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                    2009-02-06 
_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 InChI            InChI                1.02b InChI=1/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/f/h16H 
T3S InChIKey         InChI                1.02b GMOUOGHZJCSNOZ-IZLTVBEBDH                                                                                                                             
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                                                                                                               
# 
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 
# 
