data_6FC # _chem_comp.id 6FC _chem_comp.name "2'-trifluoromethylthio-2'-deoxycytidine" _chem_comp.type "RNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H15 F3 N3 O7 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 409.276 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 6FC _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 4NLF _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 6FC P P P 0 1 N N N 15.185 6.923 7.825 4.963 -0.320 0.229 P 6FC 1 6FC OP1 OP1 O 0 1 N N N 15.237 7.546 6.456 5.424 -1.592 -0.833 OP1 6FC 2 6FC "O5'" "O5'" O 0 1 N N N 16.166 7.657 8.849 3.400 -0.287 -0.490 "O5'" 6FC 3 6FC "C5'" "C5'" C 0 1 N N N 16.185 9.070 9.016 2.424 0.424 0.274 "C5'" 6FC 4 6FC "C4'" "C4'" C 0 1 N N R 16.953 9.463 10.230 1.115 0.497 -0.514 "C4'" 6FC 5 6FC "C3'" "C3'" C 0 1 N N R 18.391 8.994 10.313 0.083 1.368 0.236 "C3'" 6FC 6 6FC "O3'" "O3'" O 0 1 N N N 19.244 9.842 9.543 0.059 2.692 -0.302 "O3'" 6FC 7 6FC "C7'" "C7'" C 0 1 N N N 19.461 10.689 13.949 -2.731 3.067 0.296 "C7'" 6FC 8 6FC "F1'" "F1'" F 0 1 N N N 19.774 11.902 14.373 -1.530 3.701 0.633 "F1'" 6FC 9 6FC "F2'" "F2'" F 0 1 N N N 20.521 9.898 14.071 -3.306 2.515 1.446 "F2'" 6FC 10 6FC "F3'" "F3'" F 0 1 N N N 18.510 10.237 14.764 -3.611 4.002 -0.262 "F3'" 6FC 11 6FC "C2'" "C2'" C 0 1 N N R 18.634 9.059 11.767 -1.265 0.656 -0.017 "C2'" 6FC 12 6FC "S2'" "S2'" S 0 1 N N N 18.941 10.800 12.263 -2.404 1.751 -0.908 "S2'" 6FC 13 6FC "C1'" "C1'" C 0 1 N N R 17.368 8.497 12.320 -0.888 -0.561 -0.891 "C1'" 6FC 14 6FC "O4'" "O4'" O 0 1 N N N 16.320 8.898 11.396 0.504 -0.809 -0.597 "O4'" 6FC 15 6FC N1 N1 N 0 1 N N N 17.369 7.052 12.460 -1.702 -1.723 -0.525 N1 6FC 16 6FC C6 C6 C 0 1 N N N 16.714 6.266 11.576 -2.583 -2.243 -1.424 C6 6FC 17 6FC C5 C5 C 0 1 N N N 16.713 4.885 11.732 -3.330 -3.318 -1.074 C5 6FC 18 6FC C4 C4 C 0 1 N N N 17.422 4.393 12.828 -3.173 -3.868 0.214 C4 6FC 19 6FC N4 N4 N 0 1 N N N 17.439 3.016 13.022 -3.918 -4.959 0.596 N4 6FC 20 6FC N3 N3 N 0 1 N N N 18.061 5.195 13.686 -2.303 -3.327 1.057 N3 6FC 21 6FC C2 C2 C 0 1 N N N 18.021 6.502 13.492 -1.571 -2.273 0.696 C2 6FC 22 6FC O2 O2 O 0 1 N N N 18.593 7.244 14.275 -0.774 -1.797 1.487 O2 6FC 23 6FC OP2 OP2 O 0 1 N N N 15.503 5.457 7.928 5.210 1.318 -0.233 OP2 6FC 24 6FC H1 H1 H 0 1 N N N 14.643 7.085 5.875 6.332 -1.900 -0.706 H1 6FC 25 6FC "H5'1" "H5'1" H 0 0 N N N 16.653 9.529 8.132 2.252 -0.095 1.217 "H5'1" 6FC 26 6FC "H5'2" "H5'2" H 0 0 N N N 15.151 9.433 9.113 2.784 1.433 0.474 "H5'2" 6FC 27 6FC "H4'1" "H4'1" H 0 0 N N N 16.944 10.560 10.310 1.295 0.897 -1.512 "H4'1" 6FC 28 6FC "H3'1" "H3'1" H 0 0 N N N 18.459 7.953 9.965 0.309 1.394 1.303 "H3'1" 6FC 29 6FC H2 H2 H 0 1 N N N 20.140 9.533 9.607 0.900 3.163 -0.224 H2 6FC 30 6FC "H2'1" "H2'1" H 0 0 N N N 19.511 8.467 12.068 -1.708 0.331 0.925 "H2'1" 6FC 31 6FC "H1'1" "H1'1" H 0 0 N N N 17.179 8.955 13.302 -1.017 -0.324 -1.947 "H1'1" 6FC 32 6FC H61 H61 H 0 1 N N N 16.189 6.713 10.745 -2.685 -1.804 -2.406 H61 6FC 33 6FC H51 H51 H 0 1 N N N 16.194 4.232 11.046 -4.034 -3.746 -1.772 H51 6FC 34 6FC H41 H41 H 0 1 N N N 17.929 2.627 13.802 -4.554 -5.352 -0.022 H41 6FC 35 6FC H42 H42 H 0 1 N N N 16.962 2.415 12.381 -3.809 -5.335 1.483 H42 6FC 36 6FC H3 H3 H 0 1 N N N 15.438 5.181 8.835 5.188 1.465 -1.189 H3 6FC 37 6FC OP3 OP3 O 0 1 N Y N ? ? ? 