data_YCX # _chem_comp.id YCX _chem_comp.name "[[(2~{R},3~{S},4~{R},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{R},4~{R},5~{S})-2,3,4,5,6-pentakis(oxidanyl)hexyl] hydrogen phosphate" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C15 H27 N3 O16 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2023-12-01 _chem_comp.pdbx_modified_date 2023-12-15 _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 567.333 _chem_comp.one_letter_code ? _chem_comp.three_letter_code YCX _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 8V4H _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.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 YCX N1 N1 N 0 1 N N N N N N -8.466 1.364 -11.601 5.999 1.716 -0.490 N1 YCX 1 YCX N3 N2 N 0 1 N N N N N N -6.896 2.598 -12.846 6.782 2.546 1.544 N3 YCX 2 YCX C4 C1 C 0 1 N N N N N N -7.043 3.568 -11.927 7.004 3.736 1.001 C4 YCX 3 YCX C5 C2 C 0 1 N N N N N N -7.840 3.442 -10.891 6.717 3.944 -0.363 C5 YCX 4 YCX C6 C3 C 0 1 N N N N N N -8.544 2.375 -10.716 6.214 2.919 -1.092 C6 YCX 5 YCX O2B O1 O 0 1 N N N N N N -10.281 -1.609 -6.045 -2.374 -2.685 1.771 O2B YCX 6 YCX PB P1 P 0 1 N N N N N N -10.570 -0.531 -5.062 -1.973 -1.352 1.269 PB YCX 7 YCX O1B O2 O 0 1 N N N N N N -9.590 -0.544 -3.967 -1.738 -0.358 2.514 O1B YCX 8 YCX O6G O3 O 0 1 N N N N N N -12.045 -0.646 -4.477 -3.134 -0.762 0.323 O6G YCX 9 YCX C6G C4 C 0 1 N N N N N N -12.405 0.327 -3.487 -4.491 -0.624 0.751 C6G YCX 10 YCX C5G C5 C 0 1 N N R N N N -13.908 0.238 -3.179 -5.327 -0.036 -0.388 C5G YCX 11 YCX O5G O4 O 0 1 N N N N N N -14.371 -1.087 -2.810 -5.366 -0.960 -1.477 O5G YCX 12 YCX C4G C6 C 0 1 N N R N N N -14.238 1.247 -2.073 -6.750 0.228 0.108 C4G YCX 13 YCX O4G O5 O 0 1 N N N N N N -13.833 2.508 -2.554 -6.711 1.153 1.198 O4G YCX 14 YCX C3G C7 C 0 1 N N R N N N -15.672 1.381 -1.756 -7.586 0.817 -1.030 C3G YCX 15 YCX O3G O6 O 0 1 N N N N N N -16.483 1.529 -2.934 -6.937 1.981 -1.545 O3G YCX 16 YCX C2G C8 C 0 1 N N S N N N -15.922 2.609 -0.903 -8.971 1.197 -0.502 C2G YCX 17 YCX O2G O7 O 0 1 N N N N N N -17.334 2.624 -0.668 -8.830 2.077 0.615 O2G YCX 18 YCX C1G C9 C 0 1 N N N N N N -15.127 2.632 0.369 -9.763 1.899 -1.607 C1G YCX 19 YCX O1G O8 O 0 1 N N N N N N -15.412 3.807 1.143 -11.094 2.149 -1.153 O1G YCX 20 YCX O3B O9 O 0 1 N N N N N N -10.277 0.935 -5.676 -0.609 -1.485 0.424 O3B YCX 21 YCX PA P2 P 0 1 N N N N N N -11.168 1.790 -6.687 0.745 -2.337 0.612 PA YCX 22 YCX O1A O10 O 0 1 N N N N N N -12.630 1.733 -6.509 1.126 -2.348 2.042 O1A YCX 23 YCX O2A O11 O 0 1 N N N N N N -10.819 3.205 -6.485 0.502 -3.848 0.110 O2A YCX 24 YCX "O5'" O12 O 0 1 N N N N N N -10.904 1.353 -8.183 1.925 -1.667 -0.253 "O5'" YCX 25 YCX "C5'" C10 C 0 1 N N N N N N -11.705 0.331 -8.752 3.277 -2.129 -0.215 "C5'" YCX 26 YCX "C4'" C11 C 0 1 N N R N N N -10.847 -0.398 -9.742 4.134 -1.275 -1.151 "C4'" YCX 27 YCX "C3'" C12 C 0 1 N N S N N N -9.478 -0.801 -9.254 5.573 -1.834 -1.222 "C3'" YCX 28 YCX "O3'" O13 O 0 1 N N N N N N -9.501 -1.996 -8.459 