data_3ME # _chem_comp.id 3ME _chem_comp.name ;2'-O-{2-[2-(dimethylamino)ethoxy]ethyl}-5-methyluridine 5'-(dihydrogen phosphate) ; _chem_comp.type "RNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C16 H28 N3 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 2003-03-04 _chem_comp.pdbx_modified_date 2011-10-27 _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 453.381 _chem_comp.one_letter_code U _chem_comp.three_letter_code 3ME _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag Y _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 1NZG _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 3ME P P P 0 1 N N N -4.941 7.623 11.758 6.123 -0.190 -0.062 P 3ME 1 3ME OP1 O1P O 0 1 N N N -6.287 8.265 11.652 6.730 -1.501 -0.383 OP1 3ME 2 3ME OP2 O2P O 0 1 N N N -4.853 6.153 11.922 6.034 0.702 -1.400 OP2 3ME 3 3ME "O5'" "O5'" O 0 1 N N N -4.175 7.969 10.424 4.645 -0.414 0.534 "O5'" 3ME 4 3ME "C5'" "C5'" C 0 1 N N N -4.206 9.281 9.882 3.632 -1.152 -0.154 "C5'" 3ME 5 3ME "C4'" "C4'" C 0 1 N N R -3.317 9.358 8.681 2.355 -1.171 0.688 "C4'" 3ME 6 3ME "O4'" "O4'" O 0 1 N N N -1.947 9.106 9.055 1.811 0.156 0.781 "O4'" 3ME 7 3ME "C1'" "C1'" C 0 1 N N R -1.278 8.444 7.986 0.374 0.023 0.813 "C1'" 3ME 8 3ME N1 N1 N 0 1 N N N -0.848 7.114 8.442 -0.270 1.273 0.402 N1 3ME 9 3ME C6 C6 C 0 1 N N N -1.492 6.455 9.473 -1.209 1.849 1.212 C6 3ME 10 3ME C2 C2 C 0 1 N N N 0.229 6.561 7.794 0.073 1.846 -0.766 C2 3ME 11 3ME O2 O2 O 0 1 N N N 0.784 7.091 6.837 0.914 1.319 -1.468 O2 3ME 12 3ME N3 N3 N 0 1 N N N 0.627 5.346 8.297 -0.503 2.994 -1.168 N3 3ME 13 3ME C4 C4 C 0 1 N N N 0.061 4.641 9.344 -1.437 3.591 -0.400 C4 3ME 14 3ME O4 O4 O 0 1 N N N 0.551 3.578 9.700 -1.959 4.630 -0.763 O4 3ME 15 3ME C5 C5 C 0 1 N N N -1.093 5.262 9.957 -1.803 3.001 0.834 C5 3ME 16 3ME C5A C5A C 0 1 N N N -1.773 4.577 11.105 -2.840 3.651 1.713 C5A 3ME 17 3ME "C2'" "C2'" C 0 1 N N R -2.280 8.279 6.849 0.093 -1.100 -0.218 "C2'" 3ME 18 3ME "O2'" "O2'" O 0 1 N N N -2.286 9.484 6.091 -1.143 -1.758 0.069 "O2'" 3ME 19 3ME "CB'" "CB'" C 0 1 N N N -1.088 9.604 5.329 -1.807 -2.276 -1.086 "CB'" 3ME 20 3ME "CC'" "CC'" C 0 1 N N N -1.103 10.899 4.533 -3.111 -2.955 -0.662 "CC'" 3ME 21 3ME "OD'" "OD'" O 0 1 N N N -2.288 10.811 3.779 -4.002 -1.978 -0.120 "OD'" 3ME 22 3ME "CE'" "CE'" C 0 1 N N N -2.425 11.690 2.662 -5.257 -2.511 0.309 "CE'" 3ME 23 3ME "CF'" "CF'" C 0 1 N N N -3.723 11.360 1.904 -6.126 -1.382 0.868 "CF'" 3ME 24 3ME "NG'" "NG'" N 0 1 N N N -3.897 9.946 1.555 -6.452 -0.436 -0.207 "NG'" 3ME 25 3ME "CI'" "CI'" C 0 1 N N N -2.968 9.492 0.522 -7.308 -1.067 -1.221 "CI'" 3ME 26 3ME "CJ'" "CJ'" C 0 1 N N N -5.254 9.568 1.171 -7.080 0.778 0.331 "CJ'" 3ME 27 3ME "C3'" "C3'" C 0 1 N N R -3.585 8.312 7.617 1.292 -2.054 0.007 "C3'" 3ME 28 3ME "O3'" "O3'" O 0 1 N N N -4.668 8.592 6.780 0.917 -3.136 0.863 "O3'" 3ME 29 3ME HO2 HO2 H 0 1 N N N -5.728 5.783 11.940 5.646 1.577 -1.264 HO2 3ME 30 3ME "H5'1" "H5'1" H 0 0 N N N -5.237 9.529 9.588 3.428 -0.681 -1.115 "H5'1" 3ME 31 3ME "H5'2" "H5'2" H 0 0 N N N -3.856 9.996 10.641 3.976 -2.174 -0.316 "H5'2" 3ME 32 3ME "H4'" "H4'" H 0 1 N N N -3.514 10.365 8.285 2.573 -1.553 1.685 "H4'" 3ME 33 3ME "H1'" "H1'" H 0 1 N N N -0.401 9.020 7.655 0.038 -0.273 1.807 "H1'" 3ME 34 3ME HC6 HC6 H 0 1 N N N -2.361 6.921 9.914 -1.476 1.385 2.150 HC6 3ME 35 3ME HN3 HN3 H 0 1 N N N 1.418 4.922 7.855 -0.245 3.394 -2.013 HN3 3ME 36 3ME H5A1 H5A1 H 0 0 N N N -1.268 3.623 11.314 -2.353 4.343 2.400 H5A1 3ME 37 3ME H5A2 H5A2 H 0 0 N N N -1.725 5.220 11.996 -3.553 4.195 1.093 H5A2 3ME 38 3ME H5A3 H5A3 H 0 0 N N N -2.825 4.386 10.847 -3.366 2.884 2.282 H5A3 3ME 39 3ME "H2'" "H2'" H 0 1 N N N -2.094 7.407 6.205 0.095 -0.705 -1.234 "H2'" 3ME 40 3ME "HB'1" "HB'1" H 0 0 N N N -0.224 9.606 6.009 -2.029 -1.461 -1.774 "HB'1" 3ME 41 3ME "HB'2" "HB'2" H 0 0 N N N -1.012 8.753 4.636 -1.163 -3.004 -1.579 "HB'2" 3ME 42 3ME "HC'1" "HC'1" H 0 0 N N N -1.111 11.778 5.194 -3.573 -3.427 -1.529 "HC'1" 3ME 43 3ME "HC'2" "HC'2" H 0 0 N N N -0.219 10.983 3.884 -2.898 -3.712 0.094 "HC'2" 3ME 44 3ME "HE'1" "HE'1" H 0 0 N N N -2.463 12.730 3.017 -5.764 -2.973 -0.538 "HE'1" 3ME 45 3ME "HE'2" "HE'2" H 0 0 N N N -1.565 11.563 1.988 -5.089 -3.258 1.084 "HE'2" 3ME 46 3ME "HF'1" "HF'1" H 0 0 N N N -4.567 11.651 2.546 -7.046 -1.800 1.276 "HF'1" 3ME 47 3ME "HF'2" "HF'2" H 0 0 N N N -3.718 11.936 0.967 -5.582 -0.862 1.657 "HF'2" 3ME 48 3ME "HI'1" "HI'1" H 0 0 N N N -3.149 8.429 0.307 -8.236 -1.401 -0.756 "HI'1" 3ME 49 3ME "HI'2" "HI'2" H 0 0 N N N -3.121 10.082 -0.393 -7.534 -0.345 -2.006 "HI'2" 3ME 50 3ME "HI'3" "HI'3" H 0 0 N N N -1.935 9.623 0.875 -6.790 -1.922 -1.653 "HI'3" 3ME 51 3ME "HJ'1" "HJ'1" H 0 0 N N N -5.282 8.495 0.929 -6.396 1.263 1.027 "HJ'1" 3ME 52 3ME "HJ'2" "HJ'2" H 0 0 N N N -5.942 9.774 2.005 -7.311 1.461 -0.486 "HJ'2" 3ME 53 3ME "HJ'3" "HJ'3" H 0 0 N N N -5.561 10.150 0.290 -7.999 0.510 0.852 "HJ'3" 3ME 54 3ME "H3'" "H3'" H 0 1 N N N -3.876 7.350 8.065 1.663 -2.432 -0.946 "H3'" 3ME 55 3ME "HO3'" "HO3'" H 0 0 N Y N -4.768 7.892 6.145 1.644 -3.733 1.084 "HO3'" 3ME 56 3ME OXT OXT O 0 1 N Y N ? ? ? 7.032 0.569 1.029 OXT 3ME 57 3ME HXT H1 H 0 1 N Y N ? ? ? 