data_5SE
# 
_chem_comp.id                                    5SE 
_chem_comp.name                                  
;2'-deoxy-5-(methylselanyl)cytidine 5'-(dihydrogen phosphate)
;
_chem_comp.type                                  "DNA LINKING" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C10 H16 N3 O7 P Se" 
_chem_comp.mon_nstd_parent_comp_id               DU 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2009-08-07 
_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                        400.184 
_chem_comp.one_letter_code                       U 
_chem_comp.three_letter_code                     5SE 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   N 
_chem_comp.pdbx_ideal_coordinates_details        Corina 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        3IJN 
_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 
5SE P      P    P  0 1 N N N 12.611 26.315 -1.037 5.320  -1.337 -0.051 P    5SE 1  
5SE N1     N1   N  0 1 N N N 9.764  26.760 3.384  -1.062 0.712  -0.050 N1   5SE 2  
5SE C2     C2   C  0 1 N N N 8.708  27.066 4.229  -0.928 0.617  1.286  C2   5SE 3  
5SE O2     O2   O  0 1 N N N 8.535  26.355 5.208  0.137  0.910  1.804  O2   5SE 4  
5SE N3     N3   N  0 1 N N N 7.880  28.103 3.983  -1.938 0.208  2.051  N3   5SE 5  
5SE C4     C4   C  0 1 N N N 8.097  28.828 2.921  -3.107 -0.117 1.513  C4   5SE 6  
5SE N4     N4   N  0 1 N N N 7.259  29.832 2.723  -4.143 -0.537 2.314  N4   5SE 7  
5SE C5     C5   C  0 1 N N N 9.188  28.535 2.056  -3.280 -0.028 0.117  C5   5SE 8  
5SE C6     C6   C  0 1 N N N 10.000 27.508 2.299  -2.245 0.395  -0.647 C6   5SE 9  
5SE "C1'"  C1*  C  0 1 N N R 10.641 25.694 3.754  0.068  1.165  -0.865 C1*  5SE 10 
5SE OP3    OP3  O  0 1 N Y N 13.343 25.208 -1.665 4.940  -2.017 1.359  OP3  5SE 11 
5SE "C2'"  C2*  C  0 1 N N N 10.150 24.292 3.532  0.413  2.626  -0.517 C2*  5SE 12 
5SE OP2    OP2  O  0 1 N N N 11.496 26.977 -1.691 5.687  -2.484 -1.118 OP2  5SE 13 
5SE "C3'"  C3*  C  0 1 N N S 10.738 24.156 2.156  1.890  2.568  -0.058 C3*  5SE 14 
5SE "O3'"  O3*  O  0 1 N N N 10.683 22.800 1.748  2.628  3.679  -0.571 O3*  5SE 15 
5SE "C4'"  C4*  C  0 1 N N R 12.150 24.651 2.366  2.376  1.241  -0.695 C4*  5SE 16 
5SE "O4'"  O4*  O  0 1 N N N 11.807 25.902 2.987  1.229  0.368  -0.578 O4*  5SE 17 
5SE "C5'"  C5*  C  0 1 N N N 12.962 24.929 1.113  3.566  0.674  0.083  C5*  5SE 18 
5SE "O5'"  O5*  O  0 1 N N N 12.157 25.777 0.370  4.066  -0.483 -0.590 O5*  5SE 19 
5SE CA5    CA5  C  0 1 N N N 8.095  29.110 -0.855 -4.784 -2.439 -0.920 CA5  5SE 20 
5SE SE5    SE5  SE 0 0 N N N 9.463  29.597 0.481  -4.995 -0.502 -0.705 SE5  5SE 21 
5SE HN4    HN4  H  0 1 N N N 6.514  29.997 3.370  -3.997 -0.678 3.262  HN4  5SE 22 
5SE HN4A   HN4A H  0 0 N N N 7.370  30.427 1.927  -5.021 -0.692 1.930  HN4A 5SE 23 
5SE H6     H6   H  0 1 N N N 10.826 27.285 1.639  -2.353 0.471  -1.719 H6   5SE 24 
5SE "H1'"  H1*  H  0 1 N N N 10.772 25.740 4.845  -0.184 1.086  -1.923 H1*  5SE 25 
5SE HOP3   HOP3 H  0 0 N Y N 13.862 25.541 -2.388 4.184  -2.618 1.314  HOP3 5SE 26 
5SE "H2'"  H2*  H  0 1 N N N 10.521 23.557 4.262  0.311  3.262  -1.396 H2*  5SE 27 
5SE "H2'A" H2*A H  0 0 N N N 9.057  24.179 3.574  -0.226 2.987  0.289  H2*A 5SE 28 
5SE HOP2   HOP2 H  0 0 N N N 11.825 27.559 -2.366 6.436  -3.039 -0.858 HOP2 5SE 29 
5SE "H3'"  H3*  H  0 1 N N N 10.217 24.713 1.363  1.958  2.526  1.029  H3*  5SE 30 
5SE "HO3'" HO3* H  0 0 N N N 11.055 22.715 0.878  2.302  4.539  -0.271 HO3* 5SE 31 
5SE "H4'"  H4*  H  0 1 N N N 12.787 23.928 2.897  2.636  1.390  -1.742 H4*  5SE 32 
