data_6FU # _chem_comp.id 6FU _chem_comp.name "2'-trifluoromethylthio-2'-deoxyuridine" _chem_comp.type "RNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H14 F3 N2 O8 P S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2013-11-20 _chem_comp.pdbx_modified_date 2014-11-14 _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 410.261 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 6FU _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag Y _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 4NMG _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 6FU P P P 0 1 N N N 0.619 44.982 -16.204 5.060 -0.017 0.150 P 6FU 1 6FU OP1 OP1 O 0 1 N N N 1.800 44.728 -17.068 5.746 -0.209 -1.416 OP1 6FU 2 6FU OP2 OP2 O 0 1 N N N -0.028 43.821 -15.545 6.636 -0.009 0.839 OP2 6FU 3 6FU "O5'" "O5'" O 0 1 N N N 0.926 45.971 -15.030 3.484 -0.025 -0.539 "O5'" 6FU 4 6FU "C5'" "C5'" C 0 1 N N N 1.665 47.188 -15.238 2.508 0.676 0.235 "C5'" 6FU 5 6FU "C4'" "C4'" C 0 1 N N R 1.197 48.235 -14.251 1.160 0.634 -0.486 "C4'" 6FU 6 6FU "O4'" "O4'" O 0 1 N N N -0.089 48.654 -14.685 0.620 -0.705 -0.465 "O4'" 6FU 7 6FU "C3'" "C3'" C 0 1 N N R 1.023 47.753 -12.854 0.119 1.491 0.268 "C3'" 6FU 8 6FU "O3'" "O3'" O 0 1 N N N 2.258 47.866 -12.128 -0.005 2.778 -0.341 "O3'" 6FU 9 6FU "C2'" "C2'" C 0 1 N N R -0.040 48.632 -12.362 -1.197 0.696 0.125 "C2'" 6FU 10 6FU "S2'" "S2'" S 0 1 N N N 0.642 50.276 -11.843 -2.438 1.675 -0.765 "S2'" 6FU 11 6FU "C7'" "C7'" C 0 1 N N N -0.735 51.059 -10.984 -2.779 3.040 0.380 "C7'" 6FU 12 6FU "F1'" "F1'" F 0 1 N N N -1.798 51.390 -11.798 -3.736 3.892 -0.182 "F1'" 6FU 13 6FU "F2'" "F2'" F 0 1 N N N -1.272 50.288 -10.003 -3.265 2.526 1.588 "F2'" 6FU 14 6FU "F3'" "F3'" F 0 1 N N N -0.315 52.182 -10.406 -1.600 3.754 0.618 "F3'" 6FU 15 6FU "C1'" "C1'" C 0 1 N N R -0.957 48.804 -13.517 -0.797 -0.548 -0.699 "C1'" 6FU 16 6FU N1 N1 N 0 1 N N N -2.074 47.883 -13.609 -1.526 -1.729 -0.227 N1 6FU 17 6FU C2 C2 C 0 1 N N N -3.048 47.952 -12.664 -2.360 -2.375 -1.062 C2 6FU 18 6FU O2 O2 O 0 1 N N N -2.870 48.666 -11.658 -2.499 -1.971 -2.201 O2 6FU 19 6FU N3 N3 N 0 1 N N N -4.131 47.186 -12.768 -3.041 -3.461 -0.655 N3 6FU 20 6FU C4 C4 C 0 1 N N N -4.365 46.446 -13.852 -2.898 -3.922 0.604 C4 6FU 21 6FU O4 O4 O 0 1 N N N -5.477 45.707 -13.852 -3.514 -4.905 0.973 O4 6FU 22 6FU C5 C5 C 0 1 N N N -3.455 46.409 -14.918 -2.023 -3.251 1.493 C5 6FU 23 6FU C6 C6 C 0 1 N N N -2.275 47.163 -14.740 -1.347 -2.167 1.057 C6 6FU 24 6FU H1 H1 H 0 1 N N N 2.114 45.550 -17.425 6.712 -0.248 -1.420 H1 6FU 25 6FU H2 H2 H 0 1 N N N -0.765 44.121 -15.026 7.203 0.703 0.515 H2 6FU 26 6FU H3 H3 H 0 1 N N N 2.738 46.996 -15.088 2.412 0.205 1.213 H3 6FU 27 6FU H4 H4 H 0 1 N N N 1.497 47.549 -16.263 2.821 1.713 0.360 H4 6FU 28 6FU H5 H5 H 0 1 N N N 1.900 49.081 -14.262 1.268 0.985 -1.513 H5 6FU 29 6FU H6 H6 H 0 1 N N N 0.676 46.709 -12.862 0.394 1.589 1.318 H6 6FU 30 