data_T39
# 
_chem_comp.id                                    T39 
_chem_comp.name                                  
;2'-O-METHOXYETHYLENE 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                    2013-01-10 
_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                     T39 
_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        411D 
_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 
T39 P      P      P 0 1 N N N -4.559 6.080 7.621  5.145  0.075  -0.028 P      T39 1  
T39 OP1    OP1    O 0 1 N N N -5.756 6.865 7.275  5.833  -1.194 -0.354 OP1    T39 2  
T39 OP2    OP2    O 0 1 N N N -4.719 4.826 8.388  5.009  0.969  -1.360 OP2    T39 3  
T39 "O5'"  "O5'"  O 0 1 N N N -3.686 5.796 6.315  3.678  -0.245 0.555  "O5'"  T39 4  
T39 "C5'"  "C5'"  C 0 1 N N N -3.385 6.839 5.374  2.719  -1.040 -0.145 "C5'"  T39 5  
T39 "C4'"  "C4'"  C 0 1 N N R -2.338 6.393 4.391  1.439  -1.144 0.688  "C4'"  T39 6  
T39 "O4'"  "O4'"  O 0 1 N N N -1.089 6.154 5.094  0.814  0.147  0.786  "O4'"  T39 7  
T39 "C3'"  "C3'"  C 0 1 N N R -2.591 5.077 3.659  0.438  -2.086 -0.008 "C3'"  T39 8  
T39 "O3'"  "O3'"  O 0 1 N N N -3.489 5.187 2.560  0.127  -3.197 0.837  "O3'"  T39 9  
T39 "C2'"  "C2'"  C 0 1 N N R -1.195 4.716 3.194  -0.816 -1.207 -0.234 "C2'"  T39 10 
T39 "O2'"  "O2'"  O 0 1 N N N -0.823 5.499 2.077  -2.011 -1.942 0.039  "O2'"  T39 11 
T39 "C1'"  "C1'"  C 0 1 N N R -0.383 5.106 4.435  -0.613 -0.077 0.806  "C1'"  T39 12 
T39 N1     N1     N 0 1 N N N -0.202 3.962 5.361  -1.330 1.134  0.399  N1     T39 13 
T39 C2     C2     C 0 1 N N N 0.885  3.135 5.134  -0.963 1.781  -0.722 C2     T39 14 
T39 O2     O2     O 0 1 N N N 1.671  3.278 4.215  -0.039 1.353  -1.385 O2     T39 15 
T39 N3     N3     N 0 1 N N N 1.020  2.113 6.022  -1.605 2.895  -1.119 N3     T39 16 
T39 C4     C4     C 0 1 N N N 0.200  1.824 7.089  -2.632 3.383  -0.394 C4     T39 17 
T39 O4     O4     O 0 1 N N N 0.467  0.862 7.799  -3.214 4.391  -0.753 O4     T39 18 
T39 C5     C5     C 0 1 N N N -0.924 2.713 7.270  -3.029 2.712  0.788  C5     T39 19 
T39 C7     C7     C 0 1 N N N -1.876 2.466 8.406  -4.173 3.236  1.616  C7     T39 20 
T39 C6     C6     C 0 1 N N N -1.069 3.733 6.415  -2.371 1.593  1.160  C6     T39 21 
T39 "CA'"  "CA'"  C 0 1 N N N 0.493  5.193 1.578  -2.561 -2.602 -1.103 "CA'"  T39 22 
T39 "CD'"  "CD'"  C 0 1 N N N 0.035  7.582 -0.306 -6.059 -3.017 0.120  "CD'"  T39 23 
T39 "CB'"  "CB'"  C 0 1 N N N 1.293  6.397 1.442  -3.830 -3.353 -0.696 "CB'"  T39 24 
T39 "OC'"  "OC'"  O 0 1 N N N 0.497  7.548 1.068  -4.827 -2.416 -0.284 "OC'"  T39 25 
T39 OP3    OP3    O 0 1 N Y N -3.667 7.084 8.485  5.997  0.881  1.075  OP3    T39 26 
T39 HOP2   HOP2   H 0 0 N N N -5.640 4.681 8.570  4.566  1.817  -1.221 HOP2   T39 27 
T39 "H5'"  "H5'"  H 0 1 N N N -3.014 7.719 5.919  2.492  -0.575 -1.104 "H5'"  T39 28 
T39 "H5''" "H5''" H 0 0 N N N -4.301 7.105 4.827  3.126  -2.037 -0.312 "H5''" T39 29 
T39 "H4'"  "H4'"  H 0 1 N N N -2.192 7.186 3.643  1.674  -1.519 1.684  "H4'"  T39 30 
T39 "H3'"  "H3'"  H 0 1 N N N -2.944 4.323 4.378  0.838  -2.433 -0.960 "H3'"  T39 31 
T39 "HO3'" "HO3'" H 0 0 N Y N -4.355 5.414 2.879  0.890  -3.749 1.057  "HO3'" T39 32 
T39 H7     H7     H 0 1 N N N -1.112 3.637 2.999  -0.832 -0.805 -1.247 H7     T39 33 
T39 "H1'"  "H1'"  H 0 1 N N N 0.604  5.465 4.108  -0.936 -0.402 1.795  "H1'"  T39 34 
T39 H3     H3     H 0 1 N N N 1.801  1.504 5.884  -1.328 3.350  -1.930 H3     T39 35 
T39 H71    H71    H 0 1 N N N -1.554 1.577 8.968  -4.575 4.137  1.153  H71    T39 36 
T39 H72    H72    H 0 1 N N N -1.883 3.339 9.075  -4.955 2.479  1.676  H72    T39 37 
T39 H73    H73    H 0 1 N N N -2.888 2.301 8.007  -3.818 3.471  2.619  H73    T39 38 
T39 H6     H6     H 0 1 N N N -1.901 4.408 6.554  -2.661 1.066  2.057  H6     T39 39 
T39 HCA2   HCA2   H 0 0 N N N 0.401  4.710 0.594  -2.806 -1.863 -1.867 HCA2   T39 40 
T39 HCA1   HCA1   H 0 0 N N N 0.992  4.507 2.278  -1.833 -3.308 -1.501 HCA1   T39 41 
T39 HCD1   HCD1   H 0 0 N N N -0.555 8.495 -0.473 -6.476 -3.585 -0.712 HCD1   T39 42 
