data_TX2 # _chem_comp.id TX2 _chem_comp.name "5'-O-{(R)-hydroxy[(2-sulfanylethyl)amino]phosphoryl}thymidine" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C12 H20 N3 O7 P S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2009-10-01 _chem_comp.pdbx_modified_date 2012-01-06 _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 381.342 _chem_comp.one_letter_code ? _chem_comp.three_letter_code TX2 _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 3JY4 _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 TX2 P P P 0 1 N N N 4.784 -9.939 17.019 -3.786 0.826 0.045 P TX2 1 TX2 S S S 0 1 N N N 3.075 -5.106 16.065 -3.081 -4.321 0.358 S TX2 2 TX2 N1 N1 N 0 1 N N N 1.604 -11.276 21.398 2.886 0.295 0.414 N1 TX2 3 TX2 C2 C2 C 0 1 N N N 1.265 -11.681 22.693 2.762 -0.094 -0.868 C2 TX2 4 TX2 O2 O2 O 0 1 N N N 1.162 -12.876 22.961 1.909 0.416 -1.570 O2 TX2 5 TX2 N3 N3 N 0 1 N N N 1.045 -10.723 23.688 3.568 -1.039 -1.386 N3 TX2 6 TX2 C4 C4 C 0 1 N N N 1.161 -9.361 23.389 4.519 -1.614 -0.622 C4 TX2 7 TX2 N4 N4 N 0 1 N N N 4.529 -8.879 15.835 -3.665 -0.525 -0.953 N4 TX2 8 TX2 O4 O4 O 0 1 N N N 0.965 -8.533 24.279 5.249 -2.469 -1.089 O4 TX2 9 TX2 C5 C5 C 0 1 N N N 1.498 -8.958 22.094 4.660 -1.214 0.729 C5 TX2 10 TX2 C6 C6 C 0 1 N N N 1.720 -9.909 21.103 3.838 -0.263 1.222 C6 TX2 11 TX2 C7 C7 C 0 1 N N N 1.628 -7.466 21.760 5.714 -1.841 1.605 C7 TX2 12 TX2 "C1'" "C1'" C 0 1 N N R 1.839 -12.304 20.356 1.997 1.331 0.947 "C1'" TX2 13 TX2 "C2'" "C2'" C 0 1 N N N 0.945 -12.109 19.139 2.262 2.668 0.229 "C2'" TX2 14 TX2 "C3'" "C3'" C 0 1 N N S 1.687 -12.918 18.072 0.895 3.041 -0.394 "C3'" TX2 15 TX2 "O3'" "O3'" O 0 1 N N N 1.203 -14.274 18.030 0.634 4.439 -0.253 "O3'" TX2 16 TX2 "C4'" "C4'" C 0 1 N N R 3.142 -12.943 18.579 -0.091 2.205 0.461 "C4'" TX2 17 TX2 "O4'" "O4'" O 0 1 N N N 3.156 -12.155 19.806 0.627 0.975 0.697 "O4'" TX2 18 TX2 "C5'" "C5'" C 0 1 N N N 4.112 -12.391 17.512 -1.382 1.935 -0.315 "C5'" TX2 19 TX2 "O5'" "O5'" O 0 1 N N N 3.699 -11.119 16.975 -2.317 1.266 0.534 "O5'" TX2 20 TX2 "C7'" "C7'" C 0 1 N N N 3.479 -7.867 15.967 -3.048 -1.652 -0.240 "C7'" TX2 21 TX2 "C8'" "C8'" C 0 1 N N N 3.971 -6.546 15.375 -3.842 -2.929 -0.522 "C8'" TX2 22 TX2 OP1 OP1 O 0 1 N N N 6.128 -10.547 16.910 -4.410 1.938 -0.706 OP1 TX2 23 TX2 HS HS H 0 1 N N N 3.637 -4.114 15.441 -3.869 -5.358 0.023 HS TX2 24 TX2 HN3 HN3 H 0 1 N N N 0.804 -11.012 24.615 3.465 -1.308 -2.312 HN3 TX2 25 TX2 HN4 HN4 H 0 1 N N N 5.386 -8.376 15.725 -4.567 -0.782 -1.324 HN4 TX2 26 TX2 H6 H6 H 0 1 N N N 1.982 -9.594 20.104 3.931 0.055 2.250 H6 TX2 27 TX2 H7 H7 H 0 1 N N N 1.897 -7.349 20.700 6.272 -2.580 1.030 H7 TX2 28 TX2 H7A H7A H 0 1 N N N 0.669 -6.962 21.952 6.396 -1.069 1.962 H7A TX2 29 TX2 H7B H7B H 0 1 N N N 2.411 -7.017 22.389 5.237 -2.327 2.456 H7B TX2 30 TX2 "H1'" "H1'" H 0 1 N N N 1.660 -13.268 20.855 2.163 1.445 2.018 "H1'" TX2 31 TX2 "H2'" "H2'" H 0 1 N N N -0.074 -12.486 19.310 2.575 3.429 0.944 "H2'" TX2 32 TX2 "H2'A" "H2'A" H 0 0 N N N 0.848 -11.049 18.862 3.014 2.542 -0.549 "H2'A" TX2 33 TX2 "H3'" "H3'" H 0 1 N N N 1.563 -12.486 17.068 0.851 2.743 -1.442 "H3'" TX2 34 TX2 "HO3'" "HO3'" H 0 0 N N N 1.675 -14.759 17.363 1.279 