data_YWQ # _chem_comp.id YWQ _chem_comp.name ;uridine 5'-heptaphosphate ; _chem_comp.type "RNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C9 H19 N2 O27 P7" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2023-03-02 _chem_comp.pdbx_modified_date 2024-03-01 _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 804.061 _chem_comp.one_letter_code ? _chem_comp.three_letter_code YWQ _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 8GC9 _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_backbone_atom_flag _chem_comp_atom.pdbx_n_terminal_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 YWQ C10 C1 C 0 1 N N N N N N -37.179 1.320 10.716 5.861 5.281 -0.094 C10 YWQ 1 YWQ C15 C2 C 0 1 N N S N N N -36.998 -3.381 10.615 6.208 0.904 1.613 C15 YWQ 2 YWQ C02 C3 C 0 1 N N S N N N -38.418 -2.909 11.150 7.616 1.539 1.625 C02 YWQ 3 YWQ C03 C4 C 0 1 N N R N N N -38.350 -1.350 11.170 7.370 3.005 1.204 C03 YWQ 4 YWQ C04 C5 C 0 1 N N S N N N -37.301 -1.141 10.063 5.843 3.083 0.988 C04 YWQ 5 YWQ C06 C6 C 0 1 N N N N N N -35.353 0.344 9.446 4.925 3.441 -1.234 C06 YWQ 6 YWQ C08 C7 C 0 1 N N N N N N -35.305 2.737 10.134 4.930 5.533 -2.275 C08 YWQ 7 YWQ C09 C8 C 0 1 N N N N N N -36.575 2.544 10.761 5.574 6.084 -1.141 C09 YWQ 8 YWQ C16 C9 C 0 1 N N N N N N -36.078 -4.123 11.667 6.277 -0.536 1.100 C16 YWQ 9 YWQ N05 N1 N 0 1 N N N N N N -36.605 0.230 10.094 5.532 3.954 -0.148 N05 YWQ 10 YWQ N07 N2 N 0 1 N N N N N N -34.744 1.617 9.498 4.627 4.219 -2.291 N07 YWQ 11 YWQ O01 O1 O 0 1 N N N N N N -38.651 -3.209 12.467 8.469 0.884 0.683 O01 YWQ 12 YWQ O11 O2 O 0 1 N N N N N N -34.643 3.799 10.098 4.661 6.237 -3.231 O11 YWQ 13 YWQ O12 O3 O 0 1 N N N N N N -34.760 -0.561 8.858 4.646 2.259 -1.262 O12 YWQ 14 YWQ O13 O4 O 0 1 N N N N N N -36.375 -2.153 10.169 5.441 1.725 0.706 O13 YWQ 15 YWQ O14 O5 O 0 1 N N N N N N -37.887 -0.880 12.384 8.063 3.301 -0.010 O14 YWQ 16 YWQ O17 O6 O 0 1 N N N N N N -36.037 -5.448 11.455 4.987 -1.142 1.206 O17 YWQ 17 YWQ O19 O7 O 0 1 N N N N N N -36.574 -7.878 12.152 5.110 -2.846 -0.652 O19 YWQ 18 YWQ O20 O8 O 0 1 N N N N N N -38.480 -6.585 10.884 3.116 -2.962 0.892 O20 YWQ 19 YWQ O22 O9 O 0 1 N N N N N N -40.977 -7.333 10.487 2.294 -5.431 1.269 O22 YWQ 20 YWQ O23 O10 O 0 1 N N N N N N -40.655 -5.089 11.769 0.623 -3.611 0.368 O23 YWQ 21 YWQ O25 O11 O 0 1 N N N N N N -41.629 -6.515 13.561 -0.473 -4.583 -1.687 O25 YWQ 22 YWQ O26 O12 O 0 1 N N N N N N -42.170 -3.966 13.694 -1.818 -2.931 -0.333 O26 YWQ 23 YWQ O28 O13 O 0 1 N N N N N N -43.751 -1.910 13.886 -2.904 -2.336 -2.652 O28 YWQ 24 YWQ O29 O14 O 0 1 N N N N N N -42.676 -2.229 11.606 -4.002 -1.470 -0.426 O29 YWQ 25 YWQ O31 O15 O 0 1 N N N N N N -42.901 -2.969 9.305 -6.108 -1.167 -1.784 O31 YWQ 26 YWQ O32 O16 O 0 1 N N N N N N -44.947 -1.563 10.077 -5.626 0.553 -0.000 O32 YWQ 27 YWQ O34 O17 O 0 1 N N N N N N -46.681 0.517 9.782 -6.388 2.921 0.851 O34 YWQ 28 YWQ O35 O18 O 0 1 N N N N N N -45.557 0.001 12.006 -6.901 2.185 -1.620 O35 YWQ 29 YWQ O36 O19 O 0 1 N N N N N N -44.205 0.960 10.031 -8.065 1.105 0.342 O36 YWQ 30 YWQ O37 O20 O 0 1 N N N N N N -44.612 -3.842 11.079 -6.378 -1.889 0.619 O37 YWQ 31 YWQ O38 O21 O 0 1 N N N N N N -41.206 -1.641 13.636 -4.030 -3.918 -1.040 O38 YWQ 32 YWQ O39 O22 O 0 1 N N N N N N -39.869 -4.812 14.237 -1.334 -5.357 0.556 O39 YWQ 33 YWQ O40 O23 O 0 1 N N N N N N -39.851 -5.293 9.432 2.529 -4.463 -1.051 O40 YWQ 34 YWQ O41 O24 O 0 1 N N N N N N -37.783 -6.042 13.321 5.516 -3.670 1.699 O41 YWQ 35 YWQ O43 O25 O 0 1 N N N N N N -48.839 0.139 11.404 -7.587 5.214 0.386 O43 YWQ 36 YWQ O44 O26 O 0 1 N N N N N N -49.127 0.439 8.943 -8.477 3.589 2.101 O44 YWQ 37 YWQ O45 O27 O 0 1 N N N N N N -48.445 2.403 10.421 -6.347 4.818 2.670 O45 YWQ 38 YWQ P18 P1 P 0 1 N N N N N N -37.399 -6.631 11.988 4.692 -2.659 0.755 P18 YWQ 39 YWQ P21 P2 P 0 1 N N N N N N -40.204 -6.062 10.658 2.149 -4.124 0.339 P21 YWQ 40 YWQ P24 P3 P 0 1 N N N N N N -41.121 -5.101 13.454 -0.744 -4.130 -0.304 P24 YWQ 41 YWQ P27 P4 P 0 1 N N N N N N -42.479 -2.294 13.165 -3.207 -2.691 -1.111 P27 YWQ 42 YWQ P30 P5 P 0 1 N N N N N N -43.885 -2.706 10.426 -5.541 -0.997 -0.428 P30 YWQ 43 YWQ P33 P6 P 0 1 N N N N N N -45.326 0.080 10.517 -6.773 1.678 -0.097 P33 YWQ 44 YWQ P42 P7 P 0 1 N N N N N N -48.345 0.905 10.168 -7.227 4.124 1.515 P42 YWQ 45 YWQ H1 H1 H 0 1 N N N N N N -38.144 1.200 11.186 6.353 5.683 0.779 H1 YWQ 46 YWQ H2 H2 H 0 1 N N N N N N -37.159 -4.055 9.761 5.772 0.929 2.612 H2 YWQ 47 YWQ H3 H3 H 0 1 N N N N N N -39.213 -3.253 10.472 8.046 1.495 2.625 H3 YWQ 48 YWQ H4 H4 H 0 1 N N N N N N -39.318 -0.918 10.877 7.681 3.687 1.996 H4 YWQ 49 YWQ H5 H5 H 0 1 N N N N N N -37.823 -1.222 9.098 5.348 3.445 1.890 H5 YWQ 50 YWQ H6 H6 H 0 1 N N N N N N -37.057 3.366 11.270 5.833 7.132 -1.114 H6 YWQ 51 YWQ H7 H7 H 0 1 N N N N N N -35.057 -3.720 11.592 6.593 -0.535 0.057 H7 YWQ 52 YWQ H8 H8 H 0 1 N N N N N N -36.473 -3.937 12.677 6.994 -1.100 1.696 H8 YWQ 53 YWQ H9 H9 H 0 1 N N N N N N -33.855 1.729 9.053 4.189 3.834 -3.066 H9 YWQ 54 YWQ H10 H10 H 0 1 N N N N N N -39.514 -2.899 12.715 9.366 1.243 0.649 H10 YWQ 55 YWQ H11 H11 H 0 1 N N N N N N -38.549 -1.019 13.051 9.024 3.208 0.053 H11 YWQ 56 YWQ H12 H12 H 0 1 N N N N N N -41.145 -7.480 9.564 2.060 -5.282 2.195 H12 YWQ 57 YWQ H13 H13 H 0 1 N N N N N N -43.551 -1.279 14.567 -2.367 -1.541 -2.775 H13 YWQ 58 YWQ H14 H14 H 0 1 N N N N N N -44.925 0.550 12.455 -6.089 2.573 -1.975 H14 YWQ 59 YWQ H15 H15 H 0 1 N N N N N N -44.346 -4.661 10.678 -6.061 -1.827 1.531 H15 YWQ 60 YWQ H16 H16 H 0 1 N N N N N N -39.590 -5.599 14.690 -1.535 -5.133 1.474 H16 YWQ 61 YWQ H17 H17 H 0 1 N N N N N N -37.426 -6.578 14.019 5.293 -3.602 2.637 H17 YWQ 62 YWQ H18 H18 H 0 1 N N N N N N -49.527 -0.464 11.149 -6.814 5.607 -0.041 H18 YWQ 63 YWQ H19 H19 H 0 1 N N N N N N -48.992 2.801 9.754 -6.791 5.553 3.115 H19 YWQ 64 # 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 YWQ O12 C06 DOUB N N 1 YWQ O44 P42 DOUB N N 2 YWQ O31 P30 DOUB N N 3 YWQ O40 P21 DOUB N N 4 YWQ C06 N07 SING N N 5 YWQ C06 N05 SING N N 6 YWQ N07 C08 SING N N 7 YWQ O34 P42 SING N N 8 YWQ O34 P33 SING N N 9 YWQ O36 P33 DOUB N N 10 YWQ C04 N05 