data_U2L # _chem_comp.id U2L _chem_comp.name ;5-METHYL-3'-O-METHOXYETHYL URIDINE-5'-MONOPHOSPHATE ; _chem_comp.type "RNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C13 H21 N2 O10 P" _chem_comp.mon_nstd_parent_comp_id U _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2004-10-29 _chem_comp.pdbx_modified_date 2011-06-04 _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 396.287 _chem_comp.one_letter_code U _chem_comp.three_letter_code U2L _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag Y _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code ? _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 U2L OP3 O3P O 0 1 N Y N ? ? ? 1.198 0.588 -4.548 OP3 U2L 1 U2L P P P 0 1 N N N 0.601 1.247 13.043 2.787 0.324 -4.407 P U2L 2 U2L OP1 O1P O 0 1 N N N -0.516 1.573 13.956 3.659 1.172 -5.286 OP1 U2L 3 U2L OP2 O2P O 0 1 N N N 0.879 2.127 11.886 2.921 -1.270 -4.647 OP2 U2L 4 U2L "O5'" O5* O 0 1 N N N 1.951 1.149 13.918 3.063 0.476 -2.819 "O5'" U2L 5 U2L "C5'" C5* C 0 1 N N N 2.722 2.299 14.247 2.282 -0.292 -1.921 "C5'" U2L 6 U2L "C4'" C4* C 0 1 N N R 4.211 1.959 14.126 2.725 0.023 -0.498 "C4'" U2L 7 U2L "O4'" O4* O 0 1 N N N 4.512 0.959 15.074 2.470 1.422 -0.246 "O4'" U2L 8 U2L "C3'" C3* C 0 1 N N S 4.656 1.434 12.784 1.940 -0.742 0.560 "C3'" U2L 9 U2L "O3'" O3* O 0 1 N N N 4.830 2.505 11.848 2.742 -0.809 1.739 "O3'" U2L 10 U2L "C2'" C2* C 0 1 N N R 5.869 0.545 13.138 0.748 0.163 0.786 "C2'" U2L 11 U2L "O2'" O2* O 0 1 N N N 7.054 1.231 13.565 0.137 -0.058 2.041 "O2'" U2L 12 U2L "C1'" C1* C 0 1 N N R 5.215 -0.054 14.384 1.373 1.543 0.675 "C1'" U2L 13 U2L N1 N1 N 0 1 N N N 4.581 -1.409 14.372 0.452 2.524 0.177 N1 U2L 14 U2L C2 C2 C 0 1 N N N 4.591 -2.126 15.579 -0.300 3.336 1.055 C2 U2L 15 U2L O2 O2 O 0 1 N N N 5.086 -1.694 16.618 -0.225 3.269 2.283 O2 U2L 16 U2L N3 N3 N 0 1 N N N 4.006 -3.391 15.572 -1.159 4.248 0.431 N3 U2L 17 U2L C4 C4 C 0 1 N N N 3.413 -4.007 14.479 -1.338 4.427 -0.932 C4 U2L 18 U2L O4 O4 O 0 1 N N N 2.929 -5.131 14.592 -2.112 5.251 -1.413 O4 U2L 19 U2L C5 C5 C 0 1 N N N 3.445 -3.197 13.275 -0.514 3.537 -1.792 C5 U2L 20 U2L C6 C6 C 0 1 N N N 4.003 -1.970 13.260 0.309 2.663 -1.199 C6 U2L 21 U2L "CA'" CA* C 0 1 N N N 6.002 3.315 11.899 3.867 -1.652 1.551 "CA'" U2L 22 U2L "CB'" CB* C 0 1 N N N 5.933 4.477 10.896 4.693 -1.667 2.823 "CB'" U2L 23 U2L "OC'" OC* O 0 1 N N N 5.107 5.560 11.310 5.141 -0.346 3.101 "OC'" U2L 24 U2L "CD'" CD* C 0 1 N N N 3.718 5.273 11.339 5.904 -0.296 4.298 "CD'" U2L 25 U2L C7 C7 C 0 1 N N N 2.869 -3.653 11.965 -0.651 3.669 -3.275 C7 U2L 26 U2L HOP3 3HOP H 0 0 N N N 0.718 -0.209 -0.586 0.799 0.616 -5.443 HOP3 U2L 27 U2L HOP2 2HOP H 0 0 N N N 0.923 2.217 12.831 2.886 -1.617 -5.563 HOP2 U2L 28 U2L "H5'" 1H5* H 0 1 N N N 2.493 3.124 13.574 1.229 -0.035 -2.051 "H5'" U2L 29 U2L "H5''" 2H5* H 0 0 N N N 2.500 2.605 15.270 2.428 -1.352 -2.133 "H5''" U2L 30 U2L "H4'" H4* H 0 1 N N N 4.834 2.827 14.242 3.804 -0.139 -0.410 "H4'" U2L 31 U2L "H3'" H3* H 0 1 N N N 3.808 0.804 12.510 1.675 -1.764 0.277 "H3'" U2L 32 U2L "H2'" H2* H 0 1 N N N 6.220 -0.166 12.382 -0.000 0.004 -0.000 "H2'" U2L 33 U2L "HO2'" 2HO* H 0 0 N N N 7.800 0.684 13.783 -0.494 0.669 2.185 "HO2'" U2L 34 U2L "H1'" H1* H 0 1 N N N 6.113 -0.225 14.907 1.754 1.910 1.633 "H1'" U2L 35 U2L H3 H3 H 0 1 N N N 4.014 -3.904 16.438 -1.709 4.843 