35-/m0/s1" Y4I InChIKey InChI 1.06 JMOYBKKBBMXKAB-OTRGKRLXSA-N Y4I SMILES_CANONICAL CACTVS 3.385 "CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P@](O)(=S)N3C[C@@H](CO)O[C@H](C3)N4C=CC(=O)NC4=O)O2)C(=O)NC1=O" Y4I SMILES CACTVS 3.385 "CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=S)N3C[CH](CO)O[CH](C3)N4C=CC(=O)NC4=O)O2)C(=O)NC1=O" Y4I SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@](=S)(N3C[C@H](O[C@H](C3)N4C=CC(=O)NC4=O)CO)O)O" Y4I SMILES "OpenEye OEToolkits" 2.0.7 "CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=S)(N3CC(OC(C3)N4C=CC(=O)NC4=O)CO)O)O" # _pdbx_chem_comp_identifier.comp_id Y4I _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 "1-[(2~{R},4~{S},5~{R})-5-[[[(2~{R},6~{S})-2-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-6-(hydroxymethyl)morpholin-4-yl]-oxidanyl-phosphinothioyl]oxymethyl]-4-oxidanyl-oxolan-2-yl]-5-methyl-pyrimidine-2,4-dione" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site Y4I "Create component" 2023-11-20 PDBE Y4I "Initial release" 2023-12-06 RCSB #