data_P4U # _chem_comp.id P4U _chem_comp.name "4-propyl, uridine-5'-monophosphate" _chem_comp.type "RNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C12 H19 N2 O9 P" _chem_comp.mon_nstd_parent_comp_id U _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2017-09-25 _chem_comp.pdbx_modified_date 2019-04-29 _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 366.261 _chem_comp.one_letter_code U _chem_comp.three_letter_code P4U _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 6EK0 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site EBI # # 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 P4U "C1'" C1 C 0 1 N N R 216.423 321.536 231.669 -0.049 -1.828 0.596 "C1'" P4U 1 P4U C2 C2 C 0 1 N N N 215.802 322.267 233.984 -1.675 -0.210 -0.214 C2 P4U 2 P4U "C2'" C3 C 0 1 N N R 215.168 321.956 230.902 0.242 -2.469 -0.785 "C2'" P4U 3 P4U "C3'" C4 C 0 1 N N S 215.764 322.900 229.878 1.790 -2.447 -0.832 "C3'" P4U 4 P4U C4 C5 C 0 1 N N N 216.957 324.003 235.029 -3.831 -0.075 0.603 C4 P4U 5 P4U "C4'" C6 C 0 1 N N R 217.046 322.197 229.518 2.184 -1.366 0.192 "C4'" P4U 6 P4U C5 C7 C 0 1 N N N 217.763 324.135 233.936 -3.563 -1.143 1.480 C5 P4U 7 P4U "C5'" C8 C 0 1 N N N 218.082 323.071 228.881 3.004 -0.272 -0.495 "C5'" P4U 8 P4U C6 C9 C 0 1 N N N 217.577 323.309 232.862 -2.330 -1.707 1.472 C6 P4U 9 P4U N1 N1 N 0 1 N N N 216.624 322.386 232.858 -1.386 -1.229 0.615 N1 P4U 10 P4U N3 N2 N 0 1 N N N 215.999 323.070 235.036 -2.882 0.356 -0.213 N3 P4U 11 P4U O2 O1 O 0 1 N N N 214.894 321.421 234.056 -0.818 0.206 -0.976 O2 P4U 12 P4U "O2'" O2 O 0 1 N N N 214.615 320.808 230.283 -0.252 -3.809 -0.840 "O2'" P4U 13 P4U "O3'" O3 O 0 1 N N N 214.938 323.174 228.774 2.319 -3.719 -0.451 "O3'" P4U 14 P4U O4 O4 O 0 1 N N N 217.160 324.819 236.109 -5.050 0.507 0.594 O4 P4U 15 P4U "O4'" O5 O 0 1 N N N 217.520 321.707 230.796 0.967 -0.809 0.720 "O4'" P4U 16 P4U "O5'" O6 O 0 1 N N N 219.348 322.877 229.461 3.463 0.664 0.482 "O5'" P4U 17 P4U OP1 O7 O 0 1 N N N 219.777 324.890 230.939 5.565 1.514 -0.627 OP1 P4U 18 P4U OP2 O8 O 0 1 N N N 220.624 324.810 228.510 3.500 2.955 -0.808 OP2 P4U 19 P4U P P1 P 0 1 N N N 220.305 324.098 229.786 4.358 1.950 0.112 P P4U 20 P4U C41 C10 C 0 1 N N N 217.755 326.108 235.950 -5.248 1.584 -0.323 C41 P4U 21 P4U C42 C11 C 0 1 N N N 218.185 326.678 237.289 -6.678 2.112 -0.189 C42 P4U 22 P4U C43 C12 C 0 1 N N N 218.948 325.651 238.081 -6.890 3.266 -1.171 C43 P4U 23 P4U H1 H1 H 0 1 N N N 216.325 320.483 231.973 0.051 -2.567 1.391 H1 P4U 24 P4U H2 H2 H 0 1 N N N 214.455 322.475 231.560 -0.180 -1.867 -1.589 H2 P4U 25 P4U H3 H3 H 0 1 N N N 216.020 323.840 230.389 2.137 -2.174 -1.829 H3 P4U 26 P4U H4 H4 H 0 1 N N N 216.821 321.352 228.850 2.764 -1.814 0.999 H4 P4U 27 P4U H5 H5 H 0 1 N N N 218.540 324.885 233.919 -4.327 -1.506 2.151 H5 P4U 28 P4U H6 H6 H 0 1 N N N 217.788 324.124 229.008 3.860 -0.722 -0.998 H6 P4U 29 P4U H7 H7 H 0 1 N N N 218.140 322.833 227.809 2.381 0.242 -1.227 H7 P4U 30 P4U H8 H8 H 0 1 N N N 218.219 323.410 231.999 -2.101 -2.527 2.136 H8 P4U 31 P4U H9 H9 H 0 1 N N N 214.249 320.235 230.947 -0.093 -4.252 -1.684 H9 P4U 32 P4U H10 H10 