data_TDO
# 
_chem_comp.id                                    TDO 
_chem_comp.name                                  DTDP-4-KETO-L-RHAMNOSE 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C16 H24 N2 O15 P2" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2006-07-08 
_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                        546.314 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     TDO 
_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        2IXK 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBJ 
# 
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 
TDO O4P    O4P    O 0 1 N N N 14.328 12.338 17.887 -2.801 0.047  1.091  O4P    TDO 1  
TDO P2     P2     P 0 1 N N R 15.745 12.426 17.368 -2.877 -0.586 -0.245 P2     TDO 2  
TDO O3P    O3P    O 0 1 N N N 16.522 13.906 17.463 -3.271 -2.138 -0.081 O3P    TDO 3  
TDO O1     O1     O 0 1 N N N 16.571 11.261 18.131 -3.994 0.162  -1.130 O1     TDO 4  
TDO C1     C1     C 0 1 N N R 17.608 11.546 19.073 -5.209 0.127  -0.378 C1     TDO 5  
TDO C2     C2     C 0 1 N N R 18.490 10.303 19.201 -6.398 0.087  -1.341 C2     TDO 6  
TDO O2     O2     O 0 1 N N N 17.711 9.182  19.626 -6.452 1.305  -2.087 O2     TDO 7  
TDO C3     C3     C 0 1 N N S 19.589 10.547 20.222 -7.688 -0.077 -0.523 C3     TDO 8  
TDO O3     O3     O 0 1 N N N 20.470 9.412  20.356 -8.824 0.154  -1.357 O3     TDO 9  
TDO C4     C4     C 0 1 N N N 18.917 10.925 21.510 -7.651 0.944  0.598  C4     TDO 10 
TDO O4     O4     O 0 1 N N N 19.119 10.287 22.543 -8.618 1.618  0.861  O4     TDO 11 
TDO C5     C5     C 0 1 N N S 18.005 12.119 21.411 -6.359 1.091  1.371  C5     TDO 12 
TDO O5     O5     O 0 1 N N N 17.054 11.885 20.356 -5.285 1.286  0.449  O5     TDO 13 
TDO C6     C6     C 0 1 N N N 17.250 12.400 22.709 -6.456 2.298  2.307  C6     TDO 14 
TDO OPP    OPP    O 0 1 N N N 15.806 12.031 15.804 -1.447 -0.470 -0.976 OPP    TDO 15 
TDO P      P      P 0 1 N N R 14.808 11.046 15.006 -0.332 -0.868 0.116  P      TDO 16 
TDO O1P    O1P    O 0 1 N N N 13.420 11.640 14.930 -0.765 -2.082 0.843  O1P    TDO 17 
TDO O2P    O2P    O 0 1 N N N 14.843 9.463  15.546 -0.147 0.345  1.159  O2P    TDO 18 
TDO "O5'"  "O5'"  O 0 1 N N N 15.420 11.091 13.526 1.067  -1.157 -0.626 "O5'"  TDO 19 
TDO "C5'"  "C5'"  C 0 1 N N N 15.353 12.299 12.781 1.978  -1.616 0.375  "C5'"  TDO 20 
TDO "C4'"  "C4'"  C 0 1 N N R 15.995 12.108 11.423 3.335  -1.911 -0.267 "C4'"  TDO 21 
TDO "O4'"  "O4'"  O 0 1 N N N 17.413 11.916 11.511 3.967  -0.688 -0.703 "O4'"  TDO 22 
TDO "C3'"  "C3'"  C 0 1 N N S 15.451 10.886 10.729 4.324  -2.479 0.782  "C3'"  TDO 23 
TDO "O3'"  "O3'"  O 0 1 N N N 15.270 11.259 9.360  4.189  -3.896 0.904  "O3'"  TDO 24 
TDO "C2'"  "C2'"  C 0 1 N N N 16.527 9.828  10.881 5.697  -2.105 0.168  "C2'"  TDO 25 
TDO "C1'"  "C1'"  C 0 1 N N R 17.796 10.666 10.938 5.375  -0.958 -0.810 "C1'"  TDO 26 
TDO N11    N11    N 0 1 Y N N 18.866 10.167 11.805 6.140  0.238  -0.450 N11    TDO 27 
TDO C21    C21    C 0 1 Y N N 20.102 9.936  11.326 5.907  0.849  0.726  C21    TDO 28 
TDO O21    O21    O 0 1 N N N 20.380 10.060 10.115 5.066  0.399  1.479  O21    TDO 29 
