data_5HT
# 
_chem_comp.id                                    5HT 
_chem_comp.name                                  5-HYDROXY-THYMIDINE 
_chem_comp.type                                  "DNA LINKING" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C10 H16 N2 O6" 
_chem_comp.mon_nstd_parent_comp_id               DT 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2000-02-24 
_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                        260.244 
_chem_comp.one_letter_code                       T 
_chem_comp.three_letter_code                     5HT 
_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        1EHL 
_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 
5HT "O5'"  O5*  O 0 1 N N N -2.869 61.350 12.333 2.572  0.452  -3.637 "O5'"  5HT 1  
5HT "C5'"  C5*  C 0 1 N N N -1.704 61.611 11.567 1.181  0.775  -3.598 "C5'"  5HT 2  
5HT "C4'"  C4*  C 0 1 N N R -0.472 61.029 12.220 0.420  -0.332 -2.866 "C4'"  5HT 3  
5HT "O4'"  O4*  O 0 1 N N N -0.842 60.618 13.584 0.809  -0.386 -1.474 "O4'"  5HT 4  
5HT "C3'"  C3*  C 0 1 N N S 0.062  59.755 11.606 -1.093 -0.008 -2.809 "C3'"  5HT 5  
5HT "O3'"  O3*  O 0 1 N N N 0.937  59.962 10.500 -1.758 -0.464 -3.989 "O3'"  5HT 6  
5HT "C2'"  C2*  C 0 1 N N N 0.721  59.033 12.761 -1.551 -0.815 -1.570 "C2'"  5HT 7  
5HT "C1'"  C1*  C 0 1 N N R 0.010  59.552 14.016 -0.255 -1.046 -0.769 "C1'"  5HT 8  
5HT N1     N1   N 0 1 N N N -0.761 58.371 14.606 -0.391 -0.478 0.573  N1     5HT 9  
5HT C2     C2   C 0 1 N N N -0.369 57.820 15.683 -0.637 0.833  0.715  C2     5HT 10 
5HT O2     O2   O 0 1 N N N 0.660  58.154 16.218 -0.845 1.508  -0.273 O2     5HT 11 
5HT N3     N3   N 0 1 N N N -1.110 56.782 16.265 -0.658 1.418  1.924  N3     5HT 12 
5HT C4     C4   C 0 1 N N N -2.327 56.295 15.741 -0.201 0.774  3.014  C4     5HT 13 
5HT O4     O4   O 0 1 N N N -2.781 55.229 16.104 -0.303 1.287  4.109  O4     5HT 14 
5HT C5     C5   C 0 1 N N R -3.004 57.170 14.709 0.433  -0.585 2.874  C5     5HT 15 
5HT C5M    C5M  C 0 1 N N N -3.790 58.278 15.416 0.277  -1.360 4.184  C5M    5HT 16 
5HT O5     O5   O 0 1 N N N -3.878 56.378 13.954 1.821  -0.435 2.569  O5     5HT 17 
5HT C6     C6   C 0 1 N N N -1.917 57.829 13.744 -0.258 -1.350 1.742  C6     5HT 18 
5HT "HO5'" H5T  H 0 0 N Y N -3.643 61.715 11.922 3.014  1.173  -4.106 "HO5'" 5HT 19 
5HT "H5'"  1H5* H 0 1 N N N -1.817 61.253 10.516 0.801  0.864  -4.616 "H5'"  5HT 20 
5HT "H5''" 2H5* H 0 0 N N N -1.583 62.701 11.365 1.041  1.720  -3.074 "H5''" 5HT 21 
5HT "H4'"  H4*  H 0 1 N N N 0.300  61.827 12.124 0.589  -1.295 -3.347 "H4'"  5HT 22 
5HT "H3'"  H3*  H 0 1 N N N -0.756 59.154 11.143 -1.258 1.058  -2.660 "H3'"  5HT 23 
5HT "HO3'" H3T  H 0 0 N Y N 1.272  59.161 10.114 -2.704 -0.318 -3.851 "HO3'" 5HT 24 
5HT "H2'"  1H2* H 0 1 N N N 0.709  57.922 12.663 -1.986 -1.767 -1.874 "H2'"  5HT 25 
5HT "H2''" 2H2* H 0 0 N N N 1.829  59.148 12.790 -2.265 -0.239 -0.981 "H2''" 5HT 26 
5HT "H1'"  H1*  H 0 1 N N N 0.692  59.945 14.804 -0.047 -2.114 -0.701 "H1'"  5HT 27 
5HT H3     H3   H 0 1 N N N -0.743 56.357 17.116 -1.007 2.319  2.013  H3     5HT 28 
5HT H71    1H5M H 0 1 N N N -4.288 58.922 14.655 0.768  -0.814 4.989  H71    5HT 29 