5.007 -0.697 "HO3'" TX2 35 TX2 "H4'" "H4'" H 0 1 N N N 3.486 -13.969 18.779 -0.307 2.711 1.402 "H4'" TX2 36 TX2 "H5'" "H5'" H 0 1 N N N 5.101 -12.264 17.977 -1.809 2.880 -0.651 "H5'" TX2 37 TX2 "H5'A" "H5'A" H 0 0 N N N 4.163 -13.114 16.685 -1.162 1.308 -1.179 "H5'A" TX2 38 TX2 "H7'" "H7'" H 0 1 N N N 2.579 -8.199 15.428 -2.021 -1.779 -0.581 "H7'" TX2 39 TX2 "H7'A" "H7'A" H 0 0 N N N 3.237 -7.725 17.031 -3.053 -1.450 0.831 "H7'A" TX2 40 TX2 "H8'" "H8'" H 0 1 N N N 3.813 -6.569 14.287 -3.837 -3.130 -1.594 "H8'" TX2 41 TX2 "H8'A" "H8'A" H 0 0 N N N 5.041 -6.436 15.604 -4.869 -2.802 -0.181 "H8'A" TX2 42 TX2 OP3 OP3 O 0 1 N Y N 5.148 -9.332 18.587 -4.693 0.467 1.326 O7 TX2 43 TX2 HOP3 HOP3 H 0 0 N Y N 6.033 -9.582 18.826 -4.344 -0.255 1.865 H20 TX2 44 # 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 TX2 P N4 SING N N 1 TX2 P "O5'" SING N N 2 TX2 P OP1 DOUB N N 3 TX2 S "C8'" SING N N 4 TX2 S HS SING N N 5 TX2 N1 C2 SING N N 6 TX2 N1 C6 SING N N 7 TX2 N1 "C1'" SING N N 8 TX2 C2 O2 DOUB N N 9 TX2 C2 N3 SING N N 10 TX2 N3 C4 SING N N 11 TX2 N3 HN3 SING N N 12 TX2 C4 O4 DOUB N N 13 TX2 C4 C5 SING N N 14 TX2 N4 "C7'" SING N N 15 TX2 N4 HN4 SING N N 16 TX2 C5 C6 DOUB N N 17 TX2 C5 C7 SING N N 18 TX2 C6 H6 SING N N 19 TX2 C7 H7 SING N N 20 TX2 C7 H7A SING N N 21 TX2 C7 H7B SING N N 22 TX2 "C1'" "C2'" SING N N 23 TX2 "C1'" "O4'" SING N N 24 TX2 "C1'" "H1'" SING N N 25 TX2 "C2'" "C3'" SING N N 26 TX2 "C2'" "H2'" SING N N 27 TX2 "C2'" "H2'A" SING N N 28 TX2 "C3'" "O3'" SING N N 29 TX2 "C3'" "C4'" SING N N 30 TX2 "C3'" "H3'" SING N N 31 TX2 "O3'" "HO3'" SING N N 32 TX2 "C4'" "O4'" SING N N 33 TX2 "C4'" "C5'" SING N N 34 TX2 "C4'" "H4'" SING N N 35 TX2 "C5'" "O5'" SING N N 36 TX2 "C5'" "H5'" SING N N 37 TX2 "C5'" "H5'A" SING N N 38 TX2 "C7'" "C8'" SING N N 39 TX2 "C7'" "H7'" SING N N 40 TX2 "C7'" "H7'A" SING N N 41 TX2 "C8'" "H8'" SING N N 42 TX2 "C8'" "H8'A" SING N N 43 TX2 P OP3 SING N N 44 TX2 OP3 HOP3 SING N N 45 # 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 TX2 SMILES ACDLabs 11.02 "O=P(O)(OCC2OC(N1C(=O)NC(=O)C(=C1)C)CC2O)NCCS" TX2 SMILES_CANONICAL CACTVS 3.352 "CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(=O)NCCS)O2)C(=O)NC1=O" TX2 SMILES CACTVS 3.352 "CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=O)NCCS)O2)C(=O)NC1=O" TX2 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@@](=O)(NCCS)O)O" TX2 SMILES "OpenEye OEToolkits" 1.7.0 "CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(NCCS)O)O" TX2 InChI InChI 1.03 "InChI=1S/C12H20N3O7PS/c1-7-5-15(12(18)14-11(7)17)10-4-8(16)9(22-10)6-21-23(19,20)13-2-3-24/h5,8-10,16,24H,2-4,6H2,1H3,(H2,13,19,20)(H,14,17,18)/t8-,9+,10+/m0/s1" TX2 InChIKey InChI 1.03 NNHLQGCWACQGSN-IVZWLZJFSA-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 TX2 "SYSTEMATIC NAME" ACDLabs 11.02 "5'-O-{(R)-hydroxy[(2-sulfanylethyl)amino]phosphoryl}thymidine" TX2 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.6.1 "[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methoxy-N-(2-sulfanylethyl)phosphonamidic acid" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site TX2 "Create component" 2009-10-01 RCSB TX2 "Modify descriptor" 2011-06-04 RCSB #