data_TXS # _chem_comp.id TXS _chem_comp.name "1-(2,5-dideoxy-5-pyrrolidin-1-yl-beta-L-erythro-pentofuranosyl)-5-methylpyrimidine-2,4(1H,3H)-dione" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C14 H21 N3 O4" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "5'-deoxy-5'-pyrrolidin-1-ylthymidine" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2008-05-28 _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 295.334 _chem_comp.one_letter_code ? _chem_comp.three_letter_code TXS _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 3D8Z _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ # # 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 TXS C21 C21 C 0 1 N N N 41.988 0.383 15.087 -4.804 -0.807 0.281 C21 TXS 1 TXS C22 C22 C 0 1 N N N 42.903 -0.417 16.033 -4.880 -2.319 0.001 C22 TXS 2 TXS C23 C23 C 0 1 N N N 42.680 -1.888 15.654 -3.550 -2.667 -0.705 C23 TXS 3 TXS C24 C24 C 0 1 N N N 41.829 -1.833 14.385 -2.615 -1.510 -0.271 C24 TXS 4 TXS N25 N25 N 0 1 N N N 41.032 -0.604 14.552 -3.516 -0.329 -0.266 N25 TXS 5 TXS "C5'" "C5'" C 0 1 N N N 40.549 -0.141 13.245 -2.961 0.752 0.560 "C5'" TXS 6 TXS "C4'" "C4'" C 0 1 N N S 39.059 -0.475 13.182 -1.771 1.387 -0.162 "C4'" TXS 7 TXS "O4'" "O4'" O 0 1 N N N 38.653 -1.403 12.145 -0.729 0.409 -0.368 "O4'" TXS 8 TXS "C3'" "C3'" C 0 1 N N R 38.145 0.751 12.936 -1.122 2.474 0.723 "C3'" TXS 9 TXS "O3'" "O3'" O 0 1 N N N 37.688 1.201 14.216 -1.583 3.772 0.340 "O3'" TXS 10 TXS "C2'" "C2'" C 0 1 N N N 36.972 0.142 12.146 0.391 2.332 0.444 "C2'" TXS 11 TXS "C1'" "C1'" C 0 1 N N S 37.272 -1.306 12.522 0.477 1.176 -0.577 "C1'" TXS 12 TXS N1 N1 N 0 1 N N N 36.380 -2.479 12.341 1.659 0.351 -0.313 N1 TXS 13 TXS C6 C6 C 0 1 N N N 36.735 -3.575 13.139 1.503 -0.962 0.042 C6 TXS 14 TXS C5 C5 C 0 1 N N N 35.984 -4.738 13.121 2.592 -1.722 0.284 C5 TXS 15 TXS C5M C5M C 0 1 N N N 36.439 -5.896 13.999 2.441 -3.169 0.676 C5M TXS 16 TXS C4 C4 C 0 1 N N N 34.851 -4.815 12.311 3.878 -1.142 0.164 C4 TXS 17 TXS O4 O4 O 0 1 N N N 34.176 -5.842 12.285 4.875 -1.808 0.377 O4 TXS 18 TXS N3 N3 N 0 1 N N N 34.471 -3.717 11.515 3.989 0.155 -0.188 N3 TXS 19 TXS C2 C2 C 0 1 N N N 35.229 -2.529 11.526 2.886 0.889 -0.429 C2 TXS 20 TXS O2 O2 O 0 1 N N N 34.885 -1.578 10.830 3.002 2.056 -0.750 O2 TXS 21 TXS H21 H21 H 0 1 N N N 41.464 1.184 15.630 -5.630 -0.295 -0.213 H21 TXS 22 TXS H21A H21A H 0 0 N N N 42.558 0.878 14.287 -4.841 -0.626 1.356 H21A TXS 23 TXS H22 H22 H 0 1 N N N 43.956 -0.131 15.897 -4.969 -2.873 0.936 H22 TXS 24 TXS H22A H22A H 0 0 N N N 42.669 -0.225 17.090 -5.724 -2.541 -0.652 H22A TXS 25 TXS H23 H23 H 0 1 N N N 43.636 -2.399 15.469 -3.166 -3.625 -0.354 H23 TXS 26 TXS H23A H23A H 0 0 N N N 42.190 -2.455 16.459 -3.678 -2.674 -1.787 H23A TXS 27 TXS H24 H24 H 0 1 N N N 42.456 -1.786 13.482 -2.214 -1.692 0.726 H24 TXS 28 TXS H24A H24A H 0 0 N N N 41.204 -2.729 14.254 -1.809 -1.376 -0.993 H24A TXS 29 TXS "H5'" "H5'" H 0 1 N N N 40.703 0.943 13.142 -3.728 1.508 0.731 "H5'" TXS 30 TXS "H5'A" "H5'A" H 0 0 N N N 41.097 -0.631 12.427 -2.632 0.346 1.516 "H5'A" TXS 31 TXS "H4'" "H4'" H 0 1 N N N 38.933 -0.919 14.181 -2.088 1.810 -1.115 "H4'" TXS 32 TXS "H3'" "H3'" H 0 1 N N N 38.620 1.595 12.414 -1.338 2.289 1.775 "H3'" TXS 33 TXS "HO3'" "HO3'" H 0 0 N N N 38.430 1.301 14.801 -1.207 4.493 0.863 "HO3'" TXS 34 TXS "H2'" "H2'" H 0 1 N N N 35.980 0.496 12.462 0.788 3.252 0.014 "H2'" TXS 35 TXS "H2'A" "H2'A" H 0 0 N N N 36.914 0.379 11.073 0.925 2.075 1.358 "H2'A" TXS 36 TXS "H1'" "H1'" H 0 1 N N N 36.996 -1.459 13.576 0.506 1.568 -1.593 "H1'" TXS 37 TXS H6 H6 H 0 1 N N N 37.605 -3.512 13.776 0.514 -1.387 0.128 H6 TXS 38 TXS H5M H5M H 0 1 N N N 36.549 -6.802 13.384 2.435 -3.790 -0.221 H5M TXS 39 TXS H5MA H5MA H 0 0 N N N 37.406 -5.648 14.461 3.274 -3.462 1.315 H5MA TXS 40 TXS H5MB H5MB H 0 0 N N N 35.691 -6.075 14.786 1.504 -3.303 1.216 H5MB TXS 41 TXS HN3 HN3 H 0 1 N N N 33.657 -3.781 10.938 4.866 0.559 -0.272 HN3 TXS 42 # # 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 TXS C21 C22 SING N N 1 TXS C21 N25 SING N N 2 TXS C22 C23 SING N N 3 TXS C23 C24 SING N N 4 TXS C24 N25 SING N N 5 TXS N25 "C5'" SING N N 6 TXS "C5'" "C4'" SING N N 7 TXS "C4'" "O4'" SING N N 8 TXS "C4'" "C3'" SING N N 9 TXS "O4'" "C1'" SING N N 10 TXS "C3'" "O3'" SING N N 11 TXS "C3'" "C2'" SING N N 12 TXS "C2'" "C1'" SING N N 13 TXS "C1'" N1 SING N N 14 TXS N1 C6 SING N N 15 TXS N1 C2 SING N N 16 TXS C6 C5 DOUB N N 17 TXS C5 C5M SING N N 18 TXS C5 C4 SING N N 19 TXS C4 O4 DOUB N N 20 TXS C4 N3 SING N N 21 TXS N3 C2 SING N N 22 TXS C2 O2 DOUB N N 23 TXS C21 H21 SING N N 24 TXS C21 H21A SING N N 25 TXS C22 H22 SING N N 26 TXS C22 H22A SING N N 27 TXS C23 H23 SING N N 28 TXS C23 H23A SING N N 29 TXS C24 H24 SING N N 30 TXS C24 H24A SING N N 31 TXS "C5'" "H5'" SING N N 32 TXS "C5'" "H5'A" SING N N 33 TXS "C4'" "H4'" SING N N 34 TXS "C3'" "H3'" SING N N 35 TXS "O3'" "HO3'" SING N N 36 TXS "C2'" "H2'" SING N N 37 TXS "C2'" "H2'A" SING N N 38 TXS "C1'" "H1'" SING N N 39 TXS C6 H6 SING N N 40 TXS C5M H5M SING N N 41 TXS C5M H5MA SING N N 42 TXS C5M H5MB SING N N 43 TXS N3 HN3 SING N N 44 # # 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 TXS SMILES ACDLabs 10.04 "O=C1NC(=O)N(C=C1C)C2OC(C(O)C2)CN3CCCC3" TXS SMILES_CANONICAL CACTVS 3.341 "CC1=CN([C@@H]2C[C@@H](O)[C@H](CN3CCCC3)O2)C(=O)NC1=O" TXS SMILES CACTVS 3.341 "CC1=CN([CH]2C[CH](O)[CH](CN3CCCC3)O2)C(=O)NC1=O" TXS SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)[C@@H]2C[C@H]([C@@H](O2)CN3CCCC3)O" TXS SMILES "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)C2CC(C(O2)CN3CCCC3)O" TXS InChI InChI 1.03 "InChI=1S/C14H21N3O4/c1-9-7-17(14(20)15-13(9)19)12-6-10(18)11(21-12)8-16-4-2-3-5-16/h7,10-12,18H,2-6,8H2,1H3,(H,15,19,20)/t10-,11+,12+/m1/s1" TXS InChIKey InChI 1.03 XUSBTLVYPZUOAW-WOPDTQHZSA-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 TXS "SYSTEMATIC NAME" ACDLabs 10.04 "1-(2,5-dideoxy-5-pyrrolidin-1-yl-beta-L-erythro-pentofuranosyl)-5-methylpyrimidine-2,4(1H,3H)-dione" TXS "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "1-[(2S,4R,5S)-4-hydroxy-5-(pyrrolidin-1-ylmethyl)oxolan-2-yl]-5-methyl-pyrimidine-2,4-dione" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site TXS "Create component" 2008-05-28 PDBJ TXS "Modify descriptor" 2011-06-04 RCSB TXS "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id TXS _pdbx_chem_comp_synonyms.name "5'-deoxy-5'-pyrrolidin-1-ylthymidine" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##