data_XTH
# 
_chem_comp.id                                    XTH 
_chem_comp.name                                  "1-(2,3-DIDEOXY-6-O-PHOSPHONO-BETA-D-ERYTHRO-HEXOPYRANOSYL)-5-METHYLPYRIMIDINE-2,4(1H,3H)-DIONE" 
_chem_comp.type                                  "DNA LINKING" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C11 H17 N2 O8 P" 
_chem_comp.mon_nstd_parent_comp_id               DT 
_chem_comp.pdbx_synonyms                         
;2',3'-DI-DEOXY-BETA-D-GLUCOPYRANOSYL THYMINE
;
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2006-06-20 
_chem_comp.pdbx_modified_date                    2009-01-07 
_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                        336.235 
_chem_comp.one_letter_code                       T 
_chem_comp.three_letter_code                     XTH 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   N 
_chem_comp.pdbx_ideal_coordinates_details        ? 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        2H9S 
_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 
XTH OP3    O3P    O 0 1 N Y N -6.531 8.566  14.891 3.983  2.973  0.541  OP3    XTH 1  
XTH P      P      P 0 1 N N N -6.299 8.032  16.371 3.899  1.462  -0.009 P      XTH 2  
XTH OP1    O1P    O 0 1 N N N -5.821 6.636  16.263 3.896  1.475  -1.489 OP1    XTH 3  
XTH OP2    O2P    O 0 1 N N N -7.498 8.318  17.186 5.172  0.628  0.518  OP2    XTH 4  
XTH "O6'"  "O6'"  O 0 1 N N N -5.109 8.871  17.027 2.547  0.771  0.525  "O6'"  XTH 5  
XTH "C6'"  "C6'"  C 0 1 N N N -3.824 8.940  16.414 2.471  -0.518 -0.088 "C6'"  XTH 6  
XTH "C5'"  "C5'"  C 0 1 N N R -2.995 9.937  17.196 1.201  -1.232 0.379  "C5'"  XTH 7  
XTH "C4'"  "C4'"  C 0 1 N N S -2.811 9.542  18.654 1.184  -2.657 -0.178 "C4'"  XTH 8  
XTH "O4'"  "O4'"  O 0 1 N N N -2.242 8.206  18.677 2.344  -3.361 0.268  "O4'"  XTH 9  
XTH "C3'"  "C3'"  C 0 1 N N N -1.966 10.670 19.269 -0.075 -3.373 0.322  "C3'"  XTH 10 
XTH "C2'"  "C2'"  C 0 1 N N N -2.661 12.036 19.149 -1.299 -2.519 -0.031 "C2'"  XTH 11 
XTH "C1'"  "C1'"  C 0 1 N N R -2.856 12.250 17.645 -1.093 -1.105 0.516  "C1'"  XTH 12 
XTH "O5'"  "O5'"  O 0 1 N N N -3.691 11.195 17.213 0.058  -0.517 -0.087 "O5'"  XTH 13 
XTH N1     N1     N 0 1 N N N -3.581 13.465 17.195 -2.272 -0.290 0.212  N1     XTH 14 
XTH C2     C2     C 0 1 N N N -3.719 13.649 15.832 -2.578 -0.012 -1.069 C2     XTH 15 
XTH O2     O2     O 0 1 N N N -3.169 12.928 15.016 -1.872 -0.443 -1.961 O2     XTH 16 
XTH N3     N3     N 0 1 N N N -4.467 14.724 15.430 -3.655 0.734  -1.377 N3     XTH 17 
XTH C4     C4     C 0 1 N N N -5.104 15.587 16.287 -4.451 1.214  -0.400 C4     XTH 18 
XTH O4     O4     O 0 1 N N N -5.778 16.513 15.863 -5.426 1.889  -0.678 O4     XTH 19 
XTH C5     C5     C 0 1 N N N -4.949 15.324 17.695 -4.137 0.934  0.952  C5     XTH 20 
XTH C5M    C5M    C 0 1 N N N -5.613 16.216 18.699 -5.008 1.463  2.063  C5M    XTH 21 
XTH C6     C6     C 0 1 N N N -4.229 14.272 18.088 -3.051 0.183  1.232  C6     XTH 22 
XTH HOP3   3HOP   H 0 0 N N N -6.577 9.515  14.900 4.806  3.349  0.199  HOP3   XTH 23 
XTH HOP2   2HOP   H 0 0 N N N -7.252 8.379  18.102 5.136  0.644  1.484  HOP2   XTH 24 
XTH "H6'1" "1H6'" H 0 0 N N N -3.915 9.255  15.364 3.344  -1.106 0.195  "H6'1" XTH 25 
XTH "H6'2" "2H6'" H 0 0 N N N -3.343 7.951  16.433 2.446  -0.403 -1.172 "H6'2" XTH 26 
XTH "H5'"  "H5'"  H 0 1 N N N -2.011 9.984  16.706 1.186  -1.269 1.469  "H5'"  XTH 27 
XTH "H4'"  "H4'"  H 0 1 N N N -3.726 9.460  19.259 1.175  -2.622 -1.268 "H4'"  XTH 28 
XTH "H4T'" "H4T'" H 0 0 N N N -2.118 7.899  17.787 2.289  -4.253 -0.100 "H4T'" XTH 29 
XTH "H3'1" "1H3'" H 0 0 N N N -1.013 10.721 18.722 -0.018 -3.502 1.403  "H3'1" XTH 30 
XTH "H3'2" "2H3'" H 0 0 N N N -1.805 10.449 20.334 -0.158 -4.347 -0.161 "H3'2" XTH 31 