H 0 1 N N N 214.150 323.616 229.069 2.054 -4.445 -1.031 H10 P4U 33 P4U H12 H12 H 0 1 N N N 220.436 325.736 228.608 2.693 3.281 -0.386 H12 P4U 34 P4U H13 H13 H 0 1 N N N 218.636 326.019 235.297 -4.543 2.385 -0.100 H13 P4U 35 P4U H14 H14 H 0 1 N N N 217.023 326.787 235.488 -5.086 1.230 -1.341 H14 P4U 36 P4U H15 H15 H 0 1 N N N 218.828 327.554 237.119 -7.383 1.311 -0.412 H15 P4U 37 P4U H16 H16 H 0 1 N N N 217.293 326.982 237.856 -6.841 2.466 0.829 H16 P4U 38 P4U H17 H17 H 0 1 N N N 219.251 326.082 239.047 -6.185 4.067 -0.948 H17 P4U 39 P4U H18 H18 H 0 1 N N N 218.308 324.773 238.256 -6.728 2.911 -2.189 H18 P4U 40 P4U H19 H19 H 0 1 N N N 219.843 325.346 237.519 -7.909 3.641 -1.076 H19 P4U 41 P4U OP3 OP3 O 0 1 N Y N 221.625 323.373 230.314 4.800 2.704 1.464 OP3 P4U 42 P4U H11 H11 H 0 1 N N N 221.772 323.605 231.223 5.344 3.490 1.316 H11 P4U 43 # # 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 P4U OP2 P SING N N 1 P4U "O3'" "C3'" SING N N 2 P4U "C5'" "O5'" SING N N 3 P4U "C5'" "C4'" SING N N 4 P4U "O5'" P SING N N 5 P4U "C4'" "C3'" SING N N 6 P4U "C4'" "O4'" SING N N 7 P4U P OP1 DOUB N N 8 P4U "C3'" "C2'" SING N N 9 P4U "O2'" "C2'" SING N N 10 P4U "O4'" "C1'" SING N N 11 P4U "C2'" "C1'" SING N N 12 P4U "C1'" N1 SING N N 13 P4U N1 C6 SING N N 14 P4U N1 C2 SING N N 15 P4U C6 C5 DOUB N N 16 P4U C5 C4 SING N N 17 P4U C2 O2 DOUB N N 18 P4U C2 N3 SING N N 19 P4U C4 N3 DOUB N N 20 P4U C4 O4 SING N N 21 P4U C41 O4 SING N N 22 P4U C41 C42 SING N N 23 P4U C42 C43 SING N N 24 P4U "C1'" H1 SING N N 25 P4U "C2'" H2 SING N N 26 P4U "C3'" H3 SING N N 27 P4U "C4'" H4 SING N N 28 P4U C5 H5 SING N N 29 P4U "C5'" H6 SING N N 30 P4U "C5'" H7 SING N N 31 P4U C6 H8 SING N N 32 P4U "O2'" H9 SING N N 33 P4U "O3'" H10 SING N N 34 P4U OP2 H12 SING N N 35 P4U C41 H13 SING N N 36 P4U C41 H14 SING N N 37 P4U C42 H15 SING N N 38 P4U C42 H16 SING N N 39 P4U C43 H17 SING N N 40 P4U C43 H18 SING N N 41 P4U C43 H19 SING N N 42 P4U P OP3 SING N N 43 P4U OP3 H11 SING N N 44 # # 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 P4U InChI InChI 1.03 "InChI=1S/C12H19N2O9P/c1-2-5-21-8-3-4-14(12(17)13-8)11-10(16)9(15)7(23-11)6-22-24(18,19)20/h3-4,7,9-11,15-16H,2,5-6H2,1H3,(H2,18,19,20)/t7-,9-,10-,11-/m1/s1" P4U InChIKey InChI 1.03 YIPJYDZHQZNRLV-QCNRFFRDSA-N P4U SMILES_CANONICAL CACTVS 3.385 "CCCOC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O" P4U SMILES CACTVS 3.385 "CCCOC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O" P4U SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "CCCOC1=NC(=O)N(C=C1)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O" P4U SMILES "OpenEye OEToolkits" 2.0.6 "CCCOC1=NC(=O)N(C=C1)C2C(C(C(O2)COP(=O)(O)O)O)O" # _pdbx_chem_comp_identifier.comp_id P4U _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.6 _pdbx_chem_comp_identifier.identifier "[(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-(2-oxidanylidene-4-propoxy-pyrimidin-1-yl)oxolan-2-yl]methyl dihydrogen 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 P4U "Create component" 2017-09-25 EBI P4U "Initial release" 2018-01-24 RCSB P4U "Modify one letter code" 2019-04-29 EBI ##