data_SPT # _chem_comp.id SPT _chem_comp.name ;5'-THIO-THYMIDINE PHOSPHONIC ACID ; _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H15 N2 O7 P S" _chem_comp.mon_nstd_parent_comp_id DT _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2001-12-05 _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 338.274 _chem_comp.one_letter_code T _chem_comp.three_letter_code SPT _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag Y _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 1K4S _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 SPT "S5'" S5* S 0 1 N N N 83.518 3.220 -3.592 -2.684 -1.263 3.575 "S5'" SPT 1 SPT N1 N1 N 0 1 N N N 78.949 0.541 -5.744 1.164 -2.047 0.989 N1 SPT 2 SPT C6 C6 C 0 1 N N N 79.745 1.060 -6.744 -0.013 -2.784 0.958 C6 SPT 3 SPT C2 C2 C 0 1 N N N 77.718 -0.007 -6.019 2.333 -2.544 0.374 C2 SPT 4 SPT O2 O2 O 0 1 N N N 76.989 -0.481 -5.162 3.410 -1.945 0.363 O2 SPT 5 SPT N3 N3 N 0 1 N N N 77.372 0.017 -7.346 2.194 -3.793 -0.240 N3 SPT 6 SPT C4 C4 C 0 1 N N N 78.119 0.527 -8.394 1.047 -4.570 -0.300 C4 SPT 7 SPT O4 O4 O 0 1 N N N 77.679 0.489 -9.533 0.995 -5.663 -0.857 O4 SPT 8 SPT C5 C5 C 0 1 N N N 79.396 1.080 -8.031 -0.143 -3.980 0.369 C5 SPT 9 SPT C5M C5M C 0 1 N N N 80.268 1.651 -9.103 -1.420 -4.757 0.347 C5M SPT 10 SPT "C2'" C2* C 0 1 N N N 80.467 -0.498 -4.079 0.710 0.360 0.754 "C2'" SPT 11 SPT "C5'" C5* C 0 1 N N N 82.433 2.049 -4.396 -2.005 -0.136 2.327 "C5'" SPT 12 SPT "C4'" C4* C 0 1 N N S 81.320 1.642 -3.458 -0.611 0.328 2.728 "C4'" SPT 13 SPT "O4'" O4* O 0 1 N N N 80.045 1.823 -4.122 0.247 -0.829 2.764 "O4'" SPT 14 SPT "C1'" C1* C 0 1 N N R 79.414 0.564 -4.347 1.157 -0.778 1.657 "C1'" SPT 15 SPT "C3'" C3* C 0 1 N N S 81.374 0.169 -3.065 0.008 1.286 1.720 "C3'" SPT 16 SPT "O3'" O3* O 0 1 N N N 80.853 -0.035 -1.751 0.965 2.121 2.368 "O3'" SPT 17 SPT OP3 O3P O 0 1 N Y N ? ? ? -4.440 -2.387 1.358 OP3 SPT 18 SPT P P P 0 1 N N N ? ? ? -4.581 -1.788 2.860 P SPT 19 SPT OP1 O1P O 0 1 N N N ? ? ? -5.279 -2.733 3.800 OP1 SPT 20 SPT OP2 O2P O 0 1 N N N ? ? ? -5.432 -0.433 2.589 OP2 SPT 21 SPT H6 H6 H 0 1 N N N 80.704 1.473 -6.469 -0.857 -2.318 1.458 H6 SPT 22 SPT H3 H3 H 0 1 N N N 76.484 -0.377 -7.582 3.023 -4.171 -0.689 H3 SPT 23 SPT H71 1H5M H 0 1 N N N 79.678 1.791 -10.021 -1.735 -4.916 -0.683 H71 SPT 24 SPT H72 2H5M H 0 1 N N N 80.668 2.621 -8.772 -2.195 -4.208 0.881 H72 SPT 25 SPT H73 3H5M H 0 1 N N N 81.100 0.961 -9.305 -1.272 -5.721 0.833 H73 SPT 26 SPT "H2'" 1H2* H 0 1 N N N 80.021 -1.421 -3.680 -0.003 -0.001 0.003 "H2'" SPT 27 SPT "H2''" 2H2* H 0 0 N N N 80.998 -0.817 -4.988 1.556 0.818 0.232 "H2''" SPT 28 SPT "H5'" 1H5* H 0 1 N N N 81.999 2.514 -5.294 -1.969 -0.654 1.365 "H5'" SPT 29 SPT "H5''" 2H5* H 0 0 N N N 83.011 1.157 -4.677 -2.674 0.724 2.226 "H5''" SPT 30 SPT "H4'" H4* H 0 1 N N N 81.438 2.267 -2.560 -0.644 0.753 3.736 "H4'" SPT 31 SPT "H1'" H1* H 0 1 N N N 78.546 0.386 -3.696 2.163 -0.604 2.054 "H1'" SPT 32 SPT "H3'" H3* H 0 1 N N N 82.401 -0.224 -3.058 -0.722 1.941 1.236 "H3'" SPT 33 SPT "HO3'" H3T H 0 0 N Y N 81.570 -0.080 -1.129 0.743 3.042 2.146 "HO3'" SPT 34 SPT HOP3 3HOP H 0 0 N N N ? ? ? -5.231 -2.783 0.932 HOP3 SPT 35 SPT HOP2 2HOP H 0 0 N N N ? ? ? -6.382 -0.511 2.361 HOP2 SPT 36 # 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 SPT "S5'" "C5'" SING N N 1 SPT "S5'" P SING N N 2 SPT N1 C6 SING N N 3 SPT N1 C2 SING N N 4 SPT N1 "C1'" SING N N 5 SPT C6 C5 DOUB N N 6 SPT C6 H6 SING N N 7 SPT C2 O2 DOUB N N 8 SPT C2 N3 SING N N 9 SPT N3 C4 SING N N 10 SPT N3 H3 SING N N 11 SPT C4 O4 DOUB N N 12 SPT C4 C5 SING N N 13 SPT C5 C5M SING N N 14 SPT C5M H71 SING N N 15 SPT C5M H72 SING N N 16 SPT C5M H73 SING N N 17 SPT "C2'" "C1'" SING N N 18 SPT "C2'" "C3'" SING N N 19 SPT "C2'" "H2'" SING N N 20 SPT "C2'" "H2''" SING N N 21 SPT "C5'" "C4'" SING N N 22 SPT "C5'" "H5'" SING N N 23 SPT "C5'" "H5''" SING N N 24 SPT "C4'" "O4'" SING N N 25 SPT "C4'" "C3'" SING N N 26 SPT "C4'" "H4'" SING N N 27 SPT "O4'" "C1'" SING N N 28 SPT "C1'" "H1'" SING N N 29 SPT "C3'" "O3'" SING N N 30 SPT "C3'" "H3'" SING N N 31 SPT "O3'" "HO3'" SING N N 32 SPT OP3 P SING N N 33 SPT OP3 HOP3 SING N N 34 SPT P OP1 DOUB N N 35 SPT P OP2 SING N N 36 SPT OP2 HOP2 SING N N 37 # 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 SPT SMILES ACDLabs 10.04 "O=P(O)(O)SCC2OC(N1C(=O)NC(=O)C(=C1)C)CC2O" SPT SMILES_CANONICAL CACTVS 3.341 "CC1=CN([C@H]2C[C@H](O)[C@@H](CS[P](O)(O)=O)O2)C(=O)NC1=O" SPT SMILES CACTVS 3.341 "CC1=CN([CH]2C[CH](O)[CH](CS[P](O)(O)=O)O2)C(=O)NC1=O" SPT SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CSP(=O)(O)O)O" SPT SMILES "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)C2CC(C(O2)CSP(=O)(O)O)O" SPT InChI InChI 1.03 "InChI=1S/C10H15N2O7PS/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(19-8)4-21-20(16,17)18/h3,6-8,13H,2,4H2,1H3,(H,11,14,15)(H2,16,17,18)/t6-,7+,8+/m0/s1" SPT InChIKey InChI 1.03 NTABNFYUFIHXQE-XLPZGREQSA-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 SPT "SYSTEMATIC NAME" ACDLabs 10.04 "5'-S-phosphono-5'-thiothymidine" SPT "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2S,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methylsulfanylphosphonic 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 SPT "Create component" 2001-12-05 RCSB SPT "Modify descriptor" 2011-06-04 RCSB #