data_LSH
# 
_chem_comp.id                                    LSH 
_chem_comp.name                                  "[(1R,5R,7R,8S)-7-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-8-oxidanyl-3,3-bis(oxidanylidene)-6-oxa-3$l^{6}-thia-2-azabicyclo[3.2.1]octan-5-yl]methyl dihydrogen phosphate" 
_chem_comp.type                                  "DNA LINKING" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C11 H16 N3 O10 P S" 
_chem_comp.mon_nstd_parent_comp_id               DT 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2015-08-05 
_chem_comp.pdbx_modified_date                    2026-07-10 
_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                        413.298 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     ? 
_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        5AXE 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBJ 
_chem_comp.pdbx_pcm                              ? 
# 
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.pdbx_backbone_atom_flag 
_chem_comp_atom.pdbx_n_terminal_atom_flag 
_chem_comp_atom.pdbx_c_terminal_atom_flag 
_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 
LSH P      P1  P 0 1 N N N N N N 11.134 46.787 46.532 3.934  -1.812 -0.252 P     LSH 1  
LSH OP1    O1  O 0 1 N N N N N N 12.450 47.144 45.966 4.787  -1.615 0.941  OP1   LSH 2  
LSH OP2    O2  O 0 1 N N N N N N 11.005 46.176 47.858 3.278  -3.282 -0.206 OP2   LSH 3  
LSH "O5'"  O3  O 0 1 N N N N N N 10.089 48.060 46.451 2.767  -0.704 -0.267 "O5'" LSH 4  
LSH "C5'"  C1  C 0 1 N N N N N N 9.972  48.785 45.259 1.867  -0.507 0.826  "C5'" LSH 5  
LSH "C4'"  C2  C 0 1 N N R N N N 8.814  49.751 45.415 0.889  0.619  0.485  "C4'" LSH 6  
LSH "C6'"  C3  C 0 1 N N N N N N 8.528  50.427 44.059 1.633  1.908  0.098  "C6'" LSH 7  
LSH S      S1  S 0 1 N N N N N N 7.126  51.364 44.079 0.411  3.121  -0.493 S     LSH 8  
LSH "O7'"  O4  O 0 1 N N N N N N 7.197  52.423 43.116 0.894  4.446  -0.322 "O7'" LSH 9  
LSH "O8'"  O5  O 0 1 N N N N N N 5.994  50.476 43.936 -0.163 2.698  -1.722 "O8'" LSH 10 
LSH "N2'"  N1  N 0 1 N N N N N N 7.094  52.025 45.557 -0.826 2.980  0.615  "N2'" LSH 11 
LSH "C2'"  C4  C 0 1 N N R N N N 7.599  51.267 46.713 -1.244 1.603  0.967  "C2'" LSH 12 
LSH "C1'"  C5  C 0 1 N N R N N N 6.948  49.927 46.768 -1.297 0.810  -0.361 "C1'" LSH 13 
LSH "O4'"  O6  O 0 1 N N N N N N 7.659  49.049 45.878 0.020  0.246  -0.594 "O4'" LSH 14 
LSH N1     N2  N 0 1 N N N N N N 6.755  49.254 48.055 -2.284 -0.268 -0.257 N1    LSH 15 
LSH C2     C6  C 0 1 N N N N N N 5.736  49.656 48.849 -3.577 -0.016 -0.532 C2    LSH 16 
LSH O2     O7  O 0 1 N N N N N N 5.088  50.700 48.594 -3.912 1.105  -0.863 O2    LSH 17 
LSH N3     N3  N 0 1 N N N N N N 5.457  48.907 49.951 -4.504 -0.988 -0.445 N3    LSH 18 