SING N N 11 YWQ C04 O13 SING N N 12 YWQ C04 C03 SING N N 13 YWQ O32 P30 SING N N 14 YWQ O32 P33 SING N N 15 YWQ N05 C10 SING N N 16 YWQ O11 C08 DOUB N N 17 YWQ C08 C09 SING N N 18 YWQ P42 O45 SING N N 19 YWQ P42 O43 SING N N 20 YWQ O13 C15 SING N N 21 YWQ P30 O37 SING N N 22 YWQ P30 O29 SING N N 23 YWQ O22 P21 SING N N 24 YWQ P33 O35 SING N N 25 YWQ C15 C02 SING N N 26 YWQ C15 C16 SING N N 27 YWQ P21 O20 SING N N 28 YWQ P21 O23 SING N N 29 YWQ C10 C09 DOUB N N 30 YWQ O20 P18 SING N N 31 YWQ C02 C03 SING N N 32 YWQ C02 O01 SING N N 33 YWQ C03 O14 SING N N 34 YWQ O17 C16 SING N N 35 YWQ O17 P18 SING N N 36 YWQ O29 P27 SING N N 37 YWQ O23 P24 SING N N 38 YWQ P18 O19 DOUB N N 39 YWQ P18 O41 SING N N 40 YWQ P27 O38 DOUB N N 41 YWQ P27 O26 SING N N 42 YWQ P27 O28 SING N N 43 YWQ P24 O25 DOUB N N 44 YWQ P24 O26 SING N N 45 YWQ P24 O39 SING N N 46 YWQ C10 H1 SING N N 47 YWQ C15 H2 SING N N 48 YWQ C02 H3 SING N N 49 YWQ C03 H4 SING N N 50 YWQ C04 H5 SING N N 51 YWQ C09 H6 SING N N 52 YWQ C16 H7 SING N N 53 YWQ C16 H8 SING N N 54 YWQ N07 H9 SING N N 55 YWQ O01 H10 SING N N 56 YWQ O14 H11 SING N N 57 YWQ O22 H12 SING N N 58 YWQ O28 H13 SING N N 59 YWQ O35 H14 SING N N 60 YWQ O37 H15 SING N N 61 YWQ O39 H16 SING N N 62 YWQ O41 H17 SING N N 63 YWQ O43 H18 SING N N 64 YWQ O45 H19 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 YWQ SMILES ACDLabs 12.01 "O=P(O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)OCC1OC(N2C=CC(=O)NC2=O)C(O)C1O" YWQ InChI InChI 1.06 "InChI=1S/C9H19N2O27P7/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(32-8)3-31-40(19,20)34-42(23,24)36-44(27,28)38-45(29,30)37-43(25,26)35-41(21,22)33-39(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H,21,22)(H,23,24)(H,25,26)(H,27,28)(H,29,30)(H,10,12,15)(H2,16,17,18)/t4-,6+,7+,8-/m0/s1" YWQ InChIKey InChI 1.06 DLYGIJYUJNEFKD-IHBLQFBFSA-N YWQ 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[P](O)(=O)O[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O" YWQ 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[P](O)(=O)O[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O" YWQ SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C1=CN(C(=O)NC1=O)[C@@H]2[C@@H]([C@@H]([C@@H](O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O" YWQ SMILES "OpenEye OEToolkits" 2.0.7 "C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=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 YWQ "SYSTEMATIC NAME" ACDLabs 12.01 "1-{5-O-[(R)-hydroxy{[(R)-hydroxy{[(R)-hydroxy{[(R)-hydroxy{[(S)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]oxy}phosphoryl]oxy}phosphoryl]oxy}phosphoryl]oxy}phosphoryl]-beta-L-lyxofuranosyl}pyrimidine-2,4(1H,3H)-dione" YWQ "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[[(2~{S},3~{S},4~{R},5~{S})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [oxidanyl-[oxidanyl-[oxidanyl-[oxidanyl(phosphonooxy)phosphoryl]oxy-phosphoryl]oxy-phosphoryl]oxy-phosphoryl] 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 YWQ "Create component" 2023-03-02 RCSB YWQ "Initial release" 2024-03-06 RCSB #