data_QSK # _chem_comp.id QSK _chem_comp.name "[(2~{R},3~{R},4~{R},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3-oxidanyl-4-(trifluoromethyloxy)oxolan-2-yl]methoxyphosphinic acid" _chem_comp.type "RNA linking" _chem_comp.pdbx_type HETAIN _chem_comp.formula "C10 H13 F3 N3 O7 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2020-07-31 _chem_comp.pdbx_modified_date 2020-12-11 _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 375.195 _chem_comp.one_letter_code ? _chem_comp.three_letter_code QSK _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 6ZYB _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBE # # 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 QSK P P1 P 0 1 N N N -14.210 7.615 -6.918 5.125 0.534 -0.270 P QSK 1 QSK OP1 O1 O 0 1 N N N -15.537 7.919 -7.442 5.792 1.702 0.613 OP1 QSK 2 QSK "O5'" O2 O 0 1 N N N -13.249 6.561 -7.723 3.662 0.191 0.310 "O5'" QSK 3 QSK "C5'" C1 C 0 1 N N N -13.366 6.401 -9.087 2.694 -0.565 -0.419 "C5'" QSK 4 QSK "C4'" C2 C 0 1 N N R -12.123 5.614 -9.495 1.421 -0.705 0.419 "C4'" QSK 5 QSK "C3'" C3 C 0 1 N N R -12.101 4.195 -8.965 0.405 -1.624 -0.296 "C3'" QSK 6 QSK "O3'" O3 O 0 1 N N N -12.686 3.396 -9.684 0.470 -2.949 0.235 "O3'" QSK 7 QSK "C7'" C4 C 0 1 N N N -9.045 3.108 -10.824 -2.625 -2.707 -0.077 "C7'" QSK 8 QSK "F1'" F1 F 0 1 N N N -8.934 1.908 -10.211 -3.389 -3.555 0.733 "F1'" QSK 9 QSK "F2'" F2 F 0 1 N N N -8.028 3.947 -10.485 -1.828 -3.474 -0.933 "F2'" QSK 10 QSK "F3'" F3 F 0 1 N N N -9.007 2.910 -12.160 -3.476 -1.895 -0.835 "F3'" QSK 11 QSK "C2'" C5 C 0 1 N N R -10.591 3.996 -9.193 -0.965 -0.980 0.012 "C2'" QSK 12 QSK "C1'" C6 C 0 1 N N R -10.046 5.338 -8.624 -0.616 0.251 0.876 "C1'" QSK 13 QSK "O4'" O4 O 0 1 N N N -11.018 6.303 -8.958 0.750 0.569 0.530 "O4'" QSK 14 QSK N1 N1 N 0 1 N N N -9.754 5.385 -7.236 -1.499 1.372 0.547 N1 QSK 15 QSK C6 C7 C 0 1 N N N -10.551 6.110 -6.330 -2.366 1.850 1.484 C6 QSK 16 QSK C5 C8 C 0 1 N N N -10.233 6.156 -5.069 -3.177 2.887 1.168 C5 QSK 17 QSK C4 C9 C 0 1 N N N -8.983 5.401 -4.625 -3.102 3.444 -0.125 C4 QSK 18 QSK N4 N2 N 0 1 N N N -8.685 5.454 -3.243 -3.914 4.498 -0.472 N4 QSK 19 QSK N3 N3 N 0 1 N N N -8.251 4.732 -5.421 -2.243 2.946 -1.004 N3 QSK 20 QSK C2 C10 C 0 1 N N N -8.599 4.707 -6.802 -1.447 1.929 -0.677 C2 QSK 21 QSK O2 O5 O 0 1 N N N -7.823 4.017 -7.713 -0.662 1.492 -1.502 O2 QSK 22 QSK OP2 O6 O 0 1 N N N -13.944 7.593 -5.490 5.975 -0.676 -0.211 OP2 QSK 23 QSK "O2'" O7 O 0 1 N N N -10.281 3.668 -10.515 -1.791 -1.888 0.745 "O2'" QSK 24 QSK H1 H1 H 0 1 N N N -13.539 8.817 -7.265 5.010 0.966 -1.618 H1 QSK 25 QSK H2 H2 H 0 1 N N N -16.133 8.084 -6.721 6.677 1.960 0.320 H2 QSK 26 QSK "H5'2" H3 H 0 0 N N N -13.389 7.378 -9.591 2.460 -0.053 -1.352 "H5'2" QSK 27 QSK "H5'1" H4 H 0 0 N N N -14.279 5.839 -9.334 3.095 -1.555 -0.638 "H5'1" QSK 28 QSK "H4'1" H5 