data_BOE # _chem_comp.id BOE _chem_comp.name ;2'-O-[2-(BENZYLOXY)ETHYL] THYMIDINE-5'-MONOPHOSPHATE ; _chem_comp.type "RNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C19 H25 N2 O10 P" _chem_comp.mon_nstd_parent_comp_id DT _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2004-12-21 _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 472.383 _chem_comp.one_letter_code T _chem_comp.three_letter_code BOE _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 1YBC _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 BOE P P P 0 1 N N N -4.500 5.987 7.477 2.787 0.324 -4.407 P BOE 1 BOE OP1 O1P O 0 1 N N N -5.715 6.689 6.969 3.659 1.172 -5.286 OP1 BOE 2 BOE OP2 O2P O 0 1 N N N -4.660 4.712 8.206 1.198 0.588 -4.548 OP2 BOE 3 BOE "O5'" O5* O 0 1 N N N -3.573 5.777 6.211 3.063 0.476 -2.819 "O5'" BOE 4 BOE "C5'" C5* C 0 1 N N N -3.357 6.864 5.306 2.282 -0.292 -1.921 "C5'" BOE 5 BOE "C4'" C4* C 0 1 N N R -2.328 6.487 4.282 2.725 0.023 -0.498 "C4'" BOE 6 BOE "O4'" O4* O 0 1 N N N -1.039 6.300 4.928 2.470 1.422 -0.246 "O4'" BOE 7 BOE "C1'" C1* C 0 1 N N R -0.318 5.272 4.258 1.373 1.543 0.675 "C1'" BOE 8 BOE N1 N1 N 0 1 N N N -0.061 4.162 5.217 0.452 2.524 0.177 N1 BOE 9 BOE C6 C6 C 0 1 N N N -0.850 3.927 6.327 0.309 2.663 -1.199 C6 BOE 10 BOE C2 C2 C 0 1 N N N 1.021 3.366 4.929 -0.300 3.336 1.055 C2 BOE 11 BOE O2 O2 O 0 1 N N N 1.733 3.570 3.961 -0.225 3.269 2.283 O2 BOE 12 BOE N3 N3 N 0 1 N N N 1.234 2.326 5.808 -1.159 4.248 0.431 N3 BOE 13 BOE C4 C4 C 0 1 N N N 0.473 2.017 6.921 -1.338 4.427 -0.932 C4 BOE 14 BOE O4 O4 O 0 1 N N N 0.748 1.038 7.606 -2.112 5.251 -1.413 O4 BOE 15 BOE C5 C5 C 0 1 N N N -0.643 2.906 7.176 -0.514 3.537 -1.792 C5 BOE 16 BOE C5M C5M C 0 1 N N N -1.512 2.626 8.357 -0.651 3.669 -3.275 C5M BOE 17 BOE "C2'" C2* C 0 1 N N R -1.171 4.813 3.073 0.748 0.163 0.786 "C2'" BOE 18 BOE "O2'" O2* O 0 1 N N N -0.948 5.711 1.973 0.137 -0.058 2.041 "O2'" BOE 19 BOE "CB'" "CB'" C 0 1 N N N 0.361 5.685 1.432 -0.332 -1.396 2.174 "CB'" BOE 20 BOE "CC'" "CC'" C 0 1 N N N 0.346 6.681 0.289 -0.951 -1.569 3.547 "CC'" BOE 21 BOE "OD'" "OD'" O 0 1 N N N -0.793 6.285 -0.457 0.039 -1.320 4.537 "OD'" BOE 22 BOE "CE'" "CE'" C 0 1 N N N -0.877 6.743 -1.793 -0.494 -1.447 5.849 "CE'" BOE 23 BOE "CF'" "CF'" C 0 1 Y N N -2.013 5.991 -2.454 0.593 -1.175 6.847 "CF'" BOE 24 BOE "CG'" "CG'" C 0 1 Y N N -3.338 6.303 -2.174 1.381 -2.222 7.309 "CG'" BOE 25 BOE "CH'" "CH'" C 0 1 Y N N -4.362 5.584 -2.793 2.391 -1.969 8.237 "CH'" BOE 26 BOE "CI'" "CI'" C 0 1 Y N N -4.087 4.557 -3.689 2.606 -0.670 8.697 "CI'" BOE 27 BOE "CJ'" "CJ'" C 0 1 Y N N -2.759 4.250 -3.968 1.811 0.376 8.228 "CJ'" BOE 28 BOE "CK'" "CK'" C 0 1 Y N N -1.732 4.965 -3.352 0.801 0.123 7.300 "CK'" BOE 29 BOE "C3'" C3* C 0 1 N N R -2.563 5.165 3.567 1.940 -0.742 0.560 "C3'" BOE 30 BOE "O3'" O3* O 0 1 N N N -3.500 5.245 2.514 2.742 -0.809 1.739 "O3'" BOE 31 BOE OP3 O3P O 0 1 N Y N ? ? ? 