data_N7X # _chem_comp.id N7X _chem_comp.name "5'-O-[(R)-hydroxy(sulfanylidene)-lambda~5~-phosphanyl]-2'-O-(2-methoxyethyl)-5-methylcytidine" _chem_comp.type "RNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C13 H22 N3 O8 P S" _chem_comp.mon_nstd_parent_comp_id C _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2020-02-11 _chem_comp.pdbx_modified_date 2021-02-05 _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 411.368 _chem_comp.one_letter_code C _chem_comp.three_letter_code N7X _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 6VRD _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 N7X C C1 C 0 1 N N N 8.557 42.695 20.925 -2.778 -2.710 -1.043 C N7X 1 N7X C1 C2 C 0 1 N N N 8.082 44.129 21.033 -3.727 -3.733 -0.415 C1 N7X 2 N7X "C1'" C3 C 0 1 N N R 8.203 39.793 21.661 -0.904 0.033 0.553 "C1'" N7X 3 N7X C12 C4 C 0 1 N N N 6.313 45.183 22.370 -5.632 -3.924 1.027 C12 N7X 4 N7X C2 C5 C 0 1 N N N 10.533 39.137 21.365 -1.542 1.856 -0.927 C2 N7X 5 N7X "C2'" C6 C 0 1 N N R 7.804 40.509 20.239 -1.104 -1.084 -0.496 "C2'" N7X 6 N7X "C3'" C7 C 0 1 N N R 6.827 39.794 19.826 0.303 -1.699 -0.662 "C3'" N7X 7 N7X C4 C8 C 0 1 N N N 11.195 36.917 21.271 -3.237 3.345 -0.431 C4 N7X 8 N7X "C4'" C9 C 0 1 N N R 5.972 39.569 21.126 1.187 -0.882 0.306 "C4'" N7X 9 N7X C5 C10 C 0 1 N N N 9.863 36.522 21.405 -3.466 2.674 0.788 C5 N7X 10 N7X "C5'" C11 C 0 1 N N N 5.089 38.470 21.014 2.573 -0.655 -0.301 "C5'" N7X 11 N7X C6 C12 C 0 1 N N N 8.866 37.474 21.514 -2.703 1.600 1.099 C6 N7X 12 N7X C7 C13 C 0 1 N N N 9.479 35.021 21.432 -4.543 3.147 1.731 C7 N7X 13 N7X N1 N1 N 0 1 N N N 9.237 38.786 21.507 -1.736 1.195 0.228 N1 N7X 14 N7X N3 N2 N 0 1 N N N 11.499 38.204 21.254 -2.284 2.914 -1.247 N3 N7X 15 N7X N4 N3 N 0 1 N N N 12.280 35.983 21.153 -3.997 4.439 -0.772 N4 N7X 16 N7X O12 O1 O 0 1 N N N 7.345 44.170 22.310 -4.693 -3.055 0.391 O12 N7X 17 N7X O2 O2 O 0 1 N N N 10.825 40.317 21.318 -0.668 1.482 -1.692 O2 N7X 18 N7X "O2'" O3 O 0 1 N N N 7.406 41.880 20.632 -2.026 -2.064 -0.014 "O2'" N7X 19 N7X "O3'" O4 O 0 1 N N N 5.988 40.431 18.785 0.294 -3.078 -0.287 "O3'" N7X 20 N7X "O4'" O5 O 0 1 N N N 7.092 39.260 22.106 0.496 0.377 0.463 "O4'" N7X 21 N7X "O5'" O6 O 0 1 N N N 5.884 37.300 20.878 3.410 -0.000 0.654 "O5'" N7X 22 N7X OP2 O7 O 0 1 N N N 6.214 34.728 20.372 5.688 0.745 1.737 OP2 N7X 23 N7X P P1 P 0 1 N N N 5.212 35.776 20.946 4.942 0.394 0.354 P N7X 24 N7X S S1 S 0 1 N N N 3.291 35.930 20.154 5.802 -1.038 -0.470 S N7X 25 N7X H1 H1 H 0 1 N N N 9.011 42.377 21.875 -2.098 -3.217 -1.727 H1 N7X 26 N7X H2 H2 H 0 1 N N N 9.297 42.604 20.117 -3.357 -1.966 -1.591 H2 N7X 27 N7X H3 H3 H 0 1 N N N 8.936 44.822 21.053 -4.236 -4.287 -1.203 H3 N7X 28 N7X H4 H4 H 0 1 N N N 7.421 44.385 20.192 -3.156 -4.424 0.205 H4 N7X 29 N7X H5 H5 H 0 1 N N N 8.565 40.587 22.330 -1.141 -0.336 1.550 H5 N7X 30 N7X H6 H6 H 0 1 N N N 5.817 45.144 23.351 -5.101 -4.620 1.677 H6 N7X 31 N7X H7 H7 H 0 1 N N N 6.765 46.176 22.227 -6.330 -3.334 1.619 H7 N7X 32 N7X H8 H8 H 0 1 N N N 5.573 45.000 21.577 -6.181 -4.483 0.269 H8 N7X 33 N7X H9 H9 H 0 1 N N N 8.684 40.520 19.579 -1.453 -0.664 -1.439 H9 N7X 34 N7X H10 H10 H 0 1 N N N 7.158 38.809 19.466 0.652 -1.584 -1.688 H10 N7X 35 N7X H11 H11 H 0 1 N N N 5.454 40.499 21.404 1.271 -1.391 1.266 H11 N7X 36 N7X H12 H12 H 0 1 N N N 4.446 38.593 