data_T38
# 
_chem_comp.id                                    T38 
_chem_comp.name                                  
;2'-O-ETHOXYMETHYLENE THYMIDINE 5'-MONOPHOSPHATE
;
_chem_comp.type                                  "RNA LINKING" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C13 H21 N2 O10 P" 
_chem_comp.mon_nstd_parent_comp_id               T 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     1998-07-29 
_chem_comp.pdbx_modified_date                    2009-01-07 
_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                        396.287 
_chem_comp.one_letter_code                       T 
_chem_comp.three_letter_code                     T38 
_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        410D 
_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 
T38 P      P    P 0 1 N N N 10.758 4.422  5.368  -1.112 -0.156 -4.565 P      T38 1  
T38 O1P    O1P  O 0 1 N N N 11.966 4.955  4.715  -1.427 -1.544 -4.158 O1P    T38 2  
T38 O2P    O2P  O 0 1 N N N 9.983  3.597  4.245  0.212  -0.153 -5.480 O2P    T38 3  
T38 O3P    O3P  O 0 1 N Y N 10.874 3.608  6.597  -2.345 0.450  -5.404 O3P    T38 4  
T38 "O5'"  O5*  O 0 1 N N N 9.770  5.618  5.679  -0.860 0.742  -3.254 "O5'"  T38 5  
T38 "C5'"  C5*  C 0 1 N N N 9.469  6.568  4.659  0.240  0.156  -2.556 "C5'"  T38 6  
T38 "C4'"  C4*  C 0 1 N N R 8.380  7.490  5.121  0.532  0.967  -1.292 "C4'"  T38 7  
T38 "O4'"  O4*  O 0 1 N N N 7.125  6.763  5.242  -0.603 0.935  -0.412 "O4'"  T38 8  
T38 "C3'"  C3*  C 0 1 N N R 8.580  8.048  6.517  1.718  0.343  -0.531 "C3'"  T38 9  
T38 "O3'"  O3*  O 0 1 N N N 9.499  9.126  6.512  2.793  1.278  -0.420 "O3'"  T38 10 
T38 "C2'"  C2*  C 0 1 N N R 7.170  8.505  6.858  1.141  0.012  0.866  "C2'"  T38 11 
T38 "O2'"  O2*  O 0 1 N N N 6.865  9.702  6.164  2.081  0.329  1.894  "O2'"  T38 12 
T38 "C1'"  C1*  C 0 1 N N R 6.363  7.324  6.311  -0.092 0.948  0.937  "C1'"  T38 13 
T38 N1     N1   N 0 1 N N N 6.179  6.288  7.342  -1.091 0.421  1.872  N1     T38 14 
T38 C2     C2   C 0 1 N N N 5.117  6.419  8.199  -1.572 -0.823 1.701  C2     T38 15 
T38 O2     O2   O 0 1 N N N 4.325  7.331  8.123  -1.168 -1.500 0.775  O2     T38 16 
T38 N3     N3   N 0 1 N N N 5.019  5.437  9.145  -2.486 -1.333 2.547  N3     T38 17 
T38 C4     C4   C 0 1 N N N 5.860  4.362  9.320  -2.943 -0.596 3.579  C4     T38 18 
T38 O4     O4   O 0 1 N N N 5.656  3.576  10.243 -3.774 -1.055 4.342  O4     T38 19 
T38 C5     C5   C 0 1 N N N 6.941  4.269  8.360  -2.450 0.717  3.767  C5     T38 20 
T38 C5M    C5M  C 0 1 N N N 7.878  3.112  8.420  -2.945 1.562  4.912  C5M    T38 21 
T38 C6     C6   C 0 1 N N N 7.047  5.227  7.439  -1.529 1.202  2.906  C6     T38 22 
T38 "CA'"  CA*  C 0 1 N N N 5.586  10.284 6.378  2.802  -0.871 2.178  "CA'"  T38 23 