TDO N31    N31    N 0 1 Y N N 21.079 9.525  12.131 6.599  1.947  1.084  N31    TDO 30 
TDO C41    C41    C 0 1 Y N N 20.917 9.358  13.441 7.535  2.459  0.260  C41    TDO 31 
TDO O41    O41    O 0 1 N N N 21.863 8.977  14.145 8.158  3.455  0.581  O41    TDO 32 
TDO C51    C51    C 0 1 Y N N 19.575 9.608  14.016 7.787  1.829  -0.982 C51    TDO 33 
TDO C5A    C5A    C 0 1 N N N 19.282 9.447  15.489 8.828  2.381  -1.922 C5A    TDO 34 
TDO C61    C61    C 0 1 Y N N 18.608 10.042 13.127 7.082  0.726  -1.314 C61    TDO 35 
TDO H3PO   OH3P   H 0 0 N N N 16.669 14.129 18.375 -3.310 -2.512 -0.972 H3PO   TDO 36 
TDO H1     H1     H 0 1 N N N 18.199 12.405 18.722 -5.220 -0.765 0.248  H1     TDO 37 
TDO H2     H2     H 0 1 N N N 18.933 10.093 18.216 -6.288 -0.756 -2.023 H2     TDO 38 
TDO HA     HA     H 0 1 N N N 17.538 8.616  18.883 -7.213 1.236  -2.679 HA     TDO 39 
TDO H3     H3     H 0 1 N N N 20.248 11.365 19.894 -7.735 -1.082 -0.103 H3     TDO 40 
TDO HB     HB     H 0 1 N N N 20.664 9.058  19.496 -9.607 0.040  -0.801 HB     TDO 41 
TDO H5     H5     H 0 1 N N N 18.631 12.999 21.203 -6.179 0.190  1.956  H5     TDO 42 
TDO H6C1   1H6C   H 0 0 N N N 16.538 11.584 22.902 -6.636 3.199  1.720  H6C1   TDO 43 
TDO H6C2   2H6C   H 0 0 N N N 16.704 13.350 22.617 -7.278 2.150  3.007  H6C2   TDO 44 
TDO H6C3   3H6C   H 0 0 N N N 17.965 12.468 23.542 -5.523 2.405  2.860  H6C3   TDO 45 
TDO H2PO   OH2P   H 0 0 N N N 14.850 8.874  14.801 0.135  1.114  0.646  H2PO   TDO 46 
TDO "H5'1" "1H5'" H 0 0 N N N 15.890 13.089 13.326 2.096  -0.848 1.139  "H5'1" TDO 47 
TDO "H5'2" "2H5'" H 0 0 N N N 14.299 12.585 12.647 1.587  -2.525 0.832  "H5'2" TDO 48 
TDO "H4'"  "H4'"  H 0 1 N N N 15.766 13.027 10.864 3.221  -2.603 -1.102 "H4'"  TDO 49 
TDO "H3'"  "H3'"  H 0 1 N N N 14.498 10.508 11.129 4.184  -1.992 1.748  "H3'"  TDO 50 
TDO HC     HC     H 0 1 N N N 15.230 12.206 9.292  4.890  -4.193 1.500  HC     TDO 51 
TDO "H2'1" "1H2'" H 0 0 N N N 16.528 9.084  10.071 6.117  -2.956 -0.368 "H2'1" TDO 52 
TDO "H2'2" "2H2'" H 0 0 N N N 16.389 9.228  11.793 6.383  -1.764 0.943  "H2'2" TDO 53 
TDO "H1'"  "H1'"  H 0 1 N N N 18.195 10.683 9.913  5.618  -1.260 -1.829 "H1'"  TDO 54 
TDO H31    H31    H 0 1 N N N 21.976 9.333  11.733 6.421  2.373  1.937  H31    TDO 55 
TDO H5A1   1H5A   H 0 0 N N N 18.721 8.515  15.651 8.364  3.105  -2.592 H5A1   TDO 56 
TDO H5A2   2H5A   H 0 0 N N N 18.684 10.301 15.839 9.614  2.870  -1.346 H5A2   TDO 57 
TDO H5A3   3H5A   H 0 0 N N N 20.228 9.408  16.049 9.258  1.568  -2.506 H5A3   TDO 58 
TDO H61    H61    H 0 1 N N N 17.623 10.287 13.497 7.260  0.232  -2.258 H61    TDO 59 
# 
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 
TDO O4P   P2     DOUB N N 1  
TDO P2    O3P    SING N N 2  
TDO P2    O1     SING N N 3  
TDO P2    OPP    SING N N 4  
TDO O3P   H3PO   SING N N 5  
TDO O1    C1     SING N N 6  
TDO C1    C2     SING N N 7  
TDO C1    O5     SING N N 8  
TDO C1    H1     SING N N 9  
TDO C2    O2     SING N N 10 
TDO C2    C3     SING N N 11 
TDO C2    H2     SING N N 12 
TDO O2    HA     SING N N 13 
TDO C3    O3     SING N N 14 
TDO C3    C4     SING N N 15 
