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 2011-06-04 _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 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" D3T InChI InChI 1.03 "InChI=1S/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" D3T InChIKey InChI 1.03 URGJWIFLBWJRMF-JGVFFNPUSA-N # 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 D3T "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(hydroxy-phosphonooxy-phosphoryl) [(2S,5R)-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methyl hydrogen 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 D3T "Create component" 2004-06-28 RCSB D3T "Modify descriptor" 2011-06-04 RCSB #