data_XSX # _chem_comp.id XSX _chem_comp.name ;3-[(3R)-3-amino-3-carboxypropyl]uridine 5'-(dihydrogen phosphate) ; _chem_comp.type "RNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C13 H20 N3 O11 P" _chem_comp.mon_nstd_parent_comp_id U _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2022-12-07 _chem_comp.pdbx_modified_date 2023-09-01 _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 425.285 _chem_comp.one_letter_code U _chem_comp.three_letter_code XSX _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 8EVQ _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.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 XSX "O5'" O1 O 0 1 N N N 164.051 178.055 265.011 4.755 -0.172 -0.695 "O5'" XSX 1 XSX "C5'" C1 C 0 1 N N N 163.351 179.249 265.328 4.232 0.681 0.326 "C5'" XSX 2 XSX "C4'" C2 C 0 1 N N R 161.960 179.206 264.751 2.870 1.223 -0.111 "C4'" XSX 3 XSX "O4'" O2 O 0 1 N N N 162.065 179.263 263.311 1.886 0.166 -0.119 "O4'" XSX 4 XSX "C3'" C3 C 0 1 N N S 161.188 177.927 265.034 2.342 2.246 0.919 "C3'" XSX 5 XSX "O3'" O3 O 0 1 N N N 160.469 178.005 266.253 2.609 3.580 0.483 "O3'" XSX 6 XSX "C2'" C4 C 0 1 N N R 160.281 177.765 263.815 0.820 1.984 0.963 "C2'" XSX 7 XSX "O2'" O4 O 0 1 N N N 159.064 178.472 264.000 0.100 3.148 0.554 "O2'" XSX 8 XSX "C1'" C5 C 0 1 N N R 161.078 178.461 262.711 0.608 0.834 -0.047 "C1'" XSX 9 XSX C5 C6 C 0 1 N N N 163.682 176.265 261.190 -1.180 -1.612 2.058 C5 XSX 10 XSX C6 C7 C 0 1 N N N 162.983 177.092 262.059 -0.229 -0.763 1.611 C6 XSX 11 XSX N1 N1 N 0 1 N N N 161.756 177.543 261.765 -0.423 -0.087 0.438 N1 XSX 12 XSX C2 C8 C 0 1 N N N 161.159 177.216 260.530 -1.551 -0.259 -0.275 C2 XSX 13 XSX N3 N2 N 0 1 N N N 161.845 176.379 259.627 -2.515 -1.098 0.148 N3 XSX 14 XSX C4 C9 C 0 1 N N N 163.124 175.903 259.974 -2.360 -1.788 1.296 C4 XSX 15 XSX C1 C10 C 0 1 N N N 161.234 176.007 258.348 -3.732 -1.272 -0.649 C1 XSX 16 XSX C3 C11 C 0 1 N N N 161.491 175.575 256.914 -4.786 -0.259 -0.197 C3 XSX 17 XSX C7 C12 C 0 1 N N R 160.841 174.237 256.550 -6.057 -0.441 -1.029 C7 XSX 18 XSX C9 C13 C 0 1 N N N 161.294 173.139 257.518 -7.050 0.634 -0.670 C9 XSX 19 XSX N4 N3 N 0 1 N N N 161.212 173.847 255.163 -6.641 -1.760 -0.751 N4 XSX 20 XSX O10 O5 O 0 1 N N N 160.421 172.640 258.257 -6.925 1.865 -1.191 O10 XSX 21 XSX O11 O6 O 0 1 N N N 162.520 172.926 257.599 -7.959 0.388 0.087 O11 XSX 22 XSX O2 O7 O 0 1 N N N 160.022 177.652 260.244 -1.702 0.352 -1.315 O2 XSX 23 XSX O4 O8 O 0 1 N N N 163.758 175.159 259.197 -3.231 -2.547 1.679 O4 XSX 24 XSX OP1 O9 O 0 1 N N N 166.107 176.610 265.220 7.235 0.079 -0.299 OP1 XSX 25 XSX OP2 O10 O 0 1 N N N 166.024 178.670 263.618 6.119 -1.984 0.635 OP2 XSX 26 XSX P P1 P 0 1 N N N 165.640 178.013 264.920 6.176 -0.919 -0.571 P XSX 27 XSX H1 H1 H 0 1 N N N 163.892 180.110 264.908 4.118 0.114 1.250 H1 XSX 28 XSX H2 H2 H 0 1 N N N 163.288 179.354 266.421 4.918 1.512 0.491 H2 XSX 29 XSX H3 H3 H 0 1 N N N 161.384 180.066 265.124 2.944 1.682 -1.097 H3 XSX 30 XSX H4 H4 H 0 1 N N N 161.895 177.085 265.062 2.790 2.068 1.897 H4 XSX 31 XSX H5 H5 H 0 1 N N N 161.078 178.105 266.975 2.298 4.263 1.093 H5 XSX 32 XSX H6 H6 H 0 1 N N N 160.124 176.702 263.578 0.514 1.678 1.963 H6 XSX 33 XSX H7 H7 H 0 1 N N N 158.555 178.053 264.684 0.245 3.919 1.120 H7 XSX 34 XSX H8 H8 H 0 1 N N N 160.383 179.097 262.142 0.333 1.233 -1.024 H8 XSX 35 XSX H9 H9 H 0 1 N N N 164.662 175.903 261.462 -1.040 -2.153 2.983 H9 XSX 36 XSX H10 H10 H 0 1 N N N 163.439 177.379 262.995 0.679 -0.619 2.178 