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 
# 