TDO C3    H3     SING N N 16 
TDO O3    HB     SING N N 17 
TDO C4    O4     DOUB N N 18 
TDO C4    C5     SING N N 19 
TDO C5    O5     SING N N 20 
TDO C5    C6     SING N N 21 
TDO C5    H5     SING N N 22 
TDO C6    H6C1   SING N N 23 
TDO C6    H6C2   SING N N 24 
TDO C6    H6C3   SING N N 25 
TDO OPP   P      SING N N 26 
TDO P     O1P    DOUB N N 27 
TDO P     O2P    SING N N 28 
TDO P     "O5'"  SING N N 29 
TDO O2P   H2PO   SING N N 30 
TDO "O5'" "C5'"  SING N N 31 
TDO "C5'" "C4'"  SING N N 32 
TDO "C5'" "H5'1" SING N N 33 
TDO "C5'" "H5'2" SING N N 34 
TDO "C4'" "O4'"  SING N N 35 
TDO "C4'" "C3'"  SING N N 36 
TDO "C4'" "H4'"  SING N N 37 
TDO "O4'" "C1'"  SING N N 38 
TDO "C3'" "O3'"  SING N N 39 
TDO "C3'" "C2'"  SING N N 40 
TDO "C3'" "H3'"  SING N N 41 
TDO "O3'" HC     SING N N 42 
TDO "C2'" "C1'"  SING N N 43 
TDO "C2'" "H2'1" SING N N 44 
TDO "C2'" "H2'2" SING N N 45 
TDO "C1'" N11    SING N N 46 
TDO "C1'" "H1'"  SING N N 47 
TDO N11   C21    SING Y N 48 
TDO N11   C61    SING Y N 49 
TDO C21   O21    DOUB N N 50 
TDO C21   N31    SING Y N 51 
TDO N31   C41    SING Y N 52 
TDO N31   H31    SING N N 53 
TDO C41   O41    DOUB N N 54 
TDO C41   C51    SING Y N 55 
TDO C51   C5A    SING N N 56 
TDO C51   C61    DOUB Y N 57 
TDO C5A   H5A1   SING N N 58 
TDO C5A   H5A2   SING N N 59 
TDO C5A   H5A3   SING N N 60 
TDO C61   H61    SING N N 61 
# 
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 
TDO SMILES           ACDLabs              10.04 "O=C1C(O)C(O)C(OC1C)OP(=O)(O)OP(=O)(O)OCC3OC(N2C(=O)NC(=O)C(=C2)C)CC3O" 
TDO SMILES_CANONICAL CACTVS               3.341 "C[C@@H]1O[C@H](O[P@](O)(=O)O[P@@](O)(=O)OC[C@H]2O[C@H](C[C@@H]2O)N3C=C(C)C(=O)NC3=O)[C@H](O)[C@H](O)C1=O" 
TDO SMILES           CACTVS               3.341 "C[CH]1O[CH](O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH](C[CH]2O)N3C=C(C)C(=O)NC3=O)[CH](O)[CH](O)C1=O" 
TDO SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C[C@H]1C(=O)[C@H]([C@H]([C@H](O1)O[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]2[C@H](C[C@@H](O2)N3C=C(C(=O)NC3=O)C)O)O)O" 
TDO SMILES           "OpenEye OEToolkits" 1.5.0 "CC1C(=O)C(C(C(O1)OP(=O)(O)OP(=O)(O)OCC2C(CC(O2)N3C=C(C(=O)NC3=O)C)O)O)O" 
TDO InChI            InChI                1.03  
"InChI=1S/C16H24N2O15P2/c1-6-4-18(16(24)17-14(6)23)10-3-8(19)9(31-10)5-29-34(25,26)33-35(27,28)32-15-13(22)12(21)11(20)7(2)30-15/h4,7-10,12-13,15,19,21-22H,3,5H2,1-2H3,(H,25,26)(H,27,28)(H,17,23,24)/t7-,8-,9+,10+,12+,13+,15+/m0/s1" 
TDO InChIKey         InChI                1.03  PSXWNITXWWECNY-LPVGZGSHSA-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 
TDO "SYSTEMATIC NAME" ACDLabs              10.04 
"(2R,3R,4S,6S)-3,4-dihydroxy-6-methyl-5-oxotetrahydro-2H-pyran-2-yl [(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)" 
TDO "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3R,4S,6S)-3,4-dihydroxy-6-methyl-5-oxo-oxan-2-yl] [hydroxy-[[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methoxy]phosphoryl] hydrogen 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 
TDO "Create component"  2006-07-08 PDBJ 
TDO "Modify descriptor" 2011-06-04 RCSB 
# 