5HT H72    2H5M H 0 1 N N N -4.511 57.872 16.163 -0.781 -1.474 4.415  H72    5HT 30 
5HT H73    3H5M H 0 1 N N N -3.151 58.867 16.114 0.735  -2.344 4.080  H73    5HT 31 
5HT HO5    HO5  H 0 1 N N N -4.303 56.927 13.306 2.217  0.051  3.305  HO5    5HT 32 
5HT H61    1H6  H 0 1 N N N -2.354 58.607 13.076 0.336  -2.224 1.478  H61    5HT 33 
5HT H62    2H6  H 0 1 N N N -1.566 57.126 12.951 -1.247 -1.669 2.071  H62    5HT 34 
# 
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 
5HT "O5'" "C5'"  SING N N 1  
5HT "O5'" "HO5'" SING N N 2  
5HT "C5'" "C4'"  SING N N 3  
5HT "C5'" "H5'"  SING N N 4  
5HT "C5'" "H5''" SING N N 5  
5HT "C4'" "O4'"  SING N N 6  
5HT "C4'" "C3'"  SING N N 7  
5HT "C4'" "H4'"  SING N N 8  
5HT "O4'" "C1'"  SING N N 9  
5HT "C3'" "O3'"  SING N N 10 
5HT "C3'" "C2'"  SING N N 11 
5HT "C3'" "H3'"  SING N N 12 
5HT "O3'" "HO3'" SING N N 13 
5HT "C2'" "C1'"  SING N N 14 
5HT "C2'" "H2'"  SING N N 15 
5HT "C2'" "H2''" SING N N 16 
5HT "C1'" N1     SING N N 17 
5HT "C1'" "H1'"  SING N N 18 
5HT N1    C2     SING N N 19 
5HT N1    C6     SING N N 20 
5HT C2    O2     DOUB N N 21 
5HT C2    N3     SING N N 22 
5HT N3    C4     SING N N 23 
5HT N3    H3     SING N N 24 
5HT C4    O4     DOUB N N 25 
5HT C4    C5     SING N N 26 
5HT C5    C5M    SING N N 27 
5HT C5    O5     SING N N 28 
5HT C5    C6     SING N N 29 
5HT C5M   H71    SING N N 30 
5HT C5M   H72    SING N N 31 
5HT C5M   H73    SING N N 32 
5HT O5    HO5    SING N N 33 
5HT C6    H61    SING N N 34 
5HT C6    H62    SING N N 35 
# 
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 
5HT SMILES           ACDLabs              10.04 "O=C1N(CC(O)(C(=O)N1)C)C2OC(C(O)C2)CO"                                                                                                   
5HT InChI            InChI                1.02b "InChI=1/C10H16N2O6/c1-10(17)4-12(9(16)11-8(10)15)7-2-5(14)6(3-13)18-7/h5-7,13-14,17H,2-4H2,1H3,(H,11,15,16)/t5-,6+,7+,10+/m0/s1/f/h11H" 
5HT InChIKey         InChI                1.02b MRODUHNLAXSPFV-ZUDWTZLDDN                                                                                                                
5HT SMILES_CANONICAL CACTVS               3.341 "C[C@@]1(O)CN([C@H]2C[C@H](O)[C@@H](CO)O2)C(=O)NC1=O"                                                                                    
5HT SMILES           CACTVS               3.341 "C[C]1(O)CN([CH]2C[CH](O)[CH](CO)O2)C(=O)NC1=O"                                                                                          
5HT SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C[C@]1(CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO)O)O"                                                                                     
5HT SMILES           "OpenEye OEToolkits" 1.5.0 "CC1(CN(C(=O)NC1=O)C2CC(C(O2)CO)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 
5HT "SYSTEMATIC NAME" ACDLabs              10.04 5-hydroxythymidine                                                                                      
5HT "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(5R)-5-hydroxy-1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methyl-1,3-diazinane-2,4-dione" 
# 
