data_D3T
# 
_chem_comp.id                                    D3T 
_chem_comp.name                                  "2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE" 
_chem_comp.type                                  "DNA OH 3 PRIME TERMINUS" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C10 H17 N2 O13 P3" 
_chem_comp.mon_nstd_parent_comp_id               DT 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2004-06-28 
_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                        466.169 
_chem_comp.one_letter_code                       T 
_chem_comp.three_letter_code                     D3T 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   N 
_chem_comp.pdbx_ideal_coordinates_details        "OpenEye/OEToolkits V1.4.2" 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        1TK8 
_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 
D3T PA     PA   P 0 1 N N R 62.490 190.146 22.330 1.709  1.392  5.586 PA     D3T 1  
D3T O1A    O1A  O 0 1 N N N 62.840 188.716 22.119 2.978  1.946  6.166 O1A    D3T 2  
D3T O2A    O2A  O 0 1 N N N 61.677 190.869 21.317 0.436  2.384  5.704 O2A    D3T 3  
D3T "O5'"  O5*  O 0 1 N N N 61.815 190.239 23.773 1.798  1.054  4.005 "O5'"  D3T 4  
D3T "C5'"  C5*  C 0 1 N N N 61.102 191.401 24.184 0.670  0.525  3.329 "C5'"  D3T 5  
D3T "C4'"  C4*  C 0 1 N N S 61.494 191.783 25.597 1.027  0.302  1.866 "C4'"  D3T 6  
D3T "O4'"  O4*  O 0 1 N N N 61.229 190.675 26.499 2.097  -0.657 1.801 "O4'"  D3T 7  
D3T "C1'"  C1*  C 0 1 N N R 62.190 190.671 27.545 1.600  -1.869 1.217 "C1'"  D3T 8  
D3T N1     N1   N 0 1 N N N 62.896 189.367 27.555 2.073  -2.991 1.972 N1     D3T 9  
D3T C6     C6   C 0 1 N N N 63.020 188.603 26.410 2.255  -2.838 3.341 C6     D3T 10 
D3T C2     C2   C 0 1 N N N 63.436 188.944 28.753 2.349  -4.227 1.349 C2     D3T 11 
D3T O2     O2   O 0 1 N N N 63.357 189.586 29.785 2.211  -4.434 0.142 O2     D3T 12 
D3T N3     N3   N 0 1 N N N 64.078 187.736 28.698 2.803  -5.234 2.208 N3     D3T 13 
D3T C4     C4   C 0 1 N N N 64.241 186.921 27.598 3.003  -5.136 3.577 C4     D3T 14 
D3T O4     O4   O 0 1 N N N 64.844 185.853 27.713 3.406  -6.064 4.272 O4     D3T 15 
D3T C5     C5   C 0 1 N N N 63.661 187.422 26.370 2.690  -3.804 4.159 C5     D3T 16 
D3T C5M    C5M  C 0 1 N N N 63.804 186.614 25.117 2.879  -3.619 5.631 C5M    D3T 17 
D3T "C2'"  C2*  C 0 1 N N N 63.129 191.853 27.309 0.087  -1.764 1.201 "C2'"  D3T 18 
D3T "C3'"  C3*  C 0 1 N N N 62.968 192.081 25.809 -0.121 -0.277 1.054 "C3'"  D3T 19 
D3T O3A    O3A  O 0 1 N N N 63.817 190.975 22.639 1.185  0.025  6.267 O3A    D3T 20 
D3T PB     PB   P 0 1 N N R 64.358 192.244 21.846 0.750  -0.329 7.782 PB     D3T 21 
D3T O1B    O1B  O 0 1 N N N 65.421 192.871 22.664 -0.400 0.473  8.315 O1B    D3T 22 
D3T O2B    O2B  O 0 1 N N N 63.208 193.061 21.384 2.123  -0.193 8.625 O2B    D3T 23 
D3T O3B    O3B  O 0 1 N N N 65.045 191.501 20.611 0.508  -1.923 7.693 O3B    D3T 24 
D3T PG     PG   P 0 1 N N N 64.555 191.702 19.106 -0.573 -2.782 6.892 PG     D3T 25 
D3T O1G    O1G  O 0 1 N N N 63.069 191.596 19.063 -0.415 -2.509 5.480 O1G    D3T 26 
D3T O2G    O2G  O 0 1 N N N 65.215 192.905 18.551 -2.068 -2.375 7.297 O2G    D3T 27 
D3T O3G    O3G  O 0 1 N N N 65.096 190.409 18.521 -0.369 -4.354 7.108 O3G    D3T 28 
D3T HOA2   2HOA H 0 0 N N N 61.453 191.782 21.452 0.264  2.835  6.557 HOA2   D3T 29 
D3T "H5'1" 1H5* H 0 0 N N N 60.000 191.273 24.078 0.386  -0.420 3.803 "H5'1" D3T 30 
D3T "H5'2" 2H5* H 0 0 N N N 61.238 192.247 23.471 -0.159 1.234  3.419 "H5'2" D3T 31 
D3T "H4'"  H4*  H 0 1 N N N 60.898 192.705 25.791 1.377  1.247  1.439 "H4'"  D3T 32 
D3T "H1'"  H1*  H 0 1 N N N 61.720 190.788 28.549 2.006  -1.949 0.203 "H1'"  D3T 33 
D3T H6     H6   H 0 1 N N N 62.578 188.960 25.465 2.015  -1.852 3.725 H6     D3T 34 
D3T HN3    HN3  H 0 1 N N N 64.480 187.406 29.575 3.009  -6.134 1.782 HN3    D3T 35 
D3T H5M1   1H5M H 0 0 N N N 64.269 187.272 24.347 2.250  -4.323 6.174 H5M1   D3T 36 
D3T H5M2   2H5M H 0 0 N N N 64.336 185.635 25.084 2.607  -2.602 5.912 H5M2   D3T 37 
