data_TYD
# 
_chem_comp.id                                    TYD 
_chem_comp.name                                  "THYMIDINE-5'-DIPHOSPHATE" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C10 H16 N2 O11 P2" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     1999-07-08 
_chem_comp.pdbx_modified_date                    2008-10-14 
_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                        402.188 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     TYD 
_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        1NDC 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  EBI 
# 
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 
TYD PA     PA   P 0 1 N N S 16.634 -11.407 -21.793 -0.143 -0.002 -2.900 PA     TYD 1  
TYD O1A    O1A  O 0 1 N N N 16.219 -12.867 -21.800 0.633  1.210  -2.558 O1A    TYD 2  
TYD O2A    O2A  O 0 1 N N N 16.524 -10.610 -22.998 -1.473 0.421  -3.703 O2A    TYD 3  
TYD O3A    O3A  O 0 1 N N N 15.773 -10.641 -20.670 0.752  -0.972 -3.821 O3A    TYD 4  
TYD PB     PB   P 0 1 N N N 14.681 -11.094 -19.566 1.126  -0.140 -5.147 PB     TYD 5  
TYD O1B    O1B  O 0 1 N N N 15.443 -11.044 -18.307 1.884  1.074  -4.771 O1B    TYD 6  
TYD O2B    O2B  O 0 1 N N N 14.287 -12.514 -19.907 2.027  -1.055 -6.119 O2B    TYD 7  
TYD O3B    O3B  O 0 1 N N N 13.620 -10.096 -19.691 -0.224 0.285  -5.912 O3B    TYD 8  
TYD "O5'"  O5*  O 0 1 N N N 18.138 -11.284 -21.252 -0.555 -0.774 -1.549 "O5'"  TYD 9  
TYD "C5'"  C5*  C 0 1 N N N 18.457 -11.907 -19.996 -1.345 0.133  -0.779 "C5'"  TYD 10 
TYD "C4'"  C4*  C 0 1 N N R 19.207 -10.960 -19.107 -1.772 -0.541 0.525  "C4'"  TYD 11 
TYD "O4'"  O4*  O 0 1 N N N 20.350 -10.541 -19.811 -0.624 -0.809 1.363  "O4'"  TYD 12 
TYD "C3'"  C3*  C 0 1 N N S 18.490 -9.655  -18.781 -2.631 0.421  1.383  "C3'"  TYD 13 
TYD "O3'"  O3*  O 0 1 N N N 17.656 -10.054 -17.699 -4.008 0.349  1.007  "O3'"  TYD 14 
TYD "C2'"  C2*  C 0 1 N N N 19.648 -8.765  -18.408 -2.418 -0.137 2.811  "C2'"  TYD 15 
TYD "C1'"  C1*  C 0 1 N N R 20.741 -9.203  -19.415 -1.113 -0.949 2.708  "C1'"  TYD 16 
TYD N1     N1   N 0 1 Y N N 20.795 -8.342  -20.623 -0.124 -0.425 3.654  N1     TYD 17 
TYD C2     C2   C 0 1 Y N N 21.603 -7.208  -20.613 0.276  0.854  3.558  C2     TYD 18 
TYD O2     O2   O 0 1 N N N 22.324 -6.949  -19.653 -0.186 1.564  2.685  O2     TYD 19 
TYD N3     N3   N 0 1 Y N N 21.573 -6.390  -21.756 1.182  1.362  4.414  N3     TYD 20 
TYD C4     C4   C 0 1 Y N N 20.810 -6.645  -22.891 1.701  0.590  5.390  C4     TYD 21 
TYD O4     O4   O 0 1 N N N 20.879 -5.881  -23.847 2.522  1.048  6.165  O4     TYD 22 
TYD C5     C5   C 0 1 Y N N 19.985 -7.833  -22.803 1.292  -0.760 5.499  C5     TYD 23 
TYD C5M    C5M  C 0 1 N N N 19.146 -8.280  -23.993 1.860  -1.645 6.578  C5M    TYD 24 
TYD C6     C6   C 0 1 Y N N 19.961 -8.590  -21.694 0.381  -1.243 4.627  C6     TYD 25 
TYD HOA2   2HOA H 0 0 N N N 16.783 -9.696  -22.993 -1.949 -0.395 -3.906 HOA2   TYD 26 
TYD HOB2   2HOB H 0 0 N N N 13.645 -12.780 -19.258 2.228  -0.520 -6.899 HOB2   TYD 27 
TYD HOB3   3HOB H 0 0 N N N 12.978 -10.362 -19.042 -0.687 -0.532 -6.140 HOB3   TYD 28 
TYD "H5'1" 1H5* H 0 0 N N N 17.547 -12.311 -19.493 -2.230 0.417  -1.347 "H5'1" TYD 29 
TYD "H5'2" 2H5* H 0 0 N N N 19.010 -12.864 -20.139 -0.758 1.023  -0.552 "H5'2" TYD 30 
TYD "H4'"  H4*  H 0 1 N N N 19.376 -11.523 -18.159 -2.317 -1.462 0.319  "H4'"  TYD 31 
TYD "H3'"  H3*  H 0 1 N N N 17.864 -9.131  -19.541 -2.262 1.444  1.307  "H3'"  TYD 32 
TYD "HO3'" *HO3 H 0 0 N N N 17.209 -9.240  -17.495 -4.498 0.898  1.635  "HO3'" TYD 33 
TYD "H2'1" 1H2* H 0 0 N N N 19.420 -7.673  -18.407 -3.249 -0.784 3.095  "H2'1" TYD 34 
TYD "H2'2" 2H2* H 0 0 N N N 19.950 -8.812  -17.336 -2.306 0.676  3.527  "H2'2" TYD 35 