6.525 -0.353 0.948 OP3 6FC 38 6FC H4 H4 H 0 1 N N N ? ? ? 4.357 -0.633 1.531 H4 6FC 39 6FC H5 H5 H 0 1 N N N ? ? ? 6.755 -1.202 1.350 H5 6FC 40 # 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 6FC P OP1 SING N N 1 6FC P "O5'" SING N N 2 6FC P OP2 SING N N 3 6FC "O5'" "C5'" SING N N 4 6FC "C5'" "C4'" SING N N 5 6FC "C4'" "C3'" SING N N 6 6FC "C4'" "O4'" SING N N 7 6FC "C3'" "O3'" SING N N 8 6FC "C3'" "C2'" SING N N 9 6FC "C7'" "F1'" SING N N 10 6FC "C7'" "F2'" SING N N 11 6FC "C7'" "F3'" SING N N 12 6FC "C7'" "S2'" SING N N 13 6FC "C2'" "S2'" SING N N 14 6FC "C2'" "C1'" SING N N 15 6FC "C1'" "O4'" SING N N 16 6FC "C1'" N1 SING N N 17 6FC N1 C6 SING N N 18 6FC N1 C2 SING N N 19 6FC C6 C5 DOUB N N 20 6FC C5 C4 SING N N 21 6FC C4 N4 SING N N 22 6FC C4 N3 DOUB N N 23 6FC N3 C2 SING N N 24 6FC C2 O2 DOUB N N 25 6FC OP1 H1 SING N N 26 6FC "C5'" "H5'1" SING N N 27 6FC "C5'" "H5'2" SING N N 28 6FC "C4'" "H4'1" SING N N 29 6FC "C3'" "H3'1" SING N N 30 6FC "O3'" H2 SING N N 31 6FC "C2'" "H2'1" SING N N 32 6FC "C1'" "H1'1" SING N N 33 6FC C6 H61 SING N N 34 6FC C5 H51 SING N N 35 6FC N4 H41 SING N N 36 6FC N4 H42 SING N N 37 6FC OP2 H3 SING N N 38 6FC P OP3 SING N N 39 6FC P H4 SING N N 40 6FC OP3 H5 SING N N 41 # 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 6FC SMILES ACDLabs 12.01 "FC(F)(F)SC2C(O)C(OC2N1C(=O)N=C(N)C=C1)COP(O)(O)O" 6FC InChI InChI 1.03 "InChI=1S/C10H15F3N3O7PS/c11-10(12,13)25-7-6(17)4(3-22-24(19,20)21)23-8(7)16-2-1-5(14)15-9(16)18/h1-2,4,6-8,17,19-21,24H,3H2,(H2,14,15,18)/t4-,6-,7-,8-/m1/s1" 6FC InChIKey InChI 1.03 RXIZMKBDEBXDBO-XVFCMESISA-N 6FC SMILES_CANONICAL CACTVS 3.385 "NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[PH](O)(O)O)[C@@H](O)[C@H]2SC(F)(F)F" 6FC SMILES CACTVS 3.385 "NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[PH](O)(O)O)[CH](O)[CH]2SC(F)(F)F" 6FC SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(O)(O)O)O)SC(F)(F)F" 6FC SMILES "OpenEye OEToolkits" 1.7.6 "C1=CN(C(=O)N=C1N)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 6FC "SYSTEMATIC NAME" ACDLabs 12.01 "2'-thio-2'-S-(trifluoromethyl)-5'-O-(trihydroxy-lambda~5~-phosphanyl)cytidine" 6FC "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "4-azanyl-1-[(2R,3R,4R,5R)-4-oxidanyl-3-(trifluoromethylsulfanyl)-5-[[tris(oxidanyl)-$l^{5}-phosphanyl]oxymethyl]oxolan-2-yl]pyrimidin-2-one" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site 6FC "Create component" 2013-11-20 RCSB 6FC "Initial release" 2014-11-19 RCSB #