XTH "H2'1" "1H2'" H 0 0 N N N -2.067 12.841 19.606 -2.191 -2.958 0.417  "H2'1" XTH 32 
XTH "H2'2" "2H2'" H 0 0 N N N -3.627 12.034 19.675 -1.415 -2.479 -1.114 "H2'2" XTH 33 
XTH "H1'"  "H1'"  H 0 1 N N N -1.834 12.323 17.244 -0.953 -1.150 1.596  "H1'"  XTH 34 
XTH HN3    HN3    H 0 1 N N N -4.555 14.891 14.448 -3.862 0.924  -2.305 HN3    XTH 35 
XTH H71    1H5M   H 0 1 N N N -6.581 16.557 18.303 -4.642 2.440  2.378  H71    XTH 36 
XTH H72    2H5M   H 0 1 N N N -4.970 17.086 18.898 -6.034 1.556  1.707  H72    XTH 37 
XTH H73    3H5M   H 0 1 N N N -5.776 15.659 19.634 -4.977 0.774  2.907  H73    XTH 38 
XTH H6     H6     H 0 1 N N N -4.156 14.051 19.143 -2.798 -0.044 2.258  H6     XTH 39 
# 
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 
XTH OP3   P      SING N N 1  
XTH OP3   HOP3   SING N N 2  
XTH P     OP1    DOUB N N 3  
XTH P     OP2    SING N N 4  
XTH P     "O6'"  SING N N 5  
XTH OP2   HOP2   SING N N 6  
XTH "O6'" "C6'"  SING N N 7  
XTH "C6'" "C5'"  SING N N 8  
XTH "C6'" "H6'1" SING N N 9  
XTH "C6'" "H6'2" SING N N 10 
XTH "C5'" "C4'"  SING N N 11 
XTH "C5'" "O5'"  SING N N 12 
XTH "C5'" "H5'"  SING N N 13 
XTH "C4'" "O4'"  SING N N 14 
XTH "C4'" "C3'"  SING N N 15 
XTH "C4'" "H4'"  SING N N 16 
XTH "O4'" "H4T'" SING N N 17 
XTH "C3'" "C2'"  SING N N 18 
XTH "C3'" "H3'1" SING N N 19 
XTH "C3'" "H3'2" SING N N 20 
XTH "C2'" "C1'"  SING N N 21 
XTH "C2'" "H2'1" SING N N 22 
XTH "C2'" "H2'2" SING N N 23 
XTH "C1'" "O5'"  SING N N 24 
XTH "C1'" N1     SING N N 25 
XTH "C1'" "H1'"  SING N N 26 
XTH N1    C2     SING N N 27 
XTH N1    C6     SING N N 28 
XTH C2    O2     DOUB N N 29 
XTH C2    N3     SING N N 30 
XTH N3    C4     SING N N 31 
XTH N3    HN3    SING N N 32 
XTH C4    O4     DOUB N N 33 
XTH C4    C5     SING N N 34 
XTH C5    C5M    SING N N 35 
XTH C5    C6     DOUB N N 36 
XTH C5M   H71    SING N N 37 
XTH C5M   H72    SING N N 38 
XTH C5M   H73    SING N N 39 
XTH C6    H6     SING N N 40 
# 
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 
XTH SMILES           ACDLabs              10.04 "O=C1NC(=O)N(C=C1C)C2OC(C(O)CC2)COP(=O)(O)O"                                                                                                                      
XTH InChI            InChI                1.02b "InChI=1/C11H17N2O8P/c1-6-4-13(11(16)12-10(6)15)9-3-2-7(14)8(21-9)5-20-22(17,18)19/h4,7-9,14H,2-3,5H2,1H3,(H,12,15,16)(H2,17,18,19)/t7-,8+,9+/m0/s1/f/h12,17-18H" 
XTH InChIKey         InChI                1.02b DUSDVRPQFGBMGI-RWOLMHSVDV                                                                                                                                         
XTH SMILES_CANONICAL CACTVS               3.341 "CC1=CN([C@H]2CC[C@H](O)[C@@H](CO[P](O)(O)=O)O2)C(=O)NC1=O"                                                                                                       
XTH SMILES           CACTVS               3.341 "CC1=CN([CH]2CC[CH](O)[CH](CO[P](O)(O)=O)O2)C(=O)NC1=O"                                                                                                           
XTH SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)[C@H]2CC[C@@H]([C@H](O2)COP(=O)(O)O)O"                                                                                                         
XTH SMILES           "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)C2CCC(C(O2)COP(=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 
XTH "SYSTEMATIC NAME" ACDLabs              10.04 "1-(2,3-dideoxy-6-O-phosphono-beta-D-erythro-hexopyranosyl)-5-methylpyrimidine-2,4(1H,3H)-dione"   
XTH "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,6R)-3-hydroxy-6-(5-methyl-2,4-dioxo-pyrimidin-1-yl)oxan-2-yl]methyl dihydrogen phosphate" 
# 