5.741 -2.637 -2.391 "O3'" YCX 29 YCX "C2'" C13 C 0 1 N N R N N N -8.704 -0.919 -10.559 6.462 -0.572 -1.300 "C2'" YCX 30 YCX "O2'" O14 O 0 1 N N N N N N -9.034 -2.115 -11.186 7.209 -0.560 -2.518 "O2'" YCX 31 YCX "C1'" C14 C 0 1 N N R N N N -9.288 0.139 -11.446 5.456 0.599 -1.266 "C1'" YCX 32 YCX "O4'" O15 O 0 1 N N N N N N -10.548 0.472 -10.824 4.283 0.060 -0.619 "O4'" YCX 33 YCX N4 N3 N 0 1 N N N N N N -6.308 4.691 -12.110 7.515 4.760 1.765 N4 YCX 34 YCX C2 C15 C 0 1 N N N N N N -7.586 1.497 -12.707 6.287 1.547 0.814 C2 YCX 35 YCX O2 O16 O 0 1 N N N N N N -7.455 0.642 -13.580 6.093 0.462 1.336 O2 YCX 36 YCX H1 H1 H 0 1 N N N N N N -7.907 4.246 -10.173 6.892 4.907 -0.820 H1 YCX 37 YCX H2 H2 H 0 1 N N N N N N -9.196 2.293 -9.859 5.987 3.054 -2.139 H2 YCX 38 YCX H3 H3 H 0 1 N N N N N N -8.964 -1.245 -4.110 -1.472 0.536 2.259 H3 YCX 39 YCX H4 H4 H 0 1 N N N N N N -11.833 0.138 -2.566 -4.887 -1.602 1.024 H4 YCX 40 YCX H5 H5 H 0 1 N N N N N N -12.170 1.333 -3.864 -4.534 0.040 1.614 H5 YCX 41 YCX H6 H6 H 0 1 N N N N N N -14.447 0.554 -4.084 -4.879 0.900 -0.721 H6 YCX 42 YCX H7 H7 H 0 1 N N N N N N -15.305 -1.060 -2.636 -5.753 -1.817 -1.252 H7 YCX 43 YCX H8 H8 H 0 1 N N N N N N -13.679 0.978 -1.164 -7.198 -0.707 0.442 H8 YCX 44 YCX H9 H9 H 0 1 N N N N N N -14.018 3.171 -1.900 -6.323 2.010 0.973 H9 YCX 45 YCX H10 H10 H 0 1 N N N N N N -15.999 0.494 -1.194 -7.690 0.078 -1.824 H10 YCX 46 YCX H11 H11 H 0 1 N N N N N N -17.395 1.612 -2.683 -6.810 2.683 -0.891 H11 YCX 47 YCX H12 H12 H 0 1 N N N N N N -15.647 3.495 -1.495 -9.500 0.296 -0.191 H12 YCX 48 YCX H13 H13 H 0 1 N N N N N N -17.559 3.377 -0.134 -8.366 2.900 0.411 H13 YCX 49 YCX H14 H14 H 0 1 N N N N N N -15.378 1.742 0.964 -9.280 2.844 -1.856 H14 YCX 50 YCX H15 H15 H 0 1 N N N N N N -14.055 2.617 0.122 -9.794 1.263 -2.492 H15 YCX 51 YCX H16 H16 H 0 1 N N N N N N -14.896 3.794 1.940 -11.655 2.593 -1.804 H16 YCX 52 YCX H17 H17 H 0 1 N N N N N N -11.606 3.702 -6.297 0.249 -3.917 -0.820 H17 YCX 53 YCX H18 H18 H 0 1 N N N N N N -12.576 0.772 -9.259 3.660 -2.049 0.803 H18 YCX 54 YCX H19 H19 H 0 1 N N N N N N -12.048 -0.360 -7.968 3.314 -3.170 -0.536 H19 YCX 55 YCX H20 H20 H 0 1 N N N N N N -11.381 -1.290 -10.101 3.691 -1.241 -2.146 H20 YCX 56 YCX H21 H21 H 0 1 N N N N N N -9.053 0.027 -8.668 5.803 -2.411 -0.326 H21 YCX 57 YCX H22 H22 H 0 1 N N N N N N -9.797 -1.787 -7.581 6.626 -3.014 -2.486 H22 YCX 58 YCX H23 H23 H 0 1 N N N N N N -7.624 -0.780 -10.406 7.133 -0.524 -0.442 H23 YCX 59 YCX H24 H24 H 0 1 N N N N N N -8.695 -2.843 -10.679 7.813 -1.309 -2.616 H24 YCX 60 YCX H25 H25 H 0 1 N N N N N N -9.473 -0.295 -12.440 5.215 0.924 -2.279 H25 YCX 61 YCX H26 H26 H 0 1 N N N N N N -5.696 4.765 -12.898 7.714 4.612 2.703 H26 YCX 62 YCX H27 H27 H 0 1 N N N N N N -6.377 5.446 -11.457 7.676 5.629 1.366 H27 YCX 63 # 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 YCX O2 C2 DOUB N N 1 YCX N3 C2 SING N N 2 YCX N3 C4 DOUB N N 3 YCX C2 N1 SING N N 4 YCX N4 C4 SING N N 5 YCX C4 C5 SING N N 