2.921 -1.270 -4.647 OP3 BOE 32 BOE HOP2 2HOP H 0 0 N N N -3.887 4.265 8.529 0.799 0.616 -5.443 HOP2 BOE 33 BOE "H5'" 1H5* H 0 1 N N N -3.088 7.805 5.841 1.229 -0.035 -2.051 "H5'" BOE 34 BOE "H5''" 2H5* H 0 0 N N N -4.307 7.209 4.835 2.428 -1.352 -2.133 "H5''" BOE 35 BOE "H4'" H4* H 0 1 N N N -2.380 7.323 3.546 3.804 -0.139 -0.410 "H4'" BOE 36 BOE "H1'" H1* H 0 1 N N N 0.669 5.629 3.881 1.754 1.910 1.633 "H1'" BOE 37 BOE H6 H6 H 0 1 N N N -1.698 4.596 6.549 0.928 1.995 -1.790 H6 BOE 38 BOE HN3 HN3 H 0 1 N N N 2.035 1.725 5.616 -1.709 4.843 1.045 HN3 BOE 39 BOE H71 1H5M H 0 1 N N N -2.559 2.537 7.983 -1.057 2.748 -3.690 H71 BOE 40 BOE H72 2H5M H 0 1 N N N -1.340 1.779 9.061 0.324 3.866 -3.719 H72 BOE 41 BOE H73 3H5M H 0 1 N N N -1.552 3.559 8.966 -1.320 4.497 -3.510 H73 BOE 42 BOE "H2'" H2* H 0 1 N N N -0.984 3.757 2.768 -0.000 0.004 -0.000 "H2'" BOE 43 BOE "HB'1" "1HB'" H 0 0 N N N 0.703 4.666 1.135 -1.066 -1.580 1.383 "HB'1" BOE 44 BOE "HB'2" "2HB'" H 0 0 N N N 1.161 5.878 2.184 0.520 -2.071 2.050 "HB'2" BOE 45 BOE "HC'1" "1HC'" H 0 0 N N N 1.293 6.733 -0.297 -1.324 -2.588 3.686 "HC'1" BOE 46 BOE "HC'2" "2HC'" H 0 0 N N N 0.350 7.751 0.602 -1.768 -0.855 3.691 "HC'2" BOE 47 BOE "HE'1" "1HE'" H 0 0 N N N 0.087 6.653 -2.347 -0.897 -2.458 5.974 "HE'1" BOE 48 BOE "HE'2" "2HE'" H 0 0 N N N -0.984 7.850 -1.869 -1.320 -0.738 5.971 "HE'2" BOE 49 BOE "HG'" "HG'" H 0 1 N N N -3.575 7.115 -1.466 1.221 -3.238 6.957 "HG'" BOE 50 BOE "HH'" "HH'" H 0 1 N N N -5.413 5.833 -2.569 3.011 -2.783 8.602 "HH'" BOE 51 BOE "HI'" "HI'" H 0 1 N N N -4.907 3.997 -4.169 3.393 -0.473 9.419 "HI'" BOE 52 BOE "HJ'" "HJ'" H 0 1 N N N -2.520 3.440 -4.677 1.979 1.388 8.586 "HJ'" BOE 53 BOE "HK'" "HK'" H 0 1 N N N -0.682 4.715 -3.578 0.187 0.944 6.941 "HK'" BOE 54 BOE "H3'" H3* H 0 1 N N N -3.015 4.395 4.234 1.675 -1.764 0.277 "H3'" BOE 55 BOE "HO3'" H3T H 0 0 N Y N -3.647 4.419 2.068 3.447 -0.153 1.628 "HO3'" BOE 56 BOE HOP3 3HOP H 0 0 N N N 0.773 -0.447 0.323 2.886 -1.617 -5.563 HOP3 BOE 57 # 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 BOE P OP1 DOUB N N 1 BOE P OP2 SING N N 2 BOE P "O5'" SING N N 3 BOE P OP3 SING N N 4 BOE OP2 HOP2 SING N N 5 BOE "O5'" "C5'" SING N N 6 BOE "C5'" "C4'" SING N N 7 BOE "C5'" "H5'" SING N N 8 BOE "C5'" "H5''" SING N N 9 BOE "C4'" "O4'" SING