data_XTH # _chem_comp.id XTH _chem_comp.name "1-(2,3-DIDEOXY-6-O-PHOSPHONO-BETA-D-ERYTHRO-HEXOPYRANOSYL)-5-METHYLPYRIMIDINE-2,4(1H,3H)-DIONE" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C11 H17 N2 O8 P" _chem_comp.mon_nstd_parent_comp_id DT _chem_comp.pdbx_synonyms "2',3'-DI-DEOXY-BETA-D-GLUCOPYRANOSYL THYMINE" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2006-06-20 _chem_comp.pdbx_modified_date 2020-06-17 _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 336.235 _chem_comp.one_letter_code T _chem_comp.three_letter_code XTH _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 2H9S _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 XTH OP3 O3P O 0 1 N Y N -6.531 8.566 14.891 3.983 2.973 0.541 OP3 XTH 1 XTH P P P 0 1 N N N -6.299 8.032 16.371 3.899 1.462 -0.009 P XTH 2 XTH OP1 O1P O 0 1 N N N -5.821 6.636 16.263 3.896 1.475 -1.489 OP1 XTH 3 XTH OP2 O2P O 0 1 N N N -7.498 8.318 17.186 5.172 0.628 0.518 OP2 XTH 4 XTH "O6'" "O6'" O 0 1 N N N -5.109 8.871 17.027 2.547 0.771 0.525 "O6'" XTH 5 XTH "C6'" "C6'" C 0 1 N N N -3.824 8.940 16.414 2.471 -0.518 -0.088 "C6'" XTH 6 XTH "C5'" "C5'" C 0 1 N N R -2.995 9.937 17.196 1.201 -1.232 0.379 "C5'" XTH 7 XTH "C4'" "C4'" C 0 1 N N S -2.811 9.542 18.654 1.184 -2.657 -0.178 "C4'" XTH 8 XTH "O4'" "O4'" O 0 1 N N N -2.242 8.206 18.677 2.344 -3.361 0.268 "O4'" XTH 9 XTH "C3'" "C3'" C 0 1 N N N -1.966 10.670 19.269 -0.075 -3.373 0.322 "C3'" XTH 10 XTH "C2'" "C2'" C 0 1 N N N -2.661 12.036 19.149 -1.299 -2.519 -0.031 "C2'" XTH 11 XTH "C1'" "C1'" C 0 1 N N R -2.856 12.250 17.645 -1.093 -1.105 0.516 "C1'" XTH 12 XTH "O5'" "O5'" O 0 1 N N N -3.691 11.195 17.213 0.058 -0.517 -0.087 "O5'" XTH 13 XTH N1 N1 N 0 1 N N N -3.581 13.465 17.195 -2.272 -0.290 0.212 N1 XTH 14 XTH C2 C2 C 0 1 N N N -3.719 13.649 15.832 -2.578 -0.012 -1.069 C2 XTH 15 XTH O2 O2 O 0 1 N N N -3.169 12.928 15.016 -1.872 -0.443 -1.961 O2 XTH 16 XTH N3 N3 N 0 1 N N N -4.467 14.724 15.430 -3.655 0.734 -1.377 N3 XTH 17 XTH C4 C4 C 0 1 N N N -5.104 15.587 16.287 -4.451 1.214 -0.400 C4 XTH 18 XTH O4 O4 O 0 1 N N N -5.778 16.513 15.863 -5.426 1.889 -0.678 O4 XTH 19 XTH C5 C5 C 0 1 N N N -4.949 15.324 17.695 -4.137 0.934 0.952 C5 XTH 20 XTH C5M C5M C 0 1 N N N -5.613 16.216 18.699 -5.008 1.463 2.063 C5M XTH 21 XTH C6 C6 C 0 1 N N N -4.229 14.272 18.088 -3.051 0.183 1.232 C6 XTH 22 XTH HOP3 3HOP H 0 0 N N N -6.577 9.515 14.900 4.806 3.349 0.199 HOP3 XTH 23 XTH HOP2 2HOP H 0 0 N N N -7.252 8.379 18.102 5.136 0.644 1.484 HOP2 XTH 24 XTH "H6'1" "1H6'" H 0 0 N N N -3.915 9.255 15.364 3.344 -1.106 0.195 "H6'1" XTH 25 XTH "H6'2" "2H6'" H 0 0 N N N -3.343 7.951 16.433 2.446 -0.403 -1.172 "H6'2" XTH 26 XTH "H5'" "H5'" H 0 1 N N N -2.011 9.984 16.706 1.186 -1.269 1.469 "H5'" XTH 27 XTH "H4'" "H4'" H 0 1 N N N -3.726 9.460 19.259 1.175 -2.622 -1.268 "H4'" XTH 28 XTH "H4T'" "H4T'" H 0 0 N N N -2.118 7.899 17.787 2.289 -4.253 -0.100 "H4T'" XTH 29 XTH "H3'1" "1H3'" H 0 0 N N N -1.013 10.721 18.722 -0.018 -3.502 1.403 "H3'1" XTH 30 XTH "H3'2" "2H3'" H 0 0 N N N -1.805 10.449 20.334 -0.158 -4.347 -0.161 "H3'2" XTH 31 