D3T H5M3   3H5M H 0 0 N N N 62.780 186.452 24.706 3.923  -3.790 5.892 H5M3   D3T 38 
D3T "H2'1" 1H2* H 0 0 N N N 64.178 191.702 27.656 -0.342 -2.106 2.152 "H2'1" D3T 39 
D3T "H2'2" 2H2* H 0 0 N N N 62.937 192.746 27.948 -0.371 -2.351 0.399 "H2'2" D3T 40 
D3T "H3'1" 1H3* H 0 0 N N N 63.304 193.080 25.446 -0.001 0.001  0.000 "H3'1" D3T 41 
D3T "H3'2" 2H3* H 0 0 N N N 63.665 191.494 25.166 -1.108 0.062  1.383 "H3'2" D3T 42 
D3T HOB2   2HOB H 0 0 N N N 63.531 193.819 20.911 2.439  0.701  8.877 HOB2   D3T 43 
D3T HOG3   3HOG H 0 0 N N N 64.804 190.529 17.625 -0.451 -4.732 8.009 HOG3   D3T 44 
D3T HO1    HO1  H 0 1 N N N 65.356 193.538 19.245 -2.368 -2.502 8.222 HO1    D3T 45 
# 
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 
D3T PA    O1A    DOUB N N 1  
D3T PA    O2A    SING N N 2  
D3T PA    "O5'"  SING N N 3  
D3T PA    O3A    SING N N 4  
D3T O2A   HOA2   SING N N 5  
D3T "O5'" "C5'"  SING N N 6  
D3T "C5'" "C4'"  SING N N 7  
D3T "C5'" "H5'1" SING N N 8  
D3T "C5'" "H5'2" SING N N 9  
D3T "C4'" "O4'"  SING N N 10 
D3T "C4'" "C3'"  SING N N 11 
D3T "C4'" "H4'"  SING N N 12 
D3T "O4'" "C1'"  SING N N 13 
D3T "C1'" N1     SING N N 14 
D3T "C1'" "C2'"  SING N N 15 
D3T "C1'" "H1'"  SING N N 16 
D3T N1    C6     SING N N 17 
D3T N1    C2     SING N N 18 
D3T C6    C5     DOUB N N 19 
D3T C6    H6     SING N N 20 
D3T C2    O2     DOUB N N 21 
D3T C2    N3     SING N N 22 
D3T N3    C4     SING N N 23 
D3T N3    HN3    SING N N 24 
D3T C4    O4     DOUB N N 25 
D3T C4    C5     SING N N 26 
D3T C5    C5M    SING N N 27 
D3T C5M   H5M1   SING N N 28 
D3T C5M   H5M2   SING N N 29 
D3T C5M   H5M3   SING N N 30 
D3T "C2'" "C3'"  SING N N 31 
D3T "C2'" "H2'1" SING N N 32 
D3T "C2'" "H2'2" SING N N 33 
D3T "C3'" "H3'1" SING N N 34 
D3T "C3'" "H3'2" SING N N 35 
D3T O3A   PB     SING N N 36 
D3T PB    O1B    DOUB N N 37 
D3T PB    O2B    SING N N 38 
D3T PB    O3B    SING N N 39 
D3T O2B   HOB2   SING N N 40 
D3T O3B   PG     SING N N 41 
D3T PG    O1G    DOUB N N 42 
D3T PG    O2G    SING N N 43 
D3T PG    O3G    SING N N 44 
D3T O3G   HOG3   SING N N 45 
D3T HO1   O2G    SING N N 46 
# 
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 
D3T InChI            InChI                1.02b "InChI=1/C10H17N2O13P3/c1-6-4-12(10(14)11-9(6)13)8-3-2-7(23-8)5-22-27(18,19)25-28(20,21)24-26(15,16)17/h4,7-8H,2-3,5H2,1H3,(H,18,19)(H,20,21)(H,11,13,14)(H2,15,16,17)/t7-,8+/m0/s1/f/h11,15-16,18,20H" 
D3T InChIKey         InChI                1.02b URGJWIFLBWJRMF-PTPFDUATDW                                                                                                                                                                               
D3T SMILES_CANONICAL CACTVS               3.341 "CC1=CN([C@H]2CC[C@@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O"                                                                                                                            
D3T SMILES           CACTVS               3.341 "CC1=CN([CH]2CC[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O"                                                                                                                                  
D3T SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)[C@H]2CC[C@H](O2)CO[P@@](=O)(O)O[P@](=O)(O)OP(=O)(O)O"                                                                                                                               
D3T SMILES           "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)C2CCC(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O"                                                                                                                                              
# 
_pdbx_chem_comp_identifier.comp_id           D3T 
_pdbx_chem_comp_identifier.type              "SYSTEMATIC NAME" 
_pdbx_chem_comp_identifier.program           "OpenEye OEToolkits" 
_pdbx_chem_comp_identifier.program_version   1.5.0 
_pdbx_chem_comp_identifier.identifier        "(hydroxy-phosphonooxy-phosphoryl) [(2S,5R)-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methyl hydrogen phosphate" 
# 