N N 10 BOE "C4'" "C3'" SING N N 11 BOE "C4'" "H4'" SING N N 12 BOE "O4'" "C1'" SING N N 13 BOE "C1'" N1 SING N N 14 BOE "C1'" "C2'" SING N N 15 BOE "C1'" "H1'" SING N N 16 BOE N1 C6 SING N N 17 BOE N1 C2 SING N N 18 BOE C6 C5 DOUB N N 19 BOE C6 H6 SING N N 20 BOE C2 O2 DOUB N N 21 BOE C2 N3 SING N N 22 BOE N3 C4 SING N N 23 BOE N3 HN3 SING N N 24 BOE C4 O4 DOUB N N 25 BOE C4 C5 SING N N 26 BOE C5 C5M SING N N 27 BOE C5M H71 SING N N 28 BOE C5M H72 SING N N 29 BOE C5M H73 SING N N 30 BOE "C2'" "O2'" SING N N 31 BOE "C2'" "C3'" SING N N 32 BOE "C2'" "H2'" SING N N 33 BOE "O2'" "CB'" SING N N 34 BOE "CB'" "CC'" SING N N 35 BOE "CB'" "HB'1" SING N N 36 BOE "CB'" "HB'2" SING N N 37 BOE "CC'" "OD'" SING N N 38 BOE "CC'" "HC'1" SING N N 39 BOE "CC'" "HC'2" SING N N 40 BOE "OD'" "CE'" SING N N 41 BOE "CE'" "CF'" SING N N 42 BOE "CE'" "HE'1" SING N N 43 BOE "CE'" "HE'2" SING N N 44 BOE "CF'" "CG'" DOUB Y N 45 BOE "CF'" "CK'" SING Y N 46 BOE "CG'" "CH'" SING Y N 47 BOE "CG'" "HG'" SING N N 48 BOE "CH'" "CI'" DOUB Y N 49 BOE "CH'" "HH'" SING N N 50 BOE "CI'" "CJ'" SING Y N 51 BOE "CI'" "HI'" SING N N 52 BOE "CJ'" "CK'" DOUB Y N 53 BOE "CJ'" "HJ'" SING N N 54 BOE "CK'" "HK'" SING N N 55 BOE "C3'" "O3'" SING N N 56 BOE "C3'" "H3'" SING N N 57 BOE "O3'" "HO3'" SING N N 58 BOE OP3 HOP3 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 BOE SMILES ACDLabs 10.04 "O=C1NC(=O)N(C=C1C)C3OC(C(O)C3OCCOCc2ccccc2)COP(=O)(O)O" BOE SMILES_CANONICAL CACTVS 3.341 "CC1=CN([C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2OCCOCc3ccccc3)C(=O)NC1=O" BOE SMILES CACTVS 3.341 "CC1=CN([CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2OCCOCc3ccccc3)C(=O)NC1=O" BOE 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)O)OCCOCc3ccccc3" BOE SMILES "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)OCCOCc3ccccc3" BOE InChI InChI 1.03 "InChI=1S/C19H25N2O10P/c1-12-9-21(19(24)20-17(12)23)18-16(15(22)14(31-18)11-30-32(25,26)27)29-8-7-28-10-13-5-3-2-4-6-13/h2-6,9,14-16,18,22H,7-8,10-11H2,1H3,(H,20,23,24)(H2,25,26,27)/t14-,15-,16-,18-/m1/s1" BOE InChIKey InChI 1.03 LZEOXHFYJVFRES-YFHUEUNASA-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 BOE "SYSTEMATIC NAME" ACDLabs 10.04 ;2'-O-[2-(benzyloxy)ethyl]-5-methyluridine 5'-(dihydrogen phosphate) ; BOE "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3R,4R,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)-4-(2-phenylmethoxyethoxy)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 BOE "Create component" 2004-12-21 RCSB BOE "Modify linking type" 2011-06-04 RCSB BOE "Modify descriptor" 2011-06-04 RCSB #