data_T3S # _chem_comp.id T3S _chem_comp.name "5'-deoxy-5'-piperidin-1-ylthymidine" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C15 H23 N3 O4" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2008-05-28 _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 309.361 _chem_comp.one_letter_code ? _chem_comp.three_letter_code T3S _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 3D8Y _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 T3S C21 C21 C 0 1 N N N 42.227 -1.716 14.753 3.993 -1.012 1.319 C21 T3S 1 T3S C22 C22 C 0 1 N N N 43.125 -2.880 15.205 4.647 -2.285 0.777 C22 T3S 2 T3S C23 C23 C 0 1 N N N 42.662 -4.236 14.633 5.495 -1.936 -0.448 C23 T3S 3 T3S C24 C24 C 0 1 N N N 41.914 -4.107 13.293 4.607 -1.266 -1.500 C24 T3S 4 T3S C25 C25 C 0 1 N N N 40.751 -3.093 13.350 3.954 -0.022 -0.892 C25 T3S 5 T3S N26 N26 N 0 1 N N N 40.845 -2.194 14.531 3.154 -0.409 0.276 N26 T3S 6 T3S "C5'" "C5'" C 0 1 N N N 39.882 -1.051 14.542 2.402 0.738 0.803 "C5'" T3S 7 T3S "C4'" "C4'" C 0 1 N N R 39.470 -0.466 13.145 1.362 1.183 -0.227 "C4'" T3S 8 T3S "O4'" "O4'" O 0 1 N N N 38.720 -1.362 12.259 0.352 0.166 -0.401 "O4'" T3S 9 T3S "C3'" "C3'" C 0 1 N N S 38.511 0.685 13.421 0.561 2.402 0.297 "C3'" T3S 10 T3S "O3'" "O3'" O 0 1 N N N 38.591 1.627 12.340 1.237 3.624 -0.005 "O3'" T3S 11 T3S "C2'" "C2'" C 0 1 N N N 37.138 0.007 13.396 -0.760 2.290 -0.502 "C2'" T3S 12 T3S "C1'" "C1'" C 0 1 N N R 37.315 -0.937 12.213 -0.808 0.815 -0.948 "C1'" T3S 13 T3S N1 N1 N 0 1 N N N 36.473 -2.158 12.290 -2.024 0.179 -0.435 N1 T3S 14 T3S C6 C6 C 0 1 N N N 36.863 -3.219 13.131 -2.974 -0.273 -1.310 C6 T3S 15 T3S C5 C5 C 0 1 N N N 36.096 -4.381 13.212 -4.094 -0.860 -0.837 C5 T3S 16 T3S C5M C5M C 0 1 N N N 36.553 -5.517 14.138 -5.150 -1.365 -1.786 C5M T3S 17 T3S C4 C4 C 0 1 N N N 34.930 -4.488 12.445 -4.262 -0.996 0.562 C4 T3S 18 T3S O4 O4 O 0 1 N N N 34.225 -5.498 12.494 -5.264 -1.522 1.012 O4 T3S 19 T3S N3 N3 N 0 1 N N N 34.537 -3.437 11.602 -3.303 -0.537 1.391 N3 T3S 20 T3S C2 C2 C 0 1 N N N 35.300 -2.263 11.513 -2.194 0.040 0.893 C2 T3S 21 T3S O2 O2 O 0 1 N N N 34.928 -1.346 10.777 -1.336 0.445 1.653 O2 T3S 22 T3S H21 H21 H 0 1 N N N 42.221 -0.939 15.532 3.377 -1.259 2.184 H21 T3S 23 T3S H21A H21A H 0 0 N N N 42.620 -1.303 13.812 4.767 -0.304 1.616 H21A T3S 24 T3S H22 H22 H 0 1 N N N 44.150 -2.686 14.857 5.282 -2.724 1.547 H22 T3S 25 T3S H22A H22A H 0 0 N N N 43.071 -2.941 16.302 3.873 -2.998 0.493 H22A T3S 26 T3S H23 H23 H 0 1 N N N 43.551 -4.863 14.472 6.293 -1.252 -0.157 H23 T3S 27 T3S H23A H23A H 0 0 N N N 41.963 -4.677 15.358 5.928 -2.846 -0.863 H23A T3S 28 T3S H24 H24 H 0 1 N N N 42.629 -3.771 12.528 5.213 -0.976 -2.358 H24 T3S 29 T3S H24A H24A H 0 0 N N N 41.485 -5.092 13.056 3.832 -1.963 -1.820 H24A T3S 30 T3S H25 H25 H 0 1 N N N 40.778 -2.478 12.439 4.729 0.681 -0.585 H25 T3S 31 T3S H25A H25A H 0 0 N N N 39.811 -3.660 13.430 3.310 0.449 -1.634 H25A T3S 32 T3S "H5'" "H5'" H 0 1 N N N 38.962 -1.406 15.029 1.899 0.450 1.726 "H5'" T3S 33 T3S "H5'A" "H5'A" H 0 0 N N N 40.402 -0.233 15.062 3.088 1.561 1.004 "H5'A" T3S 34 T3S "H4'" "H4'" H 0 1 N N N 40.417 -0.220 12.642 1.840 1.415 -1.179 "H4'" T3S 35 T3S "H3'" "H3'" H 0 1 N N N 38.720 1.220 14.359 0.377 2.315 1.367 "H3'" T3S 36 T3S "HO3'" "HO3'" H 0 0 N N N 38.609 2.510 12.690 0.775 4.416 0.303 "HO3'" T3S 37 T3S "H2'" "H2'" H 0 1 N N N 36.913 -0.526 14.332 -1.613 2.523 0.136 "H2'" T3S 38 T3S "H2'A" "H2'A" H 0 0 N N N 36.290 0.701 13.301 -0.739 2.950 -1.369 "H2'A" T3S 39 T3S "H1'" "H1'" H 0 1 N N N 37.022 -0.410 11.293 -0.788 0.756 -2.036 "H1'" T3S 40 T3S H6 H6 H 0 1 N N N 37.765 -3.132 13.719 -2.828 -0.161 -2.374 H6 T3S 41 T3S H5M H5M H 0 1 N N N 36.662 -6.444 13.556 -4.939 -2.402 -2.047 H5M T3S 42 T3S H5MA H5MA H 0 0 N N N 37.520 -5.253 14.592 -6.128 -1.303 -1.308 H5MA T3S 43 T3S H5MB H5MB H 0 0 N N N 35.804 -5.668 14.930 -5.148 -0.756 -2.690 H5MB T3S 44 T3S HN3 HN3 H 0 1 N N N 33.703 -3.526 11.058 -3.412 -0.626 2.351 HN3 T3S 45 # 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 T3S C21 C22 SING N N 1 T3S C21 N26 SING N N 2 T3S C22 C23 SING N N 3 T3S C23 C24 SING N N 4 T3S C24 C25 SING N N 5 T3S C25 N26 SING N N 6 T3S N26 "C5'" SING N N 7 T3S "C5'" "C4'" SING N N 8 T3S "C4'" "O4'" SING N N 9 T3S "C4'" "C3'" SING N N 10 T3S "O4'" "C1'" SING N N 11 T3S "C3'" "O3'" SING N N 12 T3S "C3'" "C2'" SING N N 13 T3S "C2'" "C1'" SING N N 14 T3S "C1'" N1 SING N N 15 T3S N1 C6 SING N N 16 T3S N1 C2 SING N N 17 T3S C6 C5 DOUB N N 18 T3S C5 C5M SING N N 19 T3S C5 C4 SING N N 20 T3S C4 O4 DOUB N N 21 T3S C4 N3 SING N N 22 T3S N3 C2 SING N N 23 T3S C2 O2 DOUB N N 24 T3S C21 H21 SING N N 25 T3S C21 H21A SING N N 26 T3S C22 H22 SING N N 27 T3S C22 H22A SING N N 28 T3S C23 H23 SING N N 29 T3S C23 H23A SING N N 30 T3S C24 H24 SING N N 31 T3S C24 H24A SING N N 32 T3S C25 H25 SING N N 33 T3S C25 H25A SING N N 34 T3S "C5'" "H5'" SING N N 35 T3S "C5'" "H5'A" SING N N 36 T3S "C4'" "H4'" SING N N 37 T3S "C3'" "H3'" SING N N 38 T3S "O3'" "HO3'" SING N N 39 T3S "C2'" "H2'" SING N N 40 T3S "C2'" "H2'A" SING N N 41 T3S "C1'" "H1'" SING N N 42 T3S C6 H6 SING N N 43 T3S C5M H5M SING N N 44 T3S C5M H5MA SING N N 45 T3S C5M H5MB SING N N 46 T3S N3 HN3 SING N N 47 # 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 T3S SMILES ACDLabs 10.04 "O=C1NC(=O)N(C=C1C)C2OC(C(O)C2)CN3CCCCC3" T3S SMILES_CANONICAL CACTVS 3.341 "CC1=CN([C@H]2C[C@H](O)[C@@H](CN3CCCCC3)O2)C(=O)NC1=O" T3S SMILES CACTVS 3.341 "CC1=CN([CH]2C[CH](O)[CH](CN3CCCCC3)O2)C(=O)NC1=O" T3S SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CN3CCCCC3)O" T3S SMILES "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)C2CC(C(O2)CN3CCCCC3)O" T3S InChI InChI 1.03 "InChI=1S/C15H23N3O4/c1-10-8-18(15(21)16-14(10)20)13-7-11(19)12(22-13)9-17-5-3-2-4-6-17/h8,11-13,19H,2-7,9H2,1H3,(H,16,20,21)/t11-,12+,13+/m0/s1" T3S InChIKey InChI 1.03 GMOUOGHZJCSNOZ-YNEHKIRRSA-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 T3S "SYSTEMATIC NAME" ACDLabs 10.04 "5'-deoxy-5'-piperidin-1-ylthymidine" T3S "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "1-[(2R,4S,5R)-4-hydroxy-5-(piperidin-1-ylmethyl)oxolan-2-yl]-5-methyl-pyrimidine-2,4-dione" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site T3S "Create component" 2008-05-28 PDBJ T3S "Modify descriptor" 2011-06-04 RCSB #