T39 HCD2   HCD2   H 0 0 N N N 0.901  7.576 -0.984 -5.879 -3.686 0.961  HCD2   T39 43 
T39 HCD3   HCD3   H 0 0 N N N -0.592 6.700 -0.504 -6.763 -2.240 0.417  HCD3   T39 44 
T39 HCB1   HCB1   H 0 0 N N N 2.056  6.229 0.668  -4.201 -3.928 -1.545 HCB1   T39 45 
T39 HCB2   HCB2   H 0 0 N N N 1.785  6.605 2.404  -3.604 -4.029 0.129  HCB2   T39 46 
T39 HOP3   HOP3   H 0 0 N Y N -4.114 7.919 8.562  6.893  1.107  0.791  HOP3   T39 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 
T39 "CD'" "OC'"  SING N N 1  
T39 "OC'" "CB'"  SING N N 2  
T39 "CB'" "CA'"  SING N N 3  
T39 "CA'" "O2'"  SING N N 4  
T39 "O2'" "C2'"  SING N N 5  
T39 "O3'" "C3'"  SING N N 6  
T39 "C2'" "C3'"  SING N N 7  
T39 "C2'" "C1'"  SING N N 8  
T39 "C3'" "C4'"  SING N N 9  
T39 O2    C2     DOUB N N 10 
T39 "C4'" "O4'"  SING N N 11 
T39 "C4'" "C5'"  SING N N 12 
T39 "C1'" "O4'"  SING N N 13 
T39 "C1'" N1     SING N N 14 
T39 C2    N1     SING N N 15 
T39 C2    N3     SING N N 16 
T39 N1    C6     SING N N 17 
T39 "C5'" "O5'"  SING N N 18 
T39 N3    C4     SING N N 19 
T39 "O5'" P      SING N N 20 
T39 C6    C5     DOUB N N 21 
T39 C4    C5     SING N N 22 
T39 C4    O4     DOUB N N 23 
T39 C5    C7     SING N N 24 
T39 OP1   P      DOUB N N 25 
T39 P     OP2    SING N N 26 
T39 P     OP3    SING N N 27 
T39 OP2   HOP2   SING N N 28 
T39 "C5'" "H5'"  SING N N 29 
T39 "C5'" "H5''" SING N N 30 
T39 "C4'" "H4'"  SING N N 31 
T39 "C3'" "H3'"  SING N N 32 
T39 "O3'" "HO3'" SING N N 33 
T39 "C2'" H7     SING N N 34 
T39 "C1'" "H1'"  SING N N 35 
T39 N3    H3     SING N N 36 
T39 C7    H71    SING N N 37 
T39 C7    H72    SING N N 38 
T39 C7    H73    SING N N 39 
T39 C6    H6     SING N N 40 
T39 "CA'" HCA2   SING N N 41 
T39 "CA'" HCA1   SING N N 42 
T39 "CD'" HCD1   SING N N 43 
T39 "CD'" HCD2   SING N N 44 
T39 "CD'" HCD3   SING N N 45 
T39 "CB'" HCB1   SING N N 46 
T39 "CB'" HCB2   SING N N 47 
T39 OP3   HOP3   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 
T39 SMILES           ACDLabs              12.01 "O=P(O)(O)OCC2OC(N1C(=O)NC(=O)C(=C1)C)C(OCCOC)C2O"                                                                                                                             
T39 InChI            InChI                1.03  "InChI=1S/C13H21N2O10P/c1-7-5-15(13(18)14-11(7)17)12-10(23-4-3-22-2)9(16)8(25-12)6-24-26(19,20)21/h5,8-10,12,16H,3-4,6H2,1-2H3,(H,14,17,18)(H2,19,20,21)/t8-,9-,10-,12-/m1/s1" 
T39 InChIKey         InChI                1.03  BLSQXXFKLSKRRX-DNRKLUKYSA-N                                                                                                                                                    
T39 SMILES_CANONICAL CACTVS               3.370 "COCCO[C@@H]1[C@H](O)[C@@H](CO[P](O)(O)=O)O[C@H]1N2C=C(C)C(=O)NC2=O"                                                                                                           
T39 SMILES           CACTVS               3.370 "COCCO[CH]1[CH](O)[CH](CO[P](O)(O)=O)O[CH]1N2C=C(C)C(=O)NC2=O"                                                                                                                 
T39 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "CC1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)OCCOC"                                                                                                           
T39 SMILES           "OpenEye OEToolkits" 1.7.6 "CC1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)OCCOC"                                                                                                                             
# 
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 
T39 "SYSTEMATIC NAME" ACDLabs              12.01 
;2'-O-(2-methoxyethyl)-5-methyluridine 5'-(dihydrogen phosphate)
;
T39 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2R,3R,4R,5R)-4-(2-methoxyethoxy)-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 
T39 "Create component"         1998-07-29 RCSB 
T39 "Modify descriptor"        2011-06-04 RCSB 
T39 "Modify component atom id" 2013-01-10 RCSB 
# 