6 YCX N1 "C1'" SING N N 7 YCX N1 C6 SING N N 8 YCX "C1'" "O4'" SING N N 9 YCX "C1'" "C2'" SING N N 10 YCX "O2'" "C2'" SING N N 11 YCX C5 C6 DOUB N N 12 YCX "O4'" "C4'" SING N N 13 YCX "C2'" "C3'" SING N N 14 YCX "C4'" "C3'" SING N N 15 YCX "C4'" "C5'" SING N N 16 YCX "C3'" "O3'" SING N N 17 YCX "C5'" "O5'" SING N N 18 YCX "O5'" PA SING N N 19 YCX PA O1A DOUB N N 20 YCX PA O2A SING N N 21 YCX PA O3B SING N N 22 YCX O2B PB DOUB N N 23 YCX O3B PB SING N N 24 YCX PB O6G SING N N 25 YCX PB O1B SING N N 26 YCX O6G C6G SING N N 27 YCX C6G C5G SING N N 28 YCX C5G O5G SING N N 29 YCX C5G C4G SING N N 30 YCX O3G C3G SING N N 31 YCX O4G C4G SING N N 32 YCX C4G C3G SING N N 33 YCX C3G C2G SING N N 34 YCX C2G O2G SING N N 35 YCX C2G C1G SING N N 36 YCX C1G O1G SING N N 37 YCX C5 H1 SING N N 38 YCX C6 H2 SING N N 39 YCX O1B H3 SING N N 40 YCX C6G H4 SING N N 41 YCX C6G H5 SING N N 42 YCX C5G H6 SING N N 43 YCX O5G H7 SING N N 44 YCX C4G H8 SING N N 45 YCX O4G H9 SING N N 46 YCX C3G H10 SING N N 47 YCX O3G H11 SING N N 48 YCX C2G H12 SING N N 49 YCX O2G H13 SING N N 50 YCX C1G H14 SING N N 51 YCX C1G H15 SING N N 52 YCX O1G H16 SING N N 53 YCX O2A H17 SING N N 54 YCX "C5'" H18 SING N N 55 YCX "C5'" H19 SING N N 56 YCX "C4'" H20 SING N N 57 YCX "C3'" H21 SING N N 58 YCX "O3'" H22 SING N N 59 YCX "C2'" H23 SING N N 60 YCX "O2'" H24 SING N N 61 YCX "C1'" H25 SING N N 62 YCX N4 H26 SING N N 63 YCX N4 H27 SING N N 64 # 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 YCX SMILES ACDLabs 12.01 "OCC(O)C(O)C(O)C(O)COP(=O)(O)OP(=O)(O)OCC1OC(N2C=CC(N)=NC2=O)C(O)C1O" YCX InChI InChI 1.06 "InChI=1S/C15H27N3O16P2/c16-9-1-2-18(15(26)17-9)14-13(25)12(24)8(33-14)5-32-36(29,30)34-35(27,28)31-4-7(21)11(23)10(22)6(20)3-19/h1-2,6-8,10-14,19-25H,3-5H2,(H,27,28)(H,29,30)(H2,16,17,26)/t6-,7+,8+,10+,11+,12+,13+,14+/m0/s1" YCX InChIKey InChI 1.06 WSJYSDVJOUCAAL-WZWGQWAVSA-N YCX SMILES_CANONICAL CACTVS 3.385 "NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P](O)(=O)O[P](O)(=O)OC[C@@H](O)[C@@H](O)[C@H](O)[C@@H](O)CO)[C@@H](O)[C@H]2O" YCX SMILES CACTVS 3.385 "NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH](O)[CH](O)[CH](O)[CH](O)CO)[CH](O)[CH]2O" YCX SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)OP(=O)(O)OC[C@H]([C@H]([C@@H]([C@H](CO)O)O)O)O)O)O" YCX SMILES "OpenEye OEToolkits" 2.0.7 "C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OCC(C(C(C(CO)O)O)O)O)O)O" # 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 YCX "SYSTEMATIC NAME" ACDLabs 12.01 "[(2R,3S,4R,5R)-5-(4-amino-2-oxopyrimidin-1(2H)-yl)-3,4-dihydroxyoxolan-2-yl]methyl (2R,3R,4R,5S)-2,3,4,5,6-pentahydroxyhexyl dihydrogen diphosphate (non-preferred name)" YCX "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[[(2~{R},3~{S},4~{R},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{R},4~{R},5~{S})-2,3,4,5,6-pentakis(oxidanyl)hexyl] 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 YCX "Create component" 2023-12-01 RCSB YCX "Initial release" 2023-12-20 RCSB #