LSH C4     C7  C 0 1 N N N N N N 6.129  47.771 50.273 -4.148 -2.236 -0.080 C4    LSH 19 
LSH O4     O8  O 0 1 N N N N N N 5.775  47.108 51.281 -4.986 -3.116 -0.002 O4    LSH 20 
LSH C5     C8  C 0 1 N N N N N N 7.189  47.383 49.464 -2.791 -2.514 0.212  C5    LSH 21 
LSH C7     C9  C 0 1 N N N N N N 7.982  46.142 49.778 -2.367 -3.901 0.623  C7    LSH 22 
LSH C6     C10 C 0 1 N N N N N N 7.467  48.147 48.347 -1.881 -1.522 0.112  C6    LSH 23 
LSH "C3'"  C11 C 0 1 N N S N N N 9.017  50.811 46.487 -0.047 0.934  1.676  "C3'" LSH 24 
LSH "O3'"  O9  O 0 1 N N N N N N 9.879  51.845 46.034 0.560  1.868  2.572  "O3'" LSH 25 
LSH HOP2   H2  H 0 1 N N N N N N 11.867 46.067 48.242 2.705  -3.481 -0.960 H2    LSH 26 
LSH "H5'"  H3  H 0 1 N N N N N N 9.777  48.099 44.422 1.313  -1.427 1.010  H3    LSH 27 
LSH "H5''" H4  H 0 1 N N N N N N 10.901 49.342 45.067 2.433  -0.238 1.718  H4    LSH 28 
LSH "H6'"  H5  H 0 1 N N N N N N 8.417  49.645 43.293 2.154  2.307  0.969  H5    LSH 29 
LSH "H6''" H6  H 0 1 N N N N N N 9.380  51.074 43.802 2.351  1.695  -0.694 H6    LSH 30 
LSH "HN2'" H7  H 0 1 N N N N N N 7.630  52.868 45.508 -1.249 3.759  1.010  H7    LSH 31 
LSH "H2'"  H8  H 0 1 N N N N N N 7.491  51.820 47.658 -2.174 1.565  1.533  H8    LSH 32 
LSH "H1'"  H9  H 0 1 N N N N N N 5.944  50.062 46.339 -1.564 1.478  -1.180 H9    LSH 33 
LSH H3     H10 H 0 1 N N N N N N 4.719  49.209 50.555 -5.432 -0.790 -0.647 H10   LSH 34 
LSH H71    H11 H 0 1 N N N N N N 7.600  45.687 50.704 -3.237 -4.557 0.641  H11   LSH 35 
LSH H73    H12 H 0 1 N N N N N N 7.884  45.425 48.950 -1.638 -4.285 -0.091 H12   LSH 36 
LSH H72    H13 H 0 1 N N N N N N 9.041  46.407 49.910 -1.919 -3.865 1.616  H13   LSH 37 
LSH H6     H14 H 0 1 N N N N N N 8.273  47.851 47.693 -0.840 -1.717 0.326  H14   LSH 38 
LSH "H3'"  H15 H 0 1 N N N N N N 9.408  50.342 47.402 -0.335 0.023  2.200  H15   LSH 39 
LSH "HO3'" H16 H 0 1 N N N N N N 9.988  52.491 46.722 0.011  2.096  3.335  H16   LSH 40 
LSH OP3    OP3 O 0 1 N N N N N N 10.520 45.784 45.437 4.830  -1.666 -1.582 OP3   LSH 41 
LSH HOP3   H1  H 0 1 N N N N N N 11.138 45.676 44.724 5.554  -2.304 -1.641 H1    LSH 42 
# 
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 
LSH "O7'" S      DOUB N N 1  
LSH "O8'" S      DOUB N N 2  
LSH "C6'" S      SING N N 3  
LSH "C6'" "C4'"  SING N N 4  
LSH S     "N2'"  SING N N 5  
LSH "C5'" "C4'"  SING N N 6  
LSH "C5'" "O5'"  SING N N 7  
LSH "C4'" "O4'"  SING N N 8  
LSH "C4'" "C3'"  SING N N 9  
LSH "N2'" "C2'"  SING N N 10 
LSH "O4'" "C1'"  SING N N 11 
LSH OP1   P      DOUB N N 12 
LSH "O3'" "C3'"  SING N N 13 
LSH "O5'" P      SING N N 14 
LSH "C3'" "C2'"  SING N N 15 
LSH P     OP2    SING N N 16 
LSH "C2'" "C1'"  SING N N 17 
LSH "C1'" N1     SING N N 18 
LSH N1    C6     SING N N 19 