TYD "H1'"  H1*  H 0 1 N N N 21.750 -9.137  -18.945 -1.311 -1.999 2.923  "H1'"  TYD 36 
TYD HN3    HN3  H 0 1 N N N 22.148 -5.547  -21.762 1.460  2.287  4.330  HN3    TYD 37 
TYD H51    1H5  H 0 1 N N N 18.511 -9.194  -23.925 2.573  -1.078 7.176  H51    TYD 38 
TYD H52    2H5  H 0 1 N N N 18.498 -7.427  -24.304 1.053  -2.002 7.218  H52    TYD 39 
TYD H53    3H5  H 0 1 N N N 19.819 -8.386  -24.875 2.365  -2.497 6.121  H53    TYD 40 
TYD H6     H6   H 0 1 N N N 19.245 -9.428  -21.662 0.054  -2.270 4.697  H6     TYD 41 
# 
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 
TYD PA    O1A    DOUB N N 1  
TYD PA    O2A    SING N N 2  
TYD PA    O3A    SING N N 3  
TYD PA    "O5'"  SING N N 4  
TYD O2A   HOA2   SING N N 5  
TYD O3A   PB     SING N N 6  
TYD PB    O1B    DOUB N N 7  
TYD PB    O2B    SING N N 8  
TYD PB    O3B    SING N N 9  
TYD O2B   HOB2   SING N N 10 
TYD O3B   HOB3   SING N N 11 
TYD "O5'" "C5'"  SING N N 12 
TYD "C5'" "C4'"  SING N N 13 
TYD "C5'" "H5'1" SING N N 14 
TYD "C5'" "H5'2" SING N N 15 
TYD "C4'" "O4'"  SING N N 16 
TYD "C4'" "C3'"  SING N N 17 
TYD "C4'" "H4'"  SING N N 18 
TYD "O4'" "C1'"  SING N N 19 
TYD "C3'" "O3'"  SING N N 20 
TYD "C3'" "C2'"  SING N N 21 
TYD "C3'" "H3'"  SING N N 22 
TYD "O3'" "HO3'" SING N N 23 
TYD "C2'" "C1'"  SING N N 24 
TYD "C2'" "H2'1" SING N N 25 
TYD "C2'" "H2'2" SING N N 26 
TYD "C1'" N1     SING N N 27 
TYD "C1'" "H1'"  SING N N 28 
TYD N1    C2     SING Y N 29 
TYD N1    C6     SING Y N 30 
TYD C2    O2     DOUB N N 31 
TYD C2    N3     SING Y N 32 
TYD N3    C4     SING Y N 33 
TYD N3    HN3    SING N N 34 
TYD C4    O4     DOUB N N 35 
TYD C4    C5     SING Y N 36 
TYD C5    C5M    SING N N 37 
TYD C5    C6     DOUB Y N 38 
TYD C5M   H51    SING N N 39 
TYD C5M   H52    SING N N 40 
TYD C5M   H53    SING N N 41 
TYD C6    H6     SING N N 42 
# 
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 
TYD SMILES           ACDLabs              10.04 O=P(O)(O)OP(=O)(O)OCC2OC(N1C(=O)NC(=O)C(=C1)C)CC2O                                                                                                                                   
TYD InChI            InChI                1.02b InChI=1/C10H16N2O11P2/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(22-8)4-21-25(19,20)23-24(16,17)18/h3,6-8,13H,2,4H2,1H3,(H,19,20)(H,11,14,15)(H2,16,17,18)/t6-,7+,8+/m0/s1/f/h11,16-17,19H 
TYD InChIKey         InChI                1.02b UJLXYODCHAELLY-LJMMMCIGDR                                                                                                                                                            
TYD SMILES_CANONICAL CACTVS               3.341 CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P@@](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O                                                                                                                
TYD SMILES           CACTVS               3.341 CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O                                                                                                                      
TYD SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@](=O)(O)OP(=O)(O)O)O                                                                                                                   
TYD SMILES           "OpenEye OEToolkits" 1.5.0 CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)OP(=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 
TYD "SYSTEMATIC NAME" ACDLabs              10.04 
;thymidine 5'-(trihydrogen diphosphate)
;
TYD "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methyl phosphono hydrogen phosphate" 
# 