1.045 H3 U2L 36 U2L H6 H6 H 0 1 N N N 3.941 -1.493 12.308 0.928 1.995 -1.790 H6 U2L 37 U2L "HA'1" 1HA* H 0 0 N N N 6.163 3.720 12.897 3.504 -2.655 1.304 "HA'1" U2L 38 U2L "HA'2" 2HA* H 0 0 N N N 6.861 2.704 11.620 4.455 -1.258 0.717 "HA'2" U2L 39 U2L "HB'1" 1HB* H 0 0 N N N 6.943 4.869 10.778 5.572 -2.309 2.715 "HB'1" U2L 40 U2L "HB'2" 2HB* H 0 0 N N N 5.610 4.111 9.924 4.088 -2.009 3.668 "HB'2" U2L 41 U2L "HD'1" 1HD* H 0 0 N N N 3.399 4.844 10.388 5.249 -0.053 5.138 "HD'1" U2L 42 U2L "HD'2" 2HD* H 0 0 N N N 3.168 6.198 11.512 6.686 0.461 4.201 "HD'2" U2L 43 U2L "HD'3" 3HD* H 0 0 N N N 3.490 4.583 12.150 6.363 -1.273 4.468 "HD'3" U2L 44 U2L H71 1H7 H 0 1 N N N 1.864 -3.270 11.815 -1.057 2.748 -3.690 H71 U2L 45 U2L H72 2H7 H 0 1 N N N 2.895 -4.741 11.910 0.324 3.866 -3.719 H72 U2L 46 U2L H73 3H7 H 0 1 N N N 3.594 -3.270 11.223 -1.320 4.497 -3.510 H73 U2L 47 # 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 U2L OP3 P SING N N 1 U2L OP3 HOP3 SING N N 2 U2L P OP1 DOUB N N 3 U2L P OP2 SING N N 4 U2L P "O5'" SING N N 5 U2L OP2 HOP2 SING N N 6 U2L "O5'" "C5'" SING N N 7 U2L "C5'" "C4'" SING N N 8 U2L "C5'" "H5'" SING N N 9 U2L "C5'" "H5''" SING N N 10 U2L "C4'" "O4'" SING N N 11 U2L "C4'" "C3'" SING N N 12 U2L "C4'" "H4'" SING N N 13 U2L "O4'" "C1'" SING N N 14 U2L "C3'" "O3'" SING N N 15 U2L "C3'" "C2'" SING N N 16 U2L "C3'" "H3'" SING N N 17 U2L "O3'" "CA'" SING N N 18 U2L "C2'" "O2'" SING N N 19 U2L "C2'" "C1'" SING N N 20 U2L "C2'" "H2'" SING N N 21 U2L "O2'" "HO2'" SING N N 22 U2L "C1'" N1 SING N N 23 U2L "C1'" "H1'" SING N N 24 U2L N1 C2 SING N N 25 U2L N1 C6 SING N N 26 U2L C2 O2 DOUB N N 27 U2L C2 N3 SING N N 28 U2L N3 C4 SING N N 29 U2L N3 H3 SING N N 30 U2L C4 O4 DOUB N N 31 U2L C4 C5 SING N N 32 U2L C5 C6 DOUB N N 33 U2L C5 C7 SING N N 34 U2L C6 H6 SING N N 35 U2L "CA'" "CB'" SING N N 36 U2L "CA'" "HA'1" SING N N 37 U2L "CA'" "HA'2" SING N N 38 U2L "CB'" "OC'" SING N N 39 U2L "CB'" "HB'1" SING N N 40 U2L "CB'" "HB'2" SING N N 41 U2L "OC'" "CD'" SING N N 42 U2L "CD'" "HD'1" SING N N 43 U2L "CD'" "HD'2" SING N N 44 U2L "CD'" "HD'3" SING N N 45 U2L C7 H71 SING N N 46 U2L C7 H72 SING N N 47 U2L C7 H73 SING N N 48 # 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 U2L SMILES ACDLabs 10.04 "O=C1NC(=O)N(C=C1C)C2OC(C(OCCOC)C2O)COP(=O)(O)O" U2L SMILES_CANONICAL CACTVS 3.341 "COCCO[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=C(C)C(=O)NC2=O" U2L SMILES CACTVS 3.341 "COCCO[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)N2C=C(C)C(=O)NC2=O" U2L SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)OCCOC)O" U2L SMILES "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)OCCOC)O" U2L InChI InChI 1.03 "InChI=1S/C13H21N2O10P/c1-7-5-15(13(18)14-11(7)17)12-9(16)10(23-4-3-22-2)8(25-12)6-24-26(19,20)21/h5,8-10,12,16H,3-4,6H2,1-2H3,(H,14,17,18)(H2,19,20,21)/t8-,9-,10-,12-/m1/s1" U2L InChIKey InChI 1.03 KIDCHLZJMPQNHC-DNRKLUKYSA-N # 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 U2L "SYSTEMATIC NAME" ACDLabs 10.04 ;3'-O-(2-methoxyethyl)-5-methyluridine 5'-(dihydrogen phosphate) ; U2L "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,4R,5R)-4-hydroxy-3-(2-methoxyethoxy)-5-(5-methyl-2,4-dioxo-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 U2L "Create component" 2004-10-29 RCSB U2L "Modify descriptor" 2011-06-04 RCSB #