T38 "CB'"  CB*  C 0 1 N N N 5.052  10.183 4.104  5.021  -0.302 2.040  "CB'"  T38 24 
T38 "OC'"  OC*  O 0 1 N N N 4.682  9.741  5.424  3.955  -0.944 1.337  "OC'"  T38 25 
T38 "CD'"  CD*  C 0 1 N N N 4.867  9.180  3.093  6.292  -0.346 1.190  "CD'"  T38 26 
T38 H2P    H2P  H 0 1 N N N 9.203  3.253  4.666  0.382  0.767  -5.723 H2P    T38 27 
T38 H3P    H3P  H 0 1 N N N 10.094 3.264  7.018  -2.462 -0.116 -6.178 H3P    T38 28 
T38 "H5'1" 1H5* H 0 0 N N N 9.217  6.076  3.691  1.119  0.156  -3.199 "H5'1" T38 29 
T38 "H5'2" 2H5* H 0 0 N N N 10.376 7.126  4.327  -0.009 -0.868 -2.280 "H5'2" T38 30 
T38 "H4'"  H4*  H 0 1 N N N 8.262  8.327  4.394  0.765  1.998  -1.559 "H4'"  T38 31 
T38 "H3'"  H3*  H 0 1 N N N 8.915  7.248  7.217  2.055  -0.565 -1.030 "H3'"  T38 32 
T38 HA     HA   H 0 1 N N N 9.624  9.476  7.386  3.112  1.446  -1.318 HA     T38 33 
T38 "H2'"  H2*  H 0 1 N N N 7.031  8.622  7.958  0.840  -1.033 0.925  "H2'"  T38 34 
T38 "H1'"  H1*  H 0 1 N N N 5.373  7.674  5.936  0.206  1.955  1.225  "H1'"  T38 35 
T38 H3     H3   H 0 1 N N N 4.235  5.509  9.793  -2.819 -2.234 2.412  H3     T38 36 
T38 H5M1   1H5M H 0 0 N N N 7.789  2.311  9.190  -3.678 0.999  5.488  H5M1   T38 37 
T38 H5M2   2H5M H 0 0 N N N 8.914  3.520  8.475  -2.106 1.831  5.554  H5M2   T38 38 
T38 H5M3   3H5M H 0 0 N N N 7.871  2.620  7.419  -3.408 2.468  4.520  H5M3   T38 39 
T38 H6     H6   H 0 1 N N N 7.877  5.165  6.715  -1.141 2.202  3.034  H6     T38 40 
T38 "HA'1" 1HA* H 0 0 N N N 5.613  11.399 6.358  2.161  -1.732 1.991  "HA'1" T38 41 
T38 "HA'2" 2HA* H 0 0 N N N 5.228  10.160 7.427  3.114  -0.869 3.222  "HA'2" T38 42 
T38 "HB'1" 1HB* H 0 0 N N N 6.099  10.565 4.094  5.197  -0.818 2.984  "HB'1" T38 43 
T38 "HB'2" 2HB* H 0 0 N N N 4.511  11.120 3.835  4.752  0.735  2.238  "HB'2" T38 44 
T38 "HD'1" 1HD* H 0 0 N N N 5.153  9.522  2.071  7.105  0.144  1.727  "HD'1" T38 45 
T38 "HD'2" 2HD* H 0 0 N N N 3.820  8.798  3.103  6.561  -1.383 0.992  "HD'2" T38 46 
T38 "HD'3" 3HD* H 0 0 N N N 5.408  8.243  3.362  6.116  0.170  0.247  "HD'3" T38 47 
# 
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 
T38 P     O1P    DOUB N N 1  
T38 P     O2P    SING N N 2  
T38 P     O3P    SING N N 3  
T38 P     "O5'"  SING N N 4  
T38 O2P   H2P    SING N N 5  
T38 O3P   H3P    SING N N 6  
T38 "O5'" "C5'"  SING N N 7  
T38 "C5'" "C4'"  SING N N 8  
T38 "C5'" "H5'1" SING N N 9  
T38 "C5'" "H5'2" SING N N 10 
T38 "C4'" "O4'"  SING N N 11 
T38 "C4'" "C3'"  SING N N 12 
T38 "C4'" "H4'"  SING N N 13 
T38 "O4'" "C1'"  SING N N 14 
T38 "C3'" "O3'"  SING N N 15 
T38 "C3'" "C2'"  SING N N 16 
T38 "C3'" "H3'"  SING N N 17 
T38 "O3'" HA     SING N N 18 
T38 "C2'" "O2'"  SING N N 19 
T38 "C2'" "C1'"  SING N N 20 
T38 "C2'" "H2'"  SING N N 21 
