data_9V9 # _chem_comp.id 9V9 _chem_comp.name "1-{2,5-anhydro-4-[(phosphonooxy)methyl]-alpha-L-lyxofuranosyl}-5-methyl-2-sulfanylidene-2,3-dihydropyrimidin-4(1H)-one" _chem_comp.type "RNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C11 H15 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 2018-08-16 _chem_comp.pdbx_modified_date 2019-03-22 _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 366.284 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 9V9 _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 6ADV _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 9V9 C4 C1 C 0 1 N N N 1.592 -1.368 -1.261 -4.235 -1.727 0.053 C4 9V9 1 9V9 C5 C2 C 0 1 N N N 2.942 -0.937 -1.686 -2.912 -2.112 0.375 C5 9V9 2 9V9 C6 C3 C 0 1 N N N 3.157 0.426 -1.804 -1.905 -1.235 0.173 C6 9V9 3 9V9 P P1 P 0 1 N N N 7.425 2.489 -3.821 4.589 -0.763 -0.393 P 9V9 4 9V9 OP1 O1 O 0 1 N N N 8.247 3.747 -4.060 5.403 -0.284 0.747 OP1 9V9 5 9V9 OP2 O2 O 0 1 N N N 8.011 1.213 -3.326 4.352 -2.349 -0.254 OP2 9V9 6 9V9 "O5'" O3 O 0 1 N N N 6.236 2.825 -2.793 3.169 -0.005 -0.393 "O5'" 9V9 7 9V9 "C5'" C4 C 0 1 N N N 5.557 4.041 -3.099 2.291 0.003 0.734 "C5'" 9V9 8 9V9 "C4'" C5 C 0 1 N N R 4.261 4.080 -2.334 1.035 0.810 0.397 "C4'" 9V9 9 9V9 "O4'" O4 O 0 1 N N N 3.406 3.022 -2.749 0.174 0.259 -0.640 "O4'" 9V9 10 9V9 "C1'" C6 C 0 1 N N R 2.435 2.806 -1.679 -1.085 0.956 -0.554 "C1'" 9V9 11 9V9 N1 N1 N 0 1 N N N 2.187 1.335 -1.546 -2.178 0.004 -0.336 N1 9V9 12 9V9 C2 C7 C 0 1 N N N 0.899 0.888 -1.139 -3.440 0.359 -0.637 C2 9V9 13 9V9 N3 N2 N 0 1 N N N 0.652 -0.429 -1.013 -4.462 -0.497 -0.451 N3 9V9 14 9V9 O4 O5 O 0 1 N N N 1.332 -2.584 -1.134 -5.160 -2.500 0.226 O4 9V9 15 9V9 C5M C8 C 0 1 N N N 4.014 -1.972 -1.970 -2.630 -3.483 0.935 C5M 9V9 16 9V9 S1 S1 S 0 1 N N N -0.259 1.958 -0.830 -3.750 1.918 -1.273 S1 9V9 17 9V9 "C2'" C9 C 0 1 N N R 2.937 3.779 -0.645 -0.946 1.911 0.673 "C2'" 9V9 18 9V9 "O2'" O6 O 0 1 N N N 2.606 5.096 -1.188 -0.043 2.952 0.202 "O2'" 9V9 19 9V9 "C6'" C10 C 0 1 N N N 3.425 5.343 -2.334 1.256 2.297 -0.022 "C6'" 9V9 20 9V9 "C3'" C11 C 0 1 N N S 4.399 3.852 -0.847 0.005 1.032 1.563 "C3'" 9V9 21 9V9 "O3'" O7 O 0 1 N N N 4.803 5.001 -0.125 0.569 1.747 2.664 "O3'" 9V9 22 9V9 H1 H1 H 0 1 N N N 4.131 0.776 -2.112 -0.888 -1.512 0.413 H1 9V9 23 9V9 H2 H2 H 0 1 N N N 8.945 1.323 -3.194 3.825 -2.732 -0.969 H3 9V9 24 9V9 H4 H4 H 0 1 N N N 6.183 4.897 -2.808 2.010 -1.020 0.984 H4 9V9 25 9V9 H5 H5 H 0 1 N N N 5.350 4.087 -4.178 2.798 0.459 1.586 H5 9V9 26 9V9 H6 H6 H 0 1 N N N 1.488 3.231 -2.043 -1.262 1.530 -1.464 H6 9V9 27 9V9 H7 H7 H 0 1 N N N -0.259 -0.723 -0.726 -5.366 -0.227 -0.677 H7 9V9 28 9V9 H8 H8 H 0 1 N N N 3.604 -2.980 -1.807 -3.564 -4.038 1.024 H8 9V9 29 9V9 H9 H9 H 0 1 N N N 4.348 -1.877 -3.014 -1.953 -4.016 0.268 H9 9V9 30 9V9 H10 H10 H 0 1 N N N 4.868 -1.810 -1.296 -2.170 -3.386 1.918 H10 9V9 31 9V9 H11 H11 H 0 1 N N N 2.605 3.583 0.385 -1.874 2.248 1.133 H11 9V9 32 9V9 H12 H12 H 0 1 N N N 4.045 6.243 -2.207 2.043 2.747 0.583 H12 9V9 33 9V9 H13 H13 H 0 1 N N N 2.826 5.437 -3.252 1.510 2.357 -1.080 H13 9V9 34 9V9 H14 H14 H 0 1 N N N 4.935 2.926 -0.592 -0.477 0.106 1.878 H14 9V9 35 9V9 H15 H15 H 0 1 N N N 4.870 4.788 0.798 -0.048 1.895 3.394 H15 9V9 36 9V9 OP3 OP3 O 0 1 N Y N 6.646 2.166 -5.175 5.362 -0.454 -1.771 OP3 9V9 37 9V9 H3 H3 H 0 1 N Y N 6.861 2.821 -5.829 6.228 -0.879 -1.841 H2 9V9 38 # # 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 9V9 OP1 P DOUB N N 1 9V9 P OP2 SING N N 2 9V9 P "O5'" SING N N 3 9V9 "C5'" "O5'" SING N N 4 9V9 "C5