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               DT 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     1998-07-29 
_chem_comp.pdbx_modified_date                    2018-03-14 
_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                        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        Corina 
_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  -4.571 -1.370 -0.084 P      T38 1  
T38 O1P    O1P    O 0 1 N N N 11.966 4.955  4.715  -4.308 -1.823 -1.468 O1P    T38 2  
T38 O2P    O2P    O 0 1 N N N 9.983  3.597  4.245  -5.701 -0.223 -0.100 O2P    T38 3  
T38 O3P    O3P    O 0 1 N Y N 10.874 3.608  6.597  -5.082 -2.614 0.800  O3P    T38 4  
T38 "O5'"  "O5'"  O 0 1 N N N 9.770  5.618  5.679  -3.216 -0.779 0.554  "O5'"  T38 5  
T38 "C5'"  "C5'"  C 0 1 N N N 9.469  6.568  4.659  -2.458 0.266  -0.060 "C5'"  T38 6  
T38 "C4'"  "C4'"  C 0 1 N N R 8.380  7.490  5.121  -1.237 0.585  0.805  "C4'"  T38 7  
T38 "O4'"  "O4'"  O 0 1 N N N 7.125  6.763  5.242  -0.337 -0.536 0.813  "O4'"  T38 8  
T38 "C3'"  "C3'"  C 0 1 N N R 8.580  8.048  6.517  -0.471 1.782  0.208  "C3'"  T38 9  
T38 "O3'"  "O3'"  O 0 1 N N N 9.499  9.126  6.512  -0.418 2.859  1.146  "O3'"  T38 10 
T38 "C2'"  "C2'"  C 0 1 N N R 7.170  8.505  6.858  0.949  1.228  -0.062 "C2'"  T38 11 
T38 "O2'"  "O2'"  O 0 1 N N N 6.865  9.702  6.164  1.947  2.187  0.294  "O2'"  T38 12 
T38 "C1'"  "C1'"  C 0 1 N N R 6.363  7.324  6.311  1.002  -0.001 0.881  "C1'"  T38 13 
T38 N1     N1     N 0 1 N N N 6.179  6.288  7.342  1.975  -0.983 0.394  N1     T38 14 
T38 C2     C2     C 0 1 N N N 5.117  6.419  8.199  1.811  -1.538 -0.820 C2     T38 15 
T38 O2     O2     O 0 1 N N N 4.325  7.331  8.123  0.855  -1.219 -1.501 O2     T38 16 
T38 N3     N3     N 0 1 N N N 5.019  5.437  9.145  2.689  -2.443 -1.292 N3     T38 17 
T38 C4     C4     C 0 1 N N N 5.860  4.362  9.320  3.753  -2.807 -0.549 C4     T38 18 
T38 O4     O4     O 0 1 N N N 5.656  3.576  10.243 4.549  -3.625 -0.976 O4     T38 19 
T38 C5     C5     C 0 1 N N N 6.941  4.269  8.360  3.938  -2.231 0.730  C5     T38 20 
T38 C5M    C5M    C 0 1 N N N 7.878  3.112  8.420  5.120  -2.621 1.580  C5M    T38 21 
T38 C6     C6     C 0 1 N N N 7.047  5.227  7.439  3.045  -1.322 1.177  C6     T38 22 
T38 "CA'"  "CA'"  C 0 1 N N N 5.586  10.284 6.378  2.338  3.045  -0.780 "CA'"  T38 23 
T38 "CB'"  "CB'"  C 0 1 N N N 5.052  10.183 4.104  1.261  5.053  -0.035 "CB'"  T38 24 
T38 "OC'"  "OC'"  O 0 1 N N N 4.682  9.741  5.424  1.312  4.013  -1.013 "OC'"  T38 25 
T38 "CD'"  "CD'"  C 0 1 N N N 4.867  9.180  3.093  0.133  6.026  -0.384 "CD'"  T38 26 
T38 H2P    H2P    H 0 1 N N N 10.469 3.638  3.430  -5.924 0.121  0.776  H2P    T38 27 
T38 H3P    H3P    H 0 1 N N N 11.790 3.521  6.835  -5.896 -3.021 0.474  H3P    T38 28 
T38 "H5'1" "H5'1" H 0 0 N N N 10.371 7.155  4.431  -2.129 -0.056 -1.048 "H5'1" T38 29 