LSH N1    C2     SING N N 20 
LSH C6    C5     DOUB N N 21 
LSH O2    C2     DOUB N N 22 
LSH C2    N3     SING N N 23 
LSH C5    C7     SING N N 24 
LSH C5    C4     SING N N 25 
LSH N3    C4     SING N N 26 
LSH C4    O4     DOUB N N 27 
LSH OP2   HOP2   SING N N 28 
LSH "C5'" "H5'"  SING N N 29 
LSH "C5'" "H5''" SING N N 30 
LSH "C6'" "H6'"  SING N N 31 
LSH "C6'" "H6''" SING N N 32 
LSH "N2'" "HN2'" SING N N 33 
LSH "C2'" "H2'"  SING N N 34 
LSH "C1'" "H1'"  SING N N 35 
LSH N3    H3     SING N N 36 
LSH C7    H71    SING N N 37 
LSH C7    H73    SING N N 38 
LSH C7    H72    SING N N 39 
LSH C6    H6     SING N N 40 
LSH "C3'" "H3'"  SING N N 41 
LSH "O3'" "HO3'" SING N N 42 
LSH P     OP3    SING N N 43 
LSH OP3   HOP3   SING N N 44 
# 
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 
LSH InChI            InChI                1.03  "InChI=1S/C11H16N3O10PS/c1-5-2-14(10(17)12-8(5)16)9-6-7(15)11(24-9,3-23-25(18,19)20)4-26(21,22)13-6/h2,6-7,9,13,15H,3-4H2,1H3,(H,12,16,17)(H2,18,19,20)/t6-,7+,9-,11+/m1/s1" 
LSH InChIKey         InChI                1.03  BWIQWTUDCFCICX-SZVQBCOZSA-N                                                                                                                                                  
LSH SMILES_CANONICAL CACTVS               3.385 "CC1=CN([C@@H]2O[C@@]3(CO[P](O)(O)=O)C[S](=O)(=O)N[C@@H]2[C@@H]3O)C(=O)NC1=O"                                                                                                
LSH SMILES           CACTVS               3.385 "CC1=CN([CH]2O[C]3(CO[P](O)(O)=O)C[S](=O)(=O)N[CH]2[CH]3O)C(=O)NC1=O"                                                                                                        
LSH SMILES_CANONICAL "OpenEye OEToolkits" 1.9.2 "CC1=CN(C(=O)NC1=O)[C@H]2[C@H]3[C@@H]([C@@](O2)(CS(=O)(=O)N3)COP(=O)(O)O)O"                                                                                                  
LSH SMILES           "OpenEye OEToolkits" 1.9.2 "CC1=CN(C(=O)NC1=O)C2C3C(C(O2)(CS(=O)(=O)N3)COP(=O)(O)O)O"                                                                                                                   
# 
_pdbx_chem_comp_identifier.comp_id           LSH 
_pdbx_chem_comp_identifier.type              "SYSTEMATIC NAME" 
_pdbx_chem_comp_identifier.program           "OpenEye OEToolkits" 
_pdbx_chem_comp_identifier.program_version   1.9.2 
_pdbx_chem_comp_identifier.identifier        "[(1R,5R,7R,8S)-7-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-8-oxidanyl-3,3-bis(oxidanylidene)-6-oxa-3$l^{6}-thia-2-azabicyclo[3.2.1]octan-5-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 
LSH "Create component" 2015-08-05 PDBJ 
LSH "Initial release"  2016-07-20 RCSB 
LSH "Modify atom id"   2026-07-10 PDBE 
# 
