data_3TD # _chem_comp.id 3TD _chem_comp.name "(1S)-1,4-anhydro-1-(3-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-5-O-phosphono-D-ribitol" _chem_comp.type "RNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H15 N2 O9 P" _chem_comp.mon_nstd_parent_comp_id U _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2011-01-18 _chem_comp.pdbx_modified_date 2011-12-14 _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 338.208 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 3TD _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 3IZT _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 3TD P P P 0 1 N N N -0.106 0.017 -0.147 4.263 -1.099 -0.157 P 3TD 1 3TD N1 N1 N 0 1 N N N 5.169 0.693 5.003 -4.373 -0.595 -1.385 N1 3TD 2 3TD C2 C2 C 0 1 N N N 6.482 0.820 5.302 -4.459 -1.339 -0.266 C2 3TD 3 3TD O2 O2 O 0 1 N N N 6.745 1.369 6.398 -5.427 -2.054 -0.095 O2 3TD 4 3TD N3 N3 N 0 1 N N N 7.452 0.374 4.438 -3.488 -1.302 0.665 N3 3TD 5 3TD C4 C4 C 0 1 N N N 7.064 -0.184 3.239 -2.408 -0.515 0.490 C4 3TD 6 3TD O4 O4 O 0 1 N N N 7.926 -0.582 2.418 -1.528 -0.481 1.332 O4 3TD 7 3TD C5 C5 C 0 1 N N N 5.694 -0.330 2.897 -2.305 0.273 -0.682 C5 3TD 8 3TD C6 C6 C 0 1 N N N 4.759 0.133 3.844 -3.294 0.217 -1.600 C6 3TD 9 3TD "C1'" "C1'" C 0 1 N N S 5.237 -0.968 1.625 -1.108 1.162 -0.902 "C1'" 3TD 10 3TD C10 C10 C 0 1 N N N 8.853 0.516 4.782 -3.605 -2.121 1.874 C10 3TD 11 3TD "C2'" "C2'" C 0 1 N N R 5.038 -2.488 1.767 -1.078 2.274 0.164 "C2'" 3TD 12 3TD "O2'" "O2'" O 0 1 N N N 6.269 -3.208 1.718 -1.145 3.561 -0.453 "O2'" 3TD 13 3TD "C3'" "C3'" C 0 1 N N S 4.090 -2.826 0.604 0.284 2.082 0.874 "C3'" 3TD 14 3TD "O3'" "O3'" O 0 1 N N N 4.789 -3.371 -0.517 0.904 3.343 1.136 "O3'" 3TD 15 3TD "C4'" "C4'" C 0 1 N N R 3.441 -1.459 0.246 1.089 1.279 -0.179 "C4'" 3TD 16 3TD "O4'" "O4'" O 0 1 N N N 3.950 -0.502 1.189 0.101 0.399 -0.758 "O4'" 3TD 17 3TD "C5'" "C5'" C 0 1 N N N 1.894 -1.492 0.280 2.201 0.472 0.493 "C5'" 3TD 18 3TD "O5'" "O5'" O 0 1 N N N 1.380 -0.299 -0.044 2.999 -0.166 -0.507 "O5'" 3TD 19 3TD OP1 OP1 O 0 1 N N N -0.722 -0.855 -1.217 5.410 -0.210 0.540 OP1 3TD 20 3TD OP2 OP2 O 0 1 N N N -0.768 -0.240 1.149 3.841 -2.174 0.768 OP2 3TD 21 3TD HN1 HN1 H 0 1 N N N 4.486 1.021 5.655 -5.082 -0.639 -2.046 HN1 3TD 22 3TD H6 H6 H 0 1 N N N 3.702 0.039 3.641 -3.232 0.810 -2.500 H6 3TD 23 3TD "H1'" "H1'" H 0 1 N N N 5.987 -0.785 0.841 -1.153 1.604 -1.898 "H1'" 3TD 24 3TD H10 H10 H 0 1 N N N 9.473 0.104 3.973 -4.537 -2.686 1.841 H10 3TD 25 3TD H10A H10A H 0 0 N N N 9.090 1.581 4.920 -2.763 -2.811 1.929 H10A 3TD 26 3TD H10B H10B H 0 0 N N N 9.058 -0.029 5.715 -3.603 -1.475 2.752 H10B 3TD 27 3TD "H2'" "H2'" H 0 1 N N N 4.518 -2.688 2.715 -1.899 2.147 0.870 "H2'" 3TD 28 3TD "HO2'" "HO2'" H 0 0 N N N 6.096 -4.138 1.809 -1.129 4.298 0.173 "HO2'" 3TD 29 3TD "H3'" "H3'" H 0 1 N N N 3.310 -3.517 0.956 0.167 1.510 1.794 "H3'" 3TD 30 3TD "HO3'" "HO3'" H 0 0 N Y N 4.171 -3.566 -1.212 0.392 3.919 1.720 "HO3'" 3TD 31 3TD "H4'" "H4'" H 0 1 N N N 3.758 -1.184 -0.771 1.500 1.945 -0.938 "H4'" 3TD 32 3TD "H5'" "H5'" H 0 1 N N N 1.535 -2.245 -0.437 2.827 1.140 1.085 "H5'" 3TD 33 3TD "H5'A" "H5'A" H 0 0 N N N 1.562 -1.763 1.293 1.760 -0.284 1.143 "H5'A" 3TD 34 3TD O9 O9 O 0 1 N Y N -0.287 1.468 -0.527 4.839 -1.751 -1.512 O9 3TD 35 3TD H14 H14 H 0 1 N N N -1.408 -1.389 -0.835 5.734 0.516 -0.010 H14 3TD 36 3TD H15 H15 H 0 1 N N N -0.789 1.912 0.147 5.604 -2.327 -1.376 H15 3TD 37 # 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 3TD P "O5'" SING N N 1 3TD P OP1 SING N N 2 3TD P OP2 DOUB N N 3 3TD N1 C2 SING N N 4 3TD N1 C6 SING N N 5 3TD N1 HN1 SING N N 6 3TD C2 O2 DOUB N N 7 3TD C2 N3 SING N N 8 3TD N3 C4 SING N N 9 3TD N3 C10 SING N N 10 3TD C4 O4 DOUB N N 11 3TD C4 C5 SING N N 12 3TD C5 C6 DOUB N N 13 3TD C5 "C1'" SING N N 14 3TD C6 H6 SING N N 15 3TD "C1'" "C2'" SING N N 16 3TD "C1'" "O4'" SING N N 17 3TD "C1'" "H1'" SING N N 18 3TD C10 H10 SING N N 19 3TD C10 H10A SING N N 20 3TD C10 H10B SING N N 21 3TD "C2'" "O2'" SING N N 22 3TD "C2'" "C3'" SING N N 23 3TD "C2'" "H2'" SING N N 24 3TD "O2'" "HO2'" SING N N 25 3TD "C3'" "O3'" SING N N 26 3TD "C3'" "C4'" SING N N 27 3TD "C3'" "H3'" SING N N 28 3TD "O3'" "HO3'" SING N N 29 3TD "C4'" "O4'" SING N N 30 3TD "C4'" "C5'" SING N N 31 3TD "C4'" "H4'" SING N N 32 3TD "C5'" "O5'" SING N N 33 3TD "C5'" "H5'" SING N N 34 3TD "C5'" "H5'A" SING N N 35 3TD P O9 SING N N 36 3TD OP1 H14 SING N N 37 3TD O9 H15 SING N N 38 # 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 3TD SMILES ACDLabs 12.01 "O=C1NC=C(C(=O)N1C)C2OC(COP(=O)(O)O)C(O)C2O" 3TD InChI InChI 1.03 "InChI=1S/C10H15N2O9P/c1-12-9(15)4(2-11-10(12)16)8-7(14)6(13)5(21-8)3-20-22(17,18)19/h2,5-8,13-14H,3H2,1H3,(H,11,16)(H2,17,18,19)/t5-,6-,7-,8+/m1/s1" 3TD InChIKey InChI 1.03 XBPGZENOIJPXSD-XUTVFYLZSA-N 3TD SMILES_CANONICAL CACTVS 3.370 "CN1C(=O)NC=C([C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O)C1=O" 3TD SMILES CACTVS 3.370 "CN1C(=O)NC=C([CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O)C1=O" 3TD SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "CN1C(=O)C(=CNC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O" 3TD SMILES "OpenEye OEToolkits" 1.7.6 "CN1C(=O)C(=CNC1=O)C2C(C(C(O2)COP(=O)(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 3TD "SYSTEMATIC NAME" ACDLabs 12.01 "(1S)-1,4-anhydro-1-(3-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-5-O-phosphono-D-ribitol" 3TD "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2R,3S,4R,5S)-5-[3-methyl-2,4-bis(oxidanylidene)-1H-pyrimidin-5-yl]-3,4-bis(oxidanyl)oxolan-2-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 3TD "Create component" 2011-01-18 RCSB 3TD "Modify descriptor" 2011-06-04 RCSB 3TD "Modify leaving atom flag" 2011-12-14 RCSB #