T38 "H5'2" "H5'2" H 0 0 N N N 9.138  6.038  3.754  -3.078 1.157  -0.155 "H5'2" T38 30 
T38 "H4'"  "H4'"  H 0 1 N N N 8.272  8.320  4.408  -1.553 0.815  1.822  "H4'"  T38 31 
T38 "H3'"  "H3'"  H 0 1 N N N 8.895  7.249  7.204  -0.938 2.109  -0.721 "H3'"  T38 32 
T38 HA     HA     H 0 1 N N N 9.606  9.456  7.396  -1.285 3.207  1.395  HA     T38 33 
T38 "H2'"  "H2'"  H 0 1 N N N 7.038  8.600  7.946  1.057  0.925  -1.103 "H2'"  T38 34 
T38 "H1'"  "H1'"  H 0 1 N N N 5.387  7.682  5.952  1.242  0.306  1.899  "H1'"  T38 35 
T38 H3     H3     H 0 1 N N N 4.250  5.508  9.781  2.555  -2.833 -2.170 H3     T38 36 
T38 H5M1   H5M1   H 0 0 N N N 8.629  3.206  7.622  5.722  -3.358 1.048  H5M1   T38 37 
T38 H5M2   H5M2   H 0 0 N N N 8.382  3.099  9.398  5.725  -1.739 1.789  H5M2   T38 38 
T38 H5M3   H5M3   H 0 0 N N N 7.315  2.177  8.285  4.767  -3.050 2.518  H5M3   T38 39 
T38 H6     H6     H 0 1 N N N 7.860  5.166  6.730  3.172  -0.868 2.148  H6     T38 40 
T38 "HA'1" "HA'1" H 0 0 N N N 5.237  10.051 7.395  3.265  3.555  -0.518 "HA'1" T38 41 
T38 "HA'2" "HA'2" H 0 0 N N N 5.648  11.375 6.252  2.490  2.452  -1.681 "HA'2" T38 42 
T38 "HB'1" "HB'1" H 0 0 N N N 4.437  11.057 3.844  1.075  4.619  0.947  "HB'1" T38 43 
T38 "HB'2" "HB'2" H 0 0 N N N 6.113  10.472 4.118  2.211  5.587  -0.023 "HB'2" T38 44 
T38 "HD'1" "HD'1" H 0 0 N N N 5.168  9.584  2.115  0.318  6.460  -1.367 "HD'1" T38 45 
T38 "HD'2" "HD'2" H 0 0 N N N 5.484  8.301  3.332  -0.817 5.491  -0.397 "HD'2" T38 46 
T38 "HD'3" "HD'3" H 0 0 N N N 3.808  8.886  3.058  0.093  6.819  0.362  "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              12.01 "P(=O)(O)(O)OCC1OC(C(C1O)OCOCC)N2C(=O)NC(=O)C(C)=C2"                                                                                                                            
T38 InChI            InChI                1.03  "InChI=1S/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" 
T38 InChIKey         InChI                1.03  ZHEHKUXUPODKJV-DNRKLUKYSA-N                                                                                                                                                     
T38 SMILES_CANONICAL CACTVS               3.385 "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               3.385 "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" 1.7.6 "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" 1.7.6 "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              12.01 
;2'-O-(ethoxymethyl)-5-methyluridine 5'-(dihydrogen phosphate)
;
T38 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2R,3R,4R,5R)-4-(ethoxymethoxy)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-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 
T38 "Create component"      1998-07-29 RCSB 
T38 "Modify descriptor"     2011-06-04 RCSB 
T38 "Modify parent residue" 2018-03-14 RCSB 
# 
