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 #