T38 "O2'" "CA'"  SING N N 22 
T38 "C1'" N1     SING N N 23 
T38 "C1'" "H1'"  SING N N 24 
T38 N1    C2     SING N N 25 
T38 N1    C6     SING N N 26 
T38 C2    O2     DOUB N N 27 
T38 C2    N3     SING N N 28 
T38 N3    C4     SING N N 29 
T38 N3    H3     SING N N 30 
T38 C4    O4     DOUB N N 31 
T38 C4    C5     SING N N 32 
T38 C5    C5M    SING N N 33 
T38 C5    C6     DOUB N N 34 
T38 C5M   H5M1   SING N N 35 
T38 C5M   H5M2   SING N N 36 
T38 C5M   H5M3   SING N N 37 
T38 C6    H6     SING N N 38 
T38 "CA'" "OC'"  SING N N 39 
T38 "CA'" "HA'1" SING N N 40 
T38 "CA'" "HA'2" SING N N 41 
T38 "CB'" "OC'"  SING N N 42 
T38 "CB'" "CD'"  SING N N 43 
T38 "CB'" "HB'1" SING N N 44 
T38 "CB'" "HB'2" SING N N 45 
T38 "CD'" "HD'1" SING N N 46 
T38 "CD'" "HD'2" SING N N 47 
T38 "CD'" "HD'3" SING N N 48 
# 
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 
T38 SMILES           ACDLabs              10.04 "O=C1NC(=O)N(C=C1C)C2OC(C(O)C2OCOCC)COP(=O)(O)O"                                                                                                                                            
T38 InChI            InChI                1.02b "InChI=1/C13H21N2O10P/c1-3-22-6-23-10-9(16)8(5-24-26(19,20)21)25-12(10)15-4-7(2)11(17)14-13(15)18/h4,8-10,12,16H,3,5-6H2,1-2H3,(H,14,17,18)(H2,19,20,21)/t8-,9-,10-,12-/m1/s1/f/h14,19-20H" 
T38 InChIKey         InChI                1.02b ZHEHKUXUPODKJV-IHXBBRRKDE                                                                                                                                                                   
T38 SMILES_CANONICAL CACTVS               3.341 "CCOCO[C@@H]1[C@H](O)[C@@H](CO[P](O)(O)=O)O[C@H]1N2C=C(C)C(=O)NC2=O"                                                                                                                        
T38 SMILES           CACTVS               3.341 "CCOCO[CH]1[CH](O)[CH](CO[P](O)(O)=O)O[CH]1N2C=C(C)C(=O)NC2=O"                                                                                                                              
T38 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CCOCO[C@@H]1[C@@H]([C@H](O[C@H]1N2C=C(C(=O)NC2=O)C)COP(=O)(O)O)O"                                                                                                                          
T38 SMILES           "OpenEye OEToolkits" 1.5.0 "CCOCOC1C(C(OC1N2C=C(C(=O)NC2=O)C)COP(=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 
T38 "SYSTEMATIC NAME" ACDLabs              10.04 
;2'-O-(ethoxymethyl)-5-methyluridine 5'-(dihydrogen phosphate)
;
T38 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3R,4R,5R)-4-(ethoxymethoxy)-3-hydroxy-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methyl dihydrogen phosphate" 
# 