6FU H7 H7 H 0 1 N N N 2.133 47.555 -11.239 0.811 3.297 -0.333 H7 6FU 31 6FU H8 H8 H 0 1 N N N -0.558 48.205 -11.491 -1.575 0.402 1.105 H8 6FU 32 6FU H9 H9 H 0 1 N N N -1.347 49.832 -13.499 -0.990 -0.380 -1.758 H9 6FU 33 6FU H10 H10 H 0 1 N N N -4.787 47.165 -12.013 -3.639 -3.915 -1.270 H10 6FU 34 6FU H11 H11 H 0 1 N N N -3.644 45.841 -15.817 -1.892 -3.608 2.504 H11 6FU 35 6FU H12 H12 H 0 1 N N N -1.523 47.166 -15.515 -0.675 -1.643 1.721 H12 6FU 36 6FU OP3 OP3 O 0 1 N Y N ? ? ? 4.657 -1.402 1.088 OP3 6FU 37 6FU H13 H13 H 0 1 N N N ? ? ? 4.819 1.330 0.687 H13 6FU 38 6FU H14 H14 H 0 1 N N N ? ? ? 4.486 -2.196 0.563 H14 6FU 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 6FU OP1 P SING N N 1 6FU P OP2 SING N N 2 6FU P "O5'" SING N N 3 6FU "C5'" "O5'" SING N N 4 6FU "C5'" "C4'" SING N N 5 6FU C5 C6 DOUB N N 6 6FU C5 C4 SING N N 7 6FU C6 N1 SING N N 8 6FU "O4'" "C4'" SING N N 9 6FU "O4'" "C1'" SING N N 10 6FU "C4'" "C3'" SING N N 11 6FU O4 C4 DOUB N N 12 6FU C4 N3 SING N N 13 6FU N1 "C1'" SING N N 14 6FU N1 C2 SING N N 15 6FU "C1'" "C2'" SING N N 16 6FU "C3'" "C2'" SING N N 17 6FU "C3'" "O3'" SING N N 18 6FU N3 C2 SING N N 19 6FU C2 O2 DOUB N N 20 6FU "C2'" "S2'" SING N N 21 6FU "S2'" "C7'" SING N N 22 6FU "F1'" "C7'" SING N N 23 6FU "C7'" "F3'" SING N N 24 6FU "C7'" "F2'" SING N N 25 6FU OP1 H1 SING N N 26 6FU OP2 H2 SING N N 27 6FU "C5'" H3 SING N N 28 6FU "C5'" H4 SING N N 29 6FU "C4'" H5 SING N N 30 6FU "C3'" H6 SING N N 31 6FU "O3'" H7 SING N N 32 6FU "C2'" H8 SING N N 33 6FU "C1'" H9 SING N N 34 6FU N3 H10 SING N N 35 6FU C5 H11 SING N N 36 6FU C6 H12 SING N N 37 6FU P OP3 SING N N 38 6FU P H13 SING N N 39 6FU OP3 H14 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 6FU SMILES ACDLabs 12.01 "FC(F)(F)SC2C(O)C(OC2N1C(=O)NC(=O)C=C1)COP(O)(O)O" 6FU InChI InChI 1.03 "InChI=1S/C10H14F3N2O8PS/c11-10(12,13)25-7-6(17)4(3-22-24(19,20)21)23-8(7)15-2-1-5(16)14-9(15)18/h1-2,4,6-8,17,19-21,24H,3H2,(H,14,16,18)/t4-,6-,7-,8-/m1/s1" 6FU InChIKey InChI 1.03 HQACHJYAMJCNIP-XVFCMESISA-N 6FU SMILES_CANONICAL CACTVS 3.385 "O[C@@H]1[C@@H](CO[PH](O)(O)O)O[C@H]([C@@H]1SC(F)(F)F)N2C=CC(=O)NC2=O" 6FU SMILES CACTVS 3.385 "O[CH]1[CH](CO[PH](O)(O)O)O[CH]([CH]1SC(F)(F)F)N2C=CC(=O)NC2=O" 6FU SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(O)(O)O)O)SC(F)(F)F" 6FU SMILES "OpenEye OEToolkits" 1.7.6 "C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(O)(O)O)O)SC(F)(F)F" # 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 6FU "SYSTEMATIC NAME" ACDLabs 12.01 "2'-thio-2'-S-(trifluoromethyl)-5'-O-(trihydroxy-lambda~5~-phosphanyl)uridine" 6FU "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "1-[(2R,3R,4R,5R)-4-oxidanyl-3-(trifluoromethylsulfanyl)-5-[[tris(oxidanyl)-$l^{5}-phosphanyl]oxymethyl]oxolan-2-yl]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 6FU "Create component" 2013-11-20 RCSB 6FU "Initial release" 2014-11-19 RCSB #