7.939 0.738 0.737 H1 3ME 58 # 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 3ME P OP1 DOUB N N 1 3ME P OP2 SING N N 2 3ME P "O5'" SING N N 3 3ME OP2 HO2 SING N N 4 3ME "O5'" "C5'" SING N N 5 3ME "C5'" "C4'" SING N N 6 3ME "C5'" "H5'1" SING N N 7 3ME "C5'" "H5'2" SING N N 8 3ME "C4'" "O4'" SING N N 9 3ME "C4'" "C3'" SING N N 10 3ME "C4'" "H4'" SING N N 11 3ME "O4'" "C1'" SING N N 12 3ME "C1'" N1 SING N N 13 3ME "C1'" "C2'" SING N N 14 3ME "C1'" "H1'" SING N N 15 3ME N1 C6 SING N N 16 3ME N1 C2 SING N N 17 3ME C6 C5 DOUB N N 18 3ME C6 HC6 SING N N 19 3ME C2 O2 DOUB N N 20 3ME C2 N3 SING N N 21 3ME N3 C4 SING N N 22 3ME N3 HN3 SING N N 23 3ME C4 O4 DOUB N N 24 3ME C4 C5 SING N N 25 3ME C5 C5A SING N N 26 3ME C5A H5A1 SING N N 27 3ME C5A H5A2 SING N N 28 3ME C5A H5A3 SING N N 29 3ME "C2'" "O2'" SING N N 30 3ME "C2'" "C3'" SING N N 31 3ME "C2'" "H2'" SING N N 32 3ME "O2'" "CB'" SING N N 33 3ME "CB'" "CC'" SING N N 34 3ME "CB'" "HB'1" SING N N 35 3ME "CB'" "HB'2" SING N N 36 3ME "CC'" "OD'" SING N N 37 3ME "CC'" "HC'1" SING N N 38 3ME "CC'" "HC'2" SING N N 39 3ME "OD'" "CE'" SING N N 40 3ME "CE'" "CF'" SING N N 41 3ME "CE'" "HE'1" SING N N 42 3ME "CE'" "HE'2" SING N N 43 3ME "CF'" "NG'" SING N N 44 3ME "CF'" "HF'1" SING N N 45 3ME "CF'" "HF'2" SING N N 46 3ME "NG'" "CI'" SING N N 47 3ME "NG'" "CJ'" SING N N 48 3ME "CI'" "HI'1" SING N N 49 3ME "CI'" "HI'2" SING N N 50 3ME "CI'" "HI'3" SING N N 51 3ME "CJ'" "HJ'1" SING N N 52 3ME "CJ'" "HJ'2" SING N N 53 3ME "CJ'" "HJ'3" SING N N 54 3ME "C3'" "O3'" SING N N 55 3ME "C3'" "H3'" SING N N 56 3ME "O3'" "HO3'" SING N N 57 3ME P OXT SING N N 58 3ME OXT HXT SING N N 59 # 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 3ME SMILES ACDLabs 12.01 "O=P(O)(O)OCC2OC(N1C(=O)NC(=O)C(=C1)C)C(OCCOCCN(C)C)C2O" 3ME InChI InChI 1.03 "InChI=1S/C16H28N3O10P/c1-10-8-19(16(22)17-14(10)21)15-13(27-7-6-26-5-4-18(2)3)12(20)11(29-15)9-28-30(23,24)25/h8,11-13,15,20H,4-7,9H2,1-3H3,(H,17,21,22)(H2,23,24,25)/t11-,12-,13-,15-/m1/s1" 3ME InChIKey InChI 1.03 ZEPAZACIEWQAFL-RGCMKSIDSA-N 3ME SMILES_CANONICAL CACTVS 3.370 "CN(C)CCOCCO[C@@H]1[C@H](O)[C@@H](CO[P](O)(O)=O)O[C@H]1N2C=C(C)C(=O)NC2=O" 3ME SMILES CACTVS 3.370 "CN(C)CCOCCO[CH]1[CH](O)[CH](CO[P](O)(O)=O)O[CH]1N2C=C(C)C(=O)NC2=O" 3ME SMILES_CANONICAL "OpenEye OEToolkits" 1.7.2 "CC1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)OCCOCCN(C)C" 3ME SMILES "OpenEye OEToolkits" 1.7.2 "CC1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)OCCOCCN(C)C" # 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 3ME "SYSTEMATIC NAME" ACDLabs 12.01 ;2'-O-{2-[2-(dimethylamino)ethoxy]ethyl}-5-methyluridine 5'-(dihydrogen phosphate) ; 3ME "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.2 "[(2R,3R,4R,5R)-4-[2-(2-dimethylaminoethyloxy)ethoxy]-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-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 3ME "Create component" 2003-03-04 RCSB 3ME "Modify linking type" 2011-06-04 RCSB 3ME "Modify descriptor" 2011-06-04 RCSB 3ME "Other modification" 2011-10-27 RCSB #