5SE "H5'"  H5*  H  0 1 N N N 13.924 25.403 1.357  4.351  1.427  0.144  H5*  5SE 33 
5SE "H5'A" H5*A H  0 0 N N N 13.179 24.001 0.564  3.246  0.400  1.088  H5*A 5SE 34 
5SE HA5    HA5  H  0 1 N N N 8.240  29.711 -1.765 -3.875 -2.645 -1.485 HA5  5SE 35 
5SE HA5A   HA5A H  0 0 N N N 8.188  28.042 -1.103 -4.716 -2.908 0.061  HA5A 5SE 36 
5SE HA5B   HA5B H  0 0 N N N 7.094  29.305 -0.442 -5.644 -2.841 -1.456 HA5B 5SE 37 
5SE OP1    OP1  O  0 1 N N N 13.363 27.318 -2.215 6.485  -0.442 0.132  OP1  5SE 38 
# 
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 
5SE P     "O5'"  SING N N 1  
5SE N1    "C1'"  SING N N 2  
5SE N1    C2     SING N N 3  
5SE C2    O2     DOUB N N 4  
5SE N3    C2     SING N N 5  
5SE C4    N3     DOUB N N 6  
5SE N4    C4     SING N N 7  
5SE N4    HN4    SING N N 8  
5SE N4    HN4A   SING N N 9  
5SE C5    C4     SING N N 10 
5SE C5    C6     DOUB N N 11 
5SE C6    N1     SING N N 12 
5SE C6    H6     SING N N 13 
5SE "C1'" "H1'"  SING N N 14 
5SE OP3   P      SING N N 15 
5SE OP3   HOP3   SING N N 16 
5SE "C2'" "C1'"  SING N N 17 
5SE "C2'" "H2'"  SING N N 18 
5SE "C2'" "H2'A" SING N N 19 
5SE OP2   P      SING N N 20 
5SE OP2   HOP2   SING N N 21 
5SE "C3'" "C2'"  SING N N 22 
5SE "C3'" "C4'"  SING N N 23 
5SE "C3'" "H3'"  SING N N 24 
5SE "O3'" "C3'"  SING N N 25 
5SE "O3'" "HO3'" SING N N 26 
5SE "C4'" "O4'"  SING N N 27 
5SE "C4'" "H4'"  SING N N 28 
5SE "O4'" "C1'"  SING N N 29 
5SE "C5'" "C4'"  SING N N 30 
5SE "C5'" "H5'"  SING N N 31 
5SE "C5'" "H5'A" SING N N 32 
5SE "O5'" "C5'"  SING N N 33 
5SE CA5   SE5    SING N N 34 
5SE CA5   HA5    SING N N 35 
5SE CA5   HA5A   SING N N 36 
5SE CA5   HA5B   SING N N 37 
5SE SE5   C5     SING N N 38 
5SE P     OP1    DOUB N N 39 
# 
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 
5SE SMILES           ACDLabs              11.02 "O=P(O)(O)OCC2OC(N1C(=O)N=C(N)C([Se]C)=C1)CC2O"                                                                                                          
5SE SMILES_CANONICAL CACTVS               3.352 "C[Se]C1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)C(=O)N=C1N"                                                                                           
5SE SMILES           CACTVS               3.352 "C[Se]C1=CN([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)C(=O)N=C1N"                                                                                               
5SE SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "C[Se]C1=CN(C(=O)N=C1N)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O"                                                                                             
5SE SMILES           "OpenEye OEToolkits" 1.7.0 "C[Se]C1=CN(C(=O)N=C1N)C2CC(C(O2)COP(=O)(O)O)O"                                                                                                          
5SE InChI            InChI                1.03  "InChI=1S/C10H16N3O7PSe/c1-22-7-3-13(10(15)12-9(7)11)8-2-5(14)6(20-8)4-19-21(16,17)18/h3,5-6,8,14H,2,4H2,1H3,(H2,11,12,15)(H2,16,17,18)/t5-,6+,8+/m0/s1" 
5SE InChIKey         InChI                1.03  NLUQHLNACKOXLS-SHYZEUOFSA-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 
5SE "SYSTEMATIC NAME" ACDLabs              11.02 
;2'-deoxy-5-(methylselanyl)cytidine 5'-(dihydrogen phosphate)
;
5SE "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.6.1 "[(2R,3S,5R)-5-(4-azanyl-5-methylselanyl-2-oxo-pyrimidin-1-yl)-3-hydroxy-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 
5SE "Create component"  2009-08-07 RCSB 
5SE "Modify descriptor" 2011-06-04 RCSB 
# 