20.130 3.013 -1.616 -0.571 H12 N7X 37 N7X H13 H13 H 0 1 N N N 4.463 38.397 21.916 2.483 -0.034 -1.192 H13 N7X 38 N7X H14 H14 H 0 1 N N N 7.828 37.188 21.602 -2.859 1.069 2.027 H14 N7X 39 N7X H15 H15 H 0 1 N N N 8.389 34.923 21.544 -5.041 4.018 1.306 H15 N7X 40 N7X H16 H16 H 0 1 N N N 9.796 34.545 20.492 -5.270 2.349 1.880 H16 N7X 41 N7X H17 H17 H 0 1 N N N 9.980 34.530 22.279 -4.096 3.415 2.688 H17 N7X 42 N7X H18 H18 H 0 1 N N N 13.219 36.316 21.063 -4.694 4.752 -0.173 H18 N7X 43 N7X H19 H19 H 0 1 N N N 12.097 35.000 21.161 -3.837 4.899 -1.611 H19 N7X 44 N7X "HO3'" H20 H 0 0 N Y N 5.289 39.838 18.534 1.153 -3.515 -0.372 H20 N7X 45 N7X HOP2 H21 H 0 0 N N N 7.038 34.788 20.840 6.616 0.992 1.631 H21 N7X 46 N7X OP3 OP3 O 0 1 N Y N ? ? ? 4.984 1.677 -0.619 OP3 N7X 47 N7X HOP3 H22 H 0 0 N Y N ? ? ? 4.554 2.462 -0.254 H22 N7X 48 # # 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 N7X "O3'" "C3'" SING N N 1 N7X "C3'" "C2'" SING N N 2 N7X "C3'" "C4'" SING N N 3 N7X S P DOUB N N 4 N7X "C2'" "O2'" SING N N 5 N7X "C2'" "C1'" SING N N 6 N7X OP2 P SING N N 7 N7X "O2'" C SING N N 8 N7X "O5'" P SING N N 9 N7X "O5'" "C5'" SING N N 10 N7X C C1 SING N N 11 N7X "C5'" "C4'" SING N N 12 N7X C1 O12 SING N N 13 N7X "C4'" "O4'" SING N N 14 N7X N4 C4 SING N N 15 N7X N3 C4 DOUB N N 16 N7X N3 C2 SING N N 17 N7X C4 C5 SING N N 18 N7X O2 C2 DOUB N N 19 N7X C2 N1 SING N N 20 N7X C5 C7 SING N N 21 N7X C5 C6 DOUB N N 22 N7X N1 C6 SING N N 23 N7X N1 "C1'" SING N N 24 N7X "C1'" "O4'" SING N N 25 N7X O12 C12 SING N N 26 N7X C H1 SING N N 27 N7X C H2 SING N N 28 N7X C1 H3 SING N N 29 N7X C1 H4 SING N N 30 N7X "C1'" H5 SING N N 31 N7X C12 H6 SING N N 32 N7X C12 H7 SING N N 33 N7X C12 H8 SING N N 34 N7X "C2'" H9 SING N N 35 N7X "C3'" H10 SING N N 36 N7X "C4'" H11 SING N N 37 N7X "C5'" H12 SING N N 38 N7X "C5'" H13 SING N N 39 N7X C6 H14 SING N N 40 N7X C7 H15 SING N N 41 N7X C7 H16 SING N N 42 N7X C7 H17 SING N N 43 N7X N4 H18 SING N N 44 N7X N4 H19 SING N N 45 N7X "O3'" "HO3'" SING N N 46 N7X OP2 HOP2 SING N N 47 N7X P OP3 SING N N 48 N7X OP3 HOP3 SING N N 49 # # 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 N7X SMILES ACDLabs 12.01 "C(COC)OC1C(OC(C1O)COP(O)(O)=S)N2C(N=C(C(C)=C2)N)=O" N7X InChI InChI 1.03 "InChI=1S/C13H22N3O8PS/c1-7-5-16(13(18)15-11(7)14)12-10(22-4-3-21-2)9(17)8(24-12)6-23-25(19,20)26/h5,8-10,12,17H,3-4,6H2,1-2H3,(H2,14,15,18)(H2,19,20,26)/t8-,9-,10-,12-/m1/s1" N7X InChIKey InChI 1.03 UINDLFLAAYRFRN-DNRKLUKYSA-N N7X SMILES_CANONICAL CACTVS 3.385 "COCCO[C@@H]1[C@H](O)[C@@H](CO[P](O)(O)=S)O[C@H]1N2C=C(C)C(=NC2=O)N" N7X SMILES CACTVS 3.385 "COCCO[CH]1[CH](O)[CH](CO[P](O)(O)=S)O[CH]1N2C=C(C)C(=NC2=O)N" N7X SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=S)(O)O)O)OCCOC" N7X SMILES "OpenEye OEToolkits" 2.0.7 "CC1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=S)(O)O)O)OCCOC" # # 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 N7X "SYSTEMATIC NAME" ACDLabs 12.01 "2'-O-(2-methoxyethyl)-5-methyl-5'-O-thiophosphonocytidine" N7X "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "4-azanyl-1-[(2~{R},3~{R},4~{R},5~{R})-5-[bis(oxidanyl)phosphinothioyloxymethyl]-3-(2-methoxyethoxy)-4-oxidanyl-oxolan-2-yl]-5-methyl-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 N7X "Create component" 2020-02-11 RCSB N7X "Initial release" 2021-02-10 RCSB ##