XTH "H2'1" "1H2'" H 0 0 N N N -2.067 12.841 19.606 -2.191 -2.958 0.417 "H2'1" XTH 32 XTH "H2'2" "2H2'" H 0 0 N N N -3.627 12.034 19.675 -1.415 -2.479 -1.114 "H2'2" XTH 33 XTH "H1'" "H1'" H 0 1 N N N -1.834 12.323 17.244 -0.953 -1.150 1.596 "H1'" XTH 34 XTH HN3 HN3 H 0 1 N N N -4.555 14.891 14.448 -3.862 0.924 -2.305 HN3 XTH 35 XTH H71 1H5M H 0 1 N N N -6.581 16.557 18.303 -4.642 2.440 2.378 H71 XTH 36 XTH H72 2H5M H 0 1 N N N -4.970 17.086 18.898 -6.034 1.556 1.707 H72 XTH 37 XTH H73 3H5M H 0 1 N N N -5.776 15.659 19.634 -4.977 0.774 2.907 H73 XTH 38 XTH H6 H6 H 0 1 N N N -4.156 14.051 19.143 -2.798 -0.044 2.258 H6 XTH 39 # # 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 XTH OP3 P SING N N 1 XTH OP3 HOP3 SING N N 2 XTH P OP1 DOUB N N 3 XTH P OP2 SING N N 4 XTH P "O6'" SING N N 5 XTH OP2 HOP2 SING N N 6 XTH "O6'" "C6'" SING N N 7 XTH "C6'" "C5'" SING N N 8 XTH "C6'" "H6'1" SING N N 9 XTH "C6'" "H6'2" SING N N 10 XTH "C5'" "C4'" SING N N 11 XTH "C5'" "O5'" SING N N 12 XTH "C5'" "H5'" SING N N 13 XTH "C4'" "O4'" SING N N 14 XTH "C4'" "C3'" SING N N 15 XTH "C4'" "H4'" SING N N 16 XTH "O4'" "H4T'" SING N N 17 XTH "C3'" "C2'" SING N N 18 XTH "C3'" "H3'1" SING N N 19 XTH "C3'" "H3'2" SING N N 20 XTH "C2'" "C1'" SING N N 21 XTH "C2'" "H2'1" SING N N 22 XTH "C2'" "H2'2" SING N N 23 XTH "C1'" "O5'" SING N N 24 XTH "C1'" N1 SING N N 25 XTH "C1'" "H1'" SING N N 26 XTH N1 C2 SING N N 27 XTH N1 C6 SING N N 28 XTH C2 O2 DOUB N N 29 XTH C2 N3 SING N N 30 XTH N3 C4 SING N N 31 XTH N3 HN3 SING N N 32 XTH C4 O4 DOUB N N 33 XTH C4 C5 SING N N 34 XTH C5 C5M SING N N 35 XTH C5 C6 DOUB N N 36 XTH C5M H71 SING N N 37 XTH C5M H72 SING N N 38 XTH C5M H73 SING N N 39 XTH C6 H6 SING N N 40 # # 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 XTH SMILES ACDLabs 10.04 "O=C1NC(=O)N(C=C1C)C2OC(C(O)CC2)COP(=O)(O)O" XTH SMILES_CANONICAL CACTVS 3.341 "CC1=CN([C@H]2CC[C@H](O)[C@@H](CO[P](O)(O)=O)O2)C(=O)NC1=O" XTH SMILES CACTVS 3.341 "CC1=CN([CH]2CC[CH](O)[CH](CO[P](O)(O)=O)O2)C(=O)NC1=O" XTH SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)[C@H]2CC[C@@H]([C@H](O2)COP(=O)(O)O)O" XTH SMILES "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)C2CCC(C(O2)COP(=O)(O)O)O" XTH InChI InChI 1.03 "InChI=1S/C11H17N2O8P/c1-6-4-13(11(16)12-10(6)15)9-3-2-7(14)8(21-9)5-20-22(17,18)19/h4,7-9,14H,2-3,5H2,1H3,(H,12,15,16)(H2,17,18,19)/t7-,8+,9+/m0/s1" XTH InChIKey InChI 1.03 DUSDVRPQFGBMGI-DJLDLDEBSA-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 XTH "SYSTEMATIC NAME" ACDLabs 10.04 "1-(2,3-dideoxy-6-O-phosphono-beta-D-erythro-hexopyranosyl)-5-methylpyrimidine-2,4(1H,3H)-dione" XTH "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,6R)-3-hydroxy-6-(5-methyl-2,4-dioxo-pyrimidin-1-yl)oxan-2-yl]methyl dihydrogen 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 XTH "Create component" 2006-06-20 RCSB XTH "Modify descriptor" 2011-06-04 RCSB XTH "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id XTH _pdbx_chem_comp_synonyms.name "2',3'-DI-DEOXY-BETA-D-GLUCOPYRANOSYL THYMINE" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##