H10 XSX 37 XSX H11 H11 H 0 1 N N N 160.618 176.900 258.167 -3.502 -1.112 -1.702 H11 XSX 38 XSX H12 H12 H 0 1 N N N 160.591 175.179 258.681 -4.116 -2.283 -0.510 H12 XSX 39 XSX H13 H13 H 0 1 N N N 162.577 175.485 256.768 -5.015 -0.419 0.856 H13 XSX 40 XSX H14 H14 H 0 1 N N N 161.093 176.349 256.241 -4.402 0.751 -0.336 H14 XSX 41 XSX H15 H15 H 0 1 N N N 159.748 174.343 256.620 -5.811 -0.369 -2.089 H15 XSX 42 XSX H16 H16 H 0 1 N N N 160.783 172.973 254.936 -6.877 -1.852 0.226 H16 XSX 43 XSX H17 H17 H 0 1 N N N 160.897 174.549 254.524 -7.445 -1.930 -1.336 H17 XSX 44 XSX H19 H19 H 0 1 N N N 160.834 172.070 258.895 -7.586 2.521 -0.931 H19 XSX 45 XSX H21 H21 H 0 1 N N N 166.555 178.072 263.106 5.446 -2.669 0.524 H21 XSX 46 XSX OP3 OP3 O 0 1 N Y N 166.138 179.019 266.068 6.502 -1.685 -1.949 OP3 XSX 47 XSX "HO3'" H18 H 0 0 N Y N 166.634 178.537 266.719 7.345 -2.158 -1.946 "HO3'" XSX 48 # 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 XSX N4 C7 SING N N 1 XSX C7 C3 SING N N 2 XSX C7 C9 SING N N 3 XSX C3 C1 SING N N 4 XSX C9 O11 DOUB N N 5 XSX C9 O10 SING N N 6 XSX C1 N3 SING N N 7 XSX O4 C4 DOUB N N 8 XSX N3 C4 SING N N 9 XSX N3 C2 SING N N 10 XSX C4 C5 SING N N 11 XSX O2 C2 DOUB N N 12 XSX C2 N1 SING N N 13 XSX C5 C6 DOUB N N 14 XSX N1 C6 SING N N 15 XSX N1 "C1'" SING N N 16 XSX "C1'" "O4'" SING N N 17 XSX "C1'" "C2'" SING N N 18 XSX "O4'" "C4'" SING N N 19 XSX OP2 P SING N N 20 XSX "C2'" "O2'" SING N N 21 XSX "C2'" "C3'" SING N N 22 XSX "C4'" "C3'" SING N N 23 XSX "C4'" "C5'" SING N N 24 XSX P "O5'" SING N N 25 XSX P OP1 DOUB N N 26 XSX "O5'" "C5'" SING N N 27 XSX "C3'" "O3'" SING N N 28 XSX "C5'" H1 SING N N 29 XSX "C5'" H2 SING N N 30 XSX "C4'" H3 SING N N 31 XSX "C3'" H4 SING N N 32 XSX "O3'" H5 SING N N 33 XSX "C2'" H6 SING N N 34 XSX "O2'" H7 SING N N 35 XSX "C1'" H8 SING N N 36 XSX C5 H9 SING N N 37 XSX C6 H10 SING N N 38 XSX C1 H11 SING N N 39 XSX C1 H12 SING N N 40 XSX C3 H13 SING N N 41 XSX C3 H14 SING N N 42 XSX C7 H15 SING N N 43 XSX N4 H16 SING N N 44 XSX N4 H17 SING N N 45 XSX O10 H19 SING N N 46 XSX OP2 H21 SING N N 47 XSX P OP3 SING N N 48 XSX OP3 "HO3'" SING N N 49 # 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 XSX SMILES ACDLabs 12.01 "O=C(O)C(N)CCN1C(=O)C=CN(C1=O)C1OC(COP(=O)(O)O)C(O)C1O" XSX InChI InChI 1.06 "InChI=1S/C13H20N3O11P/c14-6(12(20)21)1-3-15-8(17)2-4-16(13(15)22)11-10(19)9(18)7(27-11)5-26-28(23,24)25/h2,4,6-7,9-11,18-19H,1,3,5,14H2,(H,20,21)(H2,23,24,25)/t6-,7-,9-,10-,11-/m1/s1" XSX InChIKey InChI 1.06 CJKRCYMKRHIIKR-JBSYKWBFSA-N XSX SMILES_CANONICAL CACTVS 3.385 "N[C@H](CCN1C(=O)C=CN([C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O)C1=O)C(O)=O" XSX SMILES CACTVS 3.385 "N[CH](CCN1C(=O)C=CN([CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O)C1=O)C(O)=O" XSX SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C1=CN(C(=O)N(C1=O)CC[C@H](C(=O)O)N)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O" XSX SMILES "OpenEye OEToolkits" 2.0.7 "C1=CN(C(=O)N(C1=O)CCC(C(=O)O)N)C2C(C(C(O2)COP(=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 XSX "SYSTEMATIC NAME" ACDLabs 12.01 ;3-[(3R)-3-amino-3-carboxypropyl]uridine 5'-(dihydrogen phosphate) ; XSX "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(2~{R})-2-azanyl-4-[3-[(2~{R},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]-2,6-bis(oxidanylidene)pyrimidin-1-yl]butanoic acid" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site XSX "Create component" 2022-12-07 RCSB XSX "Initial release" 2023-09-06 RCSB #