data_US3
# 
_chem_comp.id                                    US3 
_chem_comp.name                                  "1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-5-methyl-2-selanylpyrimidin-4(1H)-one" 
_chem_comp.type                                  "DNA LINKING" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C10 H15 N2 O7 P Se" 
_chem_comp.mon_nstd_parent_comp_id               DT 
_chem_comp.pdbx_synonyms                         "2-Se-Thymidine-5'-phosphate" 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2009-06-15 
_chem_comp.pdbx_modified_date                    2021-03-01 
_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                        385.169 
_chem_comp.one_letter_code                       T 
_chem_comp.three_letter_code                     US3 
_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        3HGD 
_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 
US3 P      P      P  0 1 N N N -9.241  9.704  8.212 -4.390 1.051  -0.368 P      US3 1  
US3 N1     N1     N  0 1 N N N -12.913 11.821 4.626 2.187  -0.310 -0.734 N1     US3 2  
US3 C2     C2     C  0 1 N N N -13.627 12.622 3.666 2.282  0.282  0.471  C2     US3 3  
US3 SE2    SE2    SE 0 0 N N N -14.700 12.254 2.742 0.835  0.042  1.771  SE2    US3 4  
US3 N3     N3     N  0 1 N N N -12.953 13.831 3.819 3.316  1.011  0.793  N3     US3 5  
US3 C4     C4     C  0 1 N N N -11.910 14.290 4.665 4.325  1.196  -0.076 C4     US3 6  
US3 O4     O4     O  0 1 N N N -11.418 15.480 4.750 5.289  1.879  0.234  O4     US3 7  
US3 C5     C5     C  0 1 N N N -11.272 13.348 5.525 4.259  0.588  -1.354 C5     US3 8  
US3 C6     C6     C  0 1 N N N -11.882 12.121 5.454 3.178  -0.167 -1.657 C6     US3 9  
US3 "C1'"  "C1'"  C  0 1 N N R -13.339 10.442 4.759 1.010  -1.121 -1.053 "C1'"  US3 10 
US3 OP3    OP3    O  0 1 N Y N -8.272  10.798 7.787 -4.757 2.121  -1.513 OP3    US3 11 
US3 "C2'"  "C2'"  C  0 1 N N N -12.641 9.686  3.694 0.903  -2.319 -0.085 "C2'"  US3 12 
US3 OP2    OP2    O  0 1 N N N -8.703  8.310  8.457 -5.628 0.041  -0.160 OP2    US3 13 
US3 "C3'"  "C3'"  C  0 1 N N S -11.559 8.970  4.559 -0.615 -2.470 0.161  "C3'"  US3 14 
US3 "O3'"  "O3'"  O  0 1 N N N -10.990 7.775  4.012 -1.069 -3.749 -0.285 "O3'"  US3 15 
US3 "C4'"  "C4'"  C  0 1 N N R -12.249 8.751  5.885 -1.246 -1.345 -0.689 "C4'"  US3 16 
US3 "O4'"  "O4'"  O  0 1 N N N -12.987 9.939  6.060 -0.199 -0.361 -0.834 "O4'"  US3 17 
US3 "C5'"  "C5'"  C  0 1 N N N -11.302 8.490  7.048 -2.448 -0.739 0.038  "C5'"  US3 18 
US3 "O5'"  "O5'"  O  0 1 N N N -10.394 9.591  7.103 -3.086 0.216  -0.811 "O5'"  US3 19 
US3 C5A    C5A    C  0 1 N N N -10.091 13.696 6.378 5.373  0.774  -2.352 C5A    US3 20 
US3 H6     H6     H  0 1 N N N -11.515 11.340 6.103 3.101  -0.647 -2.622 H6     US3 21 
US3 "H1'"  "H1'"  H  0 1 N N N -14.430 10.343 4.658 1.058  -1.468 -2.086 "H1'"  US3 22 
US3 HOP3   HOP3   H  0 0 N Y N -7.380  10.494 7.905 -5.535 2.660  -1.313 HOP3   US3 23 
US3 "H2'"  "H2'"  H  0 1 N N N -13.300 8.984  3.163 1.307  -3.221 -0.546 "H2'"  US3 24 
US3 "H2'A" "H2'A" H  0 0 N N N -12.210 10.336 2.918 1.422  -2.103 0.849  "H2'A" US3 25 
US3 HOP2   HOP2   H  0 0 N N N -7.753  8.331  8.453 -5.865 -0.459 -0.953 HOP2   US3 26 
US3 "H3'"  "H3'"  H  0 1 N N N -10.656 9.594  4.630 -0.847 -2.328 1.216  "H3'"  US3 27 
US3 "HO3'" "HO3'" H  0 0 N N N -10.347 7.424  4.617 -0.659 -4.495 0.174  "HO3'" US3 28 
US3 "H4'"  "H4'"  H  0 1 N N N -12.868 7.841  5.873 -1.545 -1.728 -1.664 "H4'"  US3 29 
US3 "H5'"  "H5'"  H  0 1 N N N -11.866 8.413  7.989 -3.155 -1.529 0.292  "H5'"  US3 30 
US3 "H5'A" "H5'A" H  0 0 N N N -10.753 7.550  6.889 -2.111 -0.247 0.951  "H5'A" US3 31 
US3 H5A    H5A    H  0 1 N N N -9.777  12.810 6.950 6.148  1.406  -1.919 H5A    US3 32 
US3 H5AA   H5AA   H  0 0 N N N -9.262  14.031 5.737 5.797  -0.197 -2.608 H5AA   US3 33 
US3 H5AB   H5AB   H  0 0 N N N -10.366 14.503 7.073 4.979  1.247  -3.252 H5AB   US3 34 
US3 HSE2   HSE2   H  0 0 N N N -15.035 13.401 1.902 1.372  0.882  2.971  HSE2   US3 35 
US3 OP1    OP1    O  0 1 N N N -7.411  9.704  8.212 -4.114 1.760  0.901  OP1    US3 36 
# 
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 
US3 P     OP2    SING N N 1  
US3 N1    "C1'"  SING N N 2  
US3 N1    C6     SING N N 3  
US3 C2    N1     SING N N 4  
US3 C2    N3     DOUB N N 5  
US3 SE2   C2     SING N N 6  
US3 SE2   HSE2   SING N N 7  
US3 N3    C4     SING N N 8  
US3 C4    O4     DOUB N N 9  
US3 C4    C5     SING N N 10 
US3 C5    C5A    SING N N 11 
US3 C6    C5     DOUB N N 12 
US3 C6    H6     SING N N 13 
US3 "C1'" "O4'"  SING N N 14 
US3 "C1'" "H1'"  SING N N 15 
US3 OP3   P      SING N N 16 
US3 OP3   HOP3   SING N N 17 
US3 "C2'" "C1'"  SING N N 18 
US3 "C2'" "C3'"  SING N N 19 
US3 "C2'" "H2'"  SING N N 20 
US3 "C2'" "H2'A" SING N N 21 
US3 OP2   HOP2   SING N N 22 
US3 "C3'" "C4'"  SING N N 23 
US3 "C3'" "H3'"  SING N N 24 
US3 "O3'" "C3'"  SING N N 25 
US3 "O3'" "HO3'" SING N N 26 
US3 "C4'" "O4'"  SING N N 27 
US3 "C4'" "C5'"  SING N N 28 
US3 "C4'" "H4'"  SING N N 29 
US3 "C5'" "O5'"  SING N N 30 
US3 "C5'" "H5'"  SING N N 31 
US3 "C5'" "H5'A" SING N N 32 
US3 "O5'" P      SING N N 33 
US3 C5A   H5A    SING N N 34 
US3 C5A   H5AA   SING N N 35 
US3 C5A   H5AB   SING N N 36 
US3 P     OP1    DOUB N N 37 
# 
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 
US3 SMILES           ACDLabs              11.02 "O=P(O)(O)OCC2OC(N1C(=NC(=O)C(=C1)C)[SeH])CC2O"                                                                                                    
US3 SMILES_CANONICAL CACTVS               3.352 "CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)C(=NC1=O)[SeH]"                                                                                     
US3 SMILES           CACTVS               3.352 "CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)C(=NC1=O)[SeH]"                                                                                         
US3 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "CC1=CN(C(=NC1=O)[SeH])[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O"                                                                                       
US3 SMILES           "OpenEye OEToolkits" 1.7.0 "CC1=CN(C(=NC1=O)[SeH])C2CC(C(O2)COP(=O)(O)O)O"                                                                                                    
US3 InChI            InChI                1.03  "InChI=1S/C10H15N2O7PSe/c1-5-3-12(10(21)11-9(5)14)8-2-6(13)7(19-8)4-18-20(15,16)17/h3,6-8,13H,2,4H2,1H3,(H,11,14,21)(H2,15,16,17)/t6-,7+,8+/m0/s1" 
US3 InChIKey         InChI                1.03  NJOAZAGHIQNDNL-XLPZGREQSA-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 
US3 "SYSTEMATIC NAME" ACDLabs              11.02 "1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-5-methyl-2-selanylpyrimidin-4(1H)-one"            
US3 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.6.1 "[(2R,3S,5R)-3-hydroxy-5-(5-methyl-4-oxo-2-selanyl-pyrimidin-1-yl)oxolan-2-yl]methyl dihydrogen phosphate" 
# 
_pdbx_chem_comp_synonyms.ordinal      1 
_pdbx_chem_comp_synonyms.comp_id      US3 
_pdbx_chem_comp_synonyms.name         "2-Se-Thymidine-5'-phosphate" 
_pdbx_chem_comp_synonyms.provenance   ? 
_pdbx_chem_comp_synonyms.type         ? 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
US3 "Create component"  2009-06-15 RCSB 
US3 "Modify descriptor" 2011-06-04 RCSB 
US3 "Modify synonyms"   2021-03-01 PDBE 
# 