H 0 0 N N N -12.064 5.587 -10.593 1.659 -1.098 1.407 "H4'1" QSK 29 QSK "H3'1" H6 H 0 0 N N N -12.344 4.165 -7.893 0.589 -1.634 -1.370 "H3'1" QSK 30 QSK H3 H7 H 0 1 N N N -12.637 2.529 -9.300 1.329 -3.377 0.121 H3 QSK 31 QSK H4 H8 H 0 1 N N N -10.254 3.191 -8.524 -1.459 -0.673 -0.910 H4 QSK 32 QSK "H1'1" H9 H 0 0 N N N -9.124 5.565 -9.180 -0.693 0.006 1.936 "H1'1" QSK 33 QSK H61 H10 H 0 1 N N N -11.429 6.630 -6.683 -2.405 1.406 2.468 H61 QSK 34 QSK H51 H11 H 0 1 N N N -10.833 6.709 -4.361 -3.872 3.282 1.896 H51 QSK 35 QSK H42 H12 H 0 1 N N N -7.892 4.962 -2.883 -4.541 4.861 0.173 H42 QSK 36 QSK H41 H13 H 0 1 N N N -9.267 5.983 -2.626 -3.860 4.879 -1.363 H41 QSK 37 # # 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 QSK "F3'" "C7'" SING N N 1 QSK "C7'" "O2'" SING N N 2 QSK "C7'" "F2'" SING N N 3 QSK "C7'" "F1'" SING N N 4 QSK "O2'" "C2'" SING N N 5 QSK "O3'" "C3'" SING N N 6 QSK "C4'" "C5'" SING N N 7 QSK "C4'" "C3'" SING N N 8 QSK "C4'" "O4'" SING N N 9 QSK "C2'" "C3'" SING N N 10 QSK "C2'" "C1'" SING N N 11 QSK "C5'" "O5'" SING N N 12 QSK "O4'" "C1'" SING N N 13 QSK "C1'" N1 SING N N 14 QSK "O5'" P SING N N 15 QSK O2 C2 DOUB N N 16 QSK OP1 P SING N N 17 QSK N1 C2 SING N N 18 QSK N1 C6 SING N N 19 QSK P OP2 DOUB N N 20 QSK C2 N3 SING N N 21 QSK C6 C5 DOUB N N 22 QSK N3 C4 DOUB N N 23 QSK C5 C4 SING N N 24 QSK C4 N4 SING N N 25 QSK P H1 SING N N 26 QSK OP1 H2 SING N N 27 QSK "C5'" "H5'2" SING N N 28 QSK "C5'" "H5'1" SING N N 29 QSK "C4'" "H4'1" SING N N 30 QSK "C3'" "H3'1" SING N N 31 QSK "O3'" H3 SING N N 32 QSK "C2'" H4 SING N N 33 QSK "C1'" "H1'1" SING N N 34 QSK C6 H61 SING N N 35 QSK C5 H51 SING N N 36 QSK N4 H42 SING N N 37 QSK N4 H41 SING N N 38 # # 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 QSK InChI InChI 1.03 "InChI=1S/C10H13F3N3O7P/c11-10(12,13)23-7-6(17)4(3-21-24(19)20)22-8(7)16-2-1-5(14)15-9(16)18/h1-2,4,6-8,17,24H,3H2,(H,19,20)(H2,14,15,18)/t4-,6-,7-,8-/m1/s1" QSK InChIKey InChI 1.03 IPIXNCWZLCXCPY-XVFCMESISA-N QSK SMILES_CANONICAL CACTVS 3.385 "NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[PH](O)=O)[C@@H](O)[C@H]2OC(F)(F)F" QSK SMILES CACTVS 3.385 "NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[PH](O)=O)[CH](O)[CH]2OC(F)(F)F" QSK SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)O)O)OC(F)(F)F" QSK SMILES "OpenEye OEToolkits" 2.0.7 "C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)O)O)OC(F)(F)F" # _pdbx_chem_comp_identifier.comp_id QSK _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.7 _pdbx_chem_comp_identifier.identifier "[(2~{R},3~{R},4~{R},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3-oxidanyl-4-(trifluoromethyloxy)oxolan-2-yl]methoxyphosphinic acid" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site QSK "Create component" 2020-07-31 PDBE QSK "Initial release" 2020-12-16 RCSB ##