data_75B # _chem_comp.id 75B _chem_comp.name ;5-selenophen-2-yluridine 5'-(dihydrogen phosphate) ; _chem_comp.type "RNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C13 H15 N2 O9 P Se" _chem_comp.mon_nstd_parent_comp_id U _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2016-08-26 _chem_comp.pdbx_modified_date 2017-06-30 _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 453.200 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 75B _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 5T3K _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 75B P P1 P 0 1 N N N 22.127 38.797 29.248 5.857 -1.107 -0.884 P 75B 1 75B "C5'" C1 C 0 1 N N N 20.548 37.985 31.170 4.156 0.696 0.115 "C5'" 75B 2 75B "O5'" O1 O 0 1 N N N 21.862 38.235 30.708 4.529 -0.198 -0.936 "O5'" 75B 3 75B "C4'" C2 C 0 1 N N R 20.542 37.669 32.646 2.849 1.400 -0.255 "C4'" 75B 4 75B "O4'" O2 O 0 1 N N N 21.384 36.515 32.919 1.774 0.447 -0.297 "O4'" 75B 5 75B "C3'" C3 C 0 1 N N S 21.092 38.731 33.571 2.493 2.444 0.821 "C3'" 75B 6 75B "O3'" O3 O 0 1 N N N 20.180 39.789 33.793 2.427 3.751 0.248 "O3'" 75B 7 75B "C2'" C4 C 0 1 N N R 21.408 37.926 34.830 1.099 2.004 1.330 "C2'" 75B 8 75B "O2'" O4 O 0 1 N N N 20.205 37.688 35.536 0.250 3.136 1.532 "O2'" 75B 9 75B "C1'" C5 C 0 1 N N R 21.881 36.590 34.236 0.586 1.130 0.158 "C1'" 75B 10 75B N1 N1 N 0 1 N N N 23.361 36.455 34.198 -0.413 0.168 0.630 N1 75B 11 75B C2 C6 C 0 1 N N N 24.029 36.106 35.293 -0.066 -0.736 1.561 C2 75B 12 75B O2 O5 O 0 1 N N N 23.466 35.901 36.298 1.072 -0.734 1.989 O2 75B 13 75B N3 N2 N 0 1 N N N 25.333 35.971 35.319 -0.939 -1.642 2.032 N3 75B 14 75B C4 C7 C 0 1 N N N 26.061 36.188 34.247 -2.209 -1.669 1.575 C4 75B 15 75B O4 O6 O 0 1 N N N 27.237 36.056 34.313 -3.005 -2.487 1.998 O4 75B 16 75B C5 C8 C 0 1 N N N 25.394 36.558 33.078 -2.611 -0.687 0.555 C5 75B 17 75B C6 C9 C 0 1 N N N 24.008 36.690 33.080 -1.677 0.214 0.120 C6 75B 18 75B C22 C10 C 0 1 Y N N 28.036 37.382 29.803 -6.546 -0.356 -1.199 C22 75B 19 75B C33 C11 C 0 1 Y N N 26.657 37.573 29.480 -6.311 -1.306 -0.286 C33 75B 20 75B C44 C12 C 0 1 Y N N 25.669 37.328 30.552 -5.030 -1.470 0.334 C44 75B 21 75B C55 C13 C 0 1 Y N N 26.188 36.862 31.798 -3.984 -0.667 0.026 C55 75B 22 75B OP1 O7 O 0 1 N N N 21.040 39.822 29.091 6.029 -1.886 -2.283 OP1 75B 23 75B OP2 O8 O 0 1 N N N 23.586 39.180 29.161 7.036 -0.244 -0.651 OP2 75B 24 75B SE1 SE1 SE 0 0 Y N N 28.047 36.834 31.590 -4.785 0.543 -1.324 SE1 75B 25 75B H1 H1 H 0 1 N N N 19.929 38.876 30.991 4.016 0.133 1.038 H1 75B 26 75B H2 H2 H 0 1 N N N 20.130 37.131 30.618 4.941 1.438 0.257 H2 75B 27 75B H3 H3 H 0 1 N N N 19.509 37.443 32.950 2.951 1.886 -1.226 H3 75B 28 75B H4 H4 H 0 1 N N N 22.033 39.118 33.152 3.223 2.420 1.631 H4 75B 29 75B H5 H5 H 0 1 N N N 20.571 40.427 34.378 2.207 4.448 0.881 H5 75B 30 75B H6 H6 H 0 1 N N N 22.191 38.403 35.437 1.186 1.418 2.245 H6 75B 31 75B H7 H7 H 0 1 N N N 20.392 37.187 36.321 0.577 3.760 2.194 H7 75B 32 75B H8 H8 H 0 1 N N N 21.463 35.774 34.844 0.175 1.754 -0.635 H8 75B 33 75B H9 H9 H 0 1 N N N 25.781 35.698 36.170 -0.656 -2.281 2.705 H9 75B 34 75B H10 H10 H 0 1 N N N 23.478 36.979 32.184 -1.936 0.949 -0.628 H10 75B 35 75B H11 H11 H 0 1 N N N 28.888 37.524 29.155 -7.459 -0.139 -1.734 H11 75B 36 75B H12 H12 H 0 1 N N N 26.349 37.884 28.493 -7.115 -1.972 -0.007 H12 75B 37 75B H13 H13 H 0 1 N N N 24.612 37.492 30.401 -4.895 -2.253 1.066 H13 75B 38 75B H14 H14 H 0 1 N N N 21.429 40.676 28.941 6.810 -2.454 -2.322 H14 75B 39 75B OP3 O9 O 0 1 N Y N ? ? ? 5.728 -2.176 0.313 O1 75B 40 75B HOP3 H15 H 0 0 N Y N ? ? ? 4.975 -2.776 0.226 H15 75B 41 # 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 75B OP1 P SING N N 1 75B OP2 P DOUB N N 2 75B P "O5'" SING N N 3 75B C33 C22 DOUB Y N 4 75B C33 C44 SING Y N 5 75B C22 SE1 SING Y N 6 75B C44 C55 DOUB Y N 7 75B "O5'" "C5'" SING N N 8 75B "C5'" "C4'" SING N N 9 75B SE1 C55 SING Y N 10 75B C55 C5 SING N N 11 75B "C4'" "O4'" SING N N 12 75B "C4'" "C3'" SING N N 13 75B "O4'" "C1'" SING N N 14 75B C5 C6 DOUB N N 15 75B C5 C4 SING N N 16 75B C6 N1 SING N N 17 75B "C3'" "O3'" SING N N 18 75B "C3'" "C2'" SING N N 19 75B N1 "C1'" SING N N 20 75B N1 C2 SING N N 21 75B "C1'" "C2'" SING N N 22 75B C4 O4 DOUB N N 23 75B C4 N3 SING N N 24 75B "C2'" "O2'" SING N N 25 75B C2 N3 SING N N 26 75B C2 O2 DOUB N N 27 75B "C5'" H1 SING N N 28 75B "C5'" H2 SING N N 29 75B "C4'" H3 SING N N 30 75B "C3'" H4 SING N N 31 75B "O3'" H5 SING N N 32 75B "C2'" H6 SING N N 33 75B "O2'" H7 SING N N 34 75B "C1'" H8 SING N N 35 75B N3 H9 SING N N 36 75B C6 H10 SING N N 37 75B C22 H11 SING N N 38 75B C33 H12 SING N N 39 75B C44 H13 SING N N 40 75B OP1 H14 SING N N 41 75B P OP3 SING N N 42 75B OP3 HOP3 SING N N 43 # 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 75B SMILES ACDLabs 12.01 "P(OCC1OC(C(C1O)O)N2C(NC(=O)C(=C2)c3ccc[se]3)=O)(O)(O)=O" 75B InChI InChI 1.03 "InChI=1S/C13H15N2O9PSe/c16-9-7(5-23-25(20,21)22)24-12(10(9)17)15-4-6(8-2-1-3-26-8)11(18)14-13(15)19/h1-4,7,9-10,12,16-17H,5H2,(H,14,18,19)(H2,20,21,22)/t7-,9-,10-,12-/m1/s1" 75B InChIKey InChI 1.03 XPHVOCQWRLMUPG-UGKPPGOTSA-N 75B SMILES_CANONICAL CACTVS 3.385 "O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=C(C(=O)NC2=O)c3[se]ccc3" 75B SMILES CACTVS 3.385 "O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)N2C=C(C(=O)NC2=O)c3[se]ccc3" 75B SMILES_CANONICAL "OpenEye OEToolkits" 2.0.5 "c1cc([se]c1)C2=CN(C(=O)NC2=O)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O" 75B SMILES "OpenEye OEToolkits" 2.0.5 "c1cc([se]c1)C2=CN(C(=O)NC2=O)C3C(C(C(O3)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 75B "SYSTEMATIC NAME" ACDLabs 12.01 ;5-selenophen-2-yluridine 5'-(dihydrogen phosphate) ; 75B "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.5 "[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)-5-selenophen-2-yl-pyrimidin-1-yl]-3,4-bis(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 75B "Create component" 2016-08-26 RCSB 75B "Modify parent residue" 2016-11-01 RCSB 75B "Initial release" 2017-07-05 RCSB #