data_T3P # _chem_comp.id T3P _chem_comp.name "THYMIDINE-3'-PHOSPHATE" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H15 N2 O8 P" _chem_comp.mon_nstd_parent_comp_id DT _chem_comp.pdbx_synonyms "ALPHA-ANOMERIC THYMIDINE-3'-PHOSPHATE" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 1999-08-26 _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 322.208 _chem_comp.one_letter_code T _chem_comp.three_letter_code T3P _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 1CY8 _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 T3P P P P 0 1 N N N 37.583 17.167 43.526 -1.040 -0.030 -3.573 P T3P 1 T3P OP1 O1P O 0 1 N N N 37.873 16.366 42.288 -0.250 1.195 -3.822 OP1 T3P 2 T3P OP2 O2P O 0 1 N N N 36.288 17.752 43.827 -1.427 -0.713 -4.979 OP2 T3P 3 T3P OP3 O3P O 0 1 N Y N 38.739 17.816 44.176 -2.385 0.350 -2.774 OP3 T3P 4 T3P "O5'" O5* O 0 1 N N N 37.440 22.789 41.920 3.742 0.759 -1.645 "O5'" T3P 5 T3P "C5'" C5* C 0 1 N N N 37.968 21.662 42.566 2.336 0.786 -1.900 "C5'" T3P 6 T3P "C4'" C4* C 0 1 N N R 38.057 20.549 41.522 1.669 -0.404 -1.209 "C4'" T3P 7 T3P "O4'" O4* O 0 1 N N N 38.971 20.970 40.466 1.769 -0.284 0.228 "O4'" T3P 8 T3P "C3'" C3* C 0 1 N N S 38.617 19.276 42.111 0.141 -0.400 -1.469 "C3'" T3P 9 T3P "O3'" O3* O 0 1 N N N 37.569 18.310 42.355 -0.168 -1.062 -2.697 "O3'" T3P 10 T3P "C2'" C2* C 0 1 N N N 39.627 18.752 41.132 -0.395 -1.203 -0.259 "C2'" T3P 11 T3P "C1'" C1* C 0 1 N N R 40.030 20.003 40.352 0.731 -1.105 0.788 "C1'" T3P 12 T3P N1 N1 N 0 1 N N N 41.384 20.434 40.868 0.218 -0.491 2.015 N1 T3P 13 T3P C2 C2 C 0 1 N N N 42.496 19.752 40.315 -0.299 0.749 1.973 C2 T3P 14 T3P O2 O2 O 0 1 N N N 42.420 18.862 39.474 -0.335 1.348 0.916 O2 T3P 15 T3P N3 N3 N 0 1 N N N 43.735 20.127 40.763 -0.777 1.337 3.085 N3 T3P 16 T3P C4 C4 C 0 1 N N N 43.999 21.105 41.701 -0.748 0.685 4.265 C4 T3P 17 T3P O4 O4 O 0 1 N N N 45.170 21.310 41.983 -1.181 1.216 5.272 O4 T3P 18 T3P C5 C5 C 0 1 N N N 42.838 21.798 42.264 -0.202 -0.619 4.324 C5 T3P 19 T3P C5M C5M C 0 1 N N N 43.056 22.907 43.320 -0.154 -1.368 5.631 C5M T3P 20 T3P C6 C6 C 0 1 N N N 41.580 21.451 41.839 0.270 -1.185 3.193 C6 T3P 21 T3P HOP2 2HOP H 0 0 N N N 36.104 18.258 44.609 -1.947 -0.064 -5.472 HOP2 T3P 22 T3P HOP3 3HOP H 0 0 N N N 38.555 18.322 44.958 -2.869 -0.474 -2.632 HOP3 T3P 23 T3P "H5'" H5* H 0 1 N N N 37.384 23.480 42.568 4.123 1.524 -2.097 "H5'" T3P 24 T3P "H5'1" 1H5* H 0 0 N N N 38.939 21.863 43.075 2.161 0.727 -2.974 "H5'1" T3P 25 T3P "H5''" 2H5* H 0 0 N N N 37.390 21.366 43.473 1.915 1.714 -1.513 "H5''" T3P 26 T3P "H4'" H4* H 0 1 N N N 37.027 20.358 41.139 2.114 -1.340 -1.546 "H4'" T3P 27 T3P "H3'" H3* H 0 1 N N N 39.095 19.473 43.098 -0.250 0.616 -1.467 "H3'" T3P 28 T3P "H2'" 1H2* H 0 1 N N N 40.477 18.196 41.592 -0.568 -2.242 -0.536 "H2'" T3P 29 T3P "H2''" 2H2* H 0 0 N N N 39.268 17.905 40.501 -1.310 -0.751 0.122 "H2''" T3P 30 T3P "H1'" H1* H 0 1 N N N 40.152 19.839 39.255 1.121 -2.099 1.006 "H1'" T3P 31 T3P H3 H3 H 0 1 N N N 44.532 19.633 40.362 -1.147 2.233 3.038 H3 T3P 32 T3P H51 1H5 H 0 1 N N N 42.172 23.434 43.748 -0.579 -0.749 6.421 H51 T3P 33 T3P H52 2H5 H 0 1 N N N 43.662 22.488 44.157 -0.729 -2.290 5.543 H52 T3P 34 T3P H53 3H5 H 0 1 N N N 43.756 23.666 42.900 0.880 -1.608 5.874 H53 T3P 35 T3P H6 H6 H 0 1 N N N 40.724 21.990 42.278 0.687 -2.181 3.218 H6 T3P 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 T3P P OP1 DOUB N N 1 T3P P OP2 SING N N 2 T3P P OP3 SING N N 3 T3P P "O3'" SING N N 4 T3P OP2 HOP2 SING N N 5 T3P OP3 HOP3 SING N N 6 T3P "O5'" "C5'" SING N N 7 T3P "O5'" "H5'" SING N N 8 T3P "C5'" "C4'" SING N N 9 T3P "C5'" "H5'1" SING N N 10 T3P "C5'" "H5''" SING N N 11 T3P "C4'" "O4'" SING N N 12 T3P "C4'" "C3'" SING N N 13 T3P "C4'" "H4'" SING N N 14 T3P "O4'" "C1'" SING N N 15 T3P "C3'" "O3'" SING N N 16 T3P "C3'" "C2'" SING N N 17 T3P "C3'" "H3'" SING N N 18 T3P "C2'" "C1'" SING N N 19 T3P "C2'" "H2'" SING N N 20 T3P "C2'" "H2''" SING N N 21 T3P "C1'" N1 SING N N 22 T3P "C1'" "H1'" SING N N 23 T3P N1 C2 SING N N 24 T3P N1 C6 SING N N 25 T3P C2 O2 DOUB N N 26 T3P C2 N3 SING N N 27 T3P N3 C4 SING N N 28 T3P N3 H3 SING N N 29 T3P C4 O4 DOUB N N 30 T3P C4 C5 SING N N 31 T3P C5 C5M SING N N 32 T3P C5 C6 DOUB N N 33 T3P C5M H51 SING N N 34 T3P C5M H52 SING N N 35 T3P C5M H53 SING N N 36 T3P C6 H6 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 T3P SMILES ACDLabs 10.04 "O=C1NC(=O)N(C=C1C)C2OC(C(OP(=O)(O)O)C2)CO" T3P SMILES_CANONICAL CACTVS 3.341 "CC1=CN([C@H]2C[C@H](O[P](O)(O)=O)[C@@H](CO)O2)C(=O)NC1=O" T3P SMILES CACTVS 3.341 "CC1=CN([CH]2C[CH](O[P](O)(O)=O)[CH](CO)O2)C(=O)NC1=O" T3P SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO)OP(=O)(O)O" T3P SMILES "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)C2CC(C(O2)CO)OP(=O)(O)O" T3P InChI InChI 1.03 "InChI=1S/C10H15N2O8P/c1-5-3-12(10(15)11-9(5)14)8-2-6(7(4-13)19-8)20-21(16,17)18/h3,6-8,13H,2,4H2,1H3,(H,11,14,15)(H2,16,17,18)/t6-,7+,8+/m0/s1" T3P InChIKey InChI 1.03 XXYIANZGUOSQHY-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 T3P "SYSTEMATIC NAME" ACDLabs 10.04 "3'-thymidylic acid" T3P "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,5R)-2-(hydroxymethyl)-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)oxolan-3-yl] 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 T3P "Create component" 1999-08-26 RCSB T3P "Modify descriptor" 2011-06-04 RCSB T3P "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id T3P _pdbx_chem_comp_synonyms.name "ALPHA-ANOMERIC THYMIDINE-3'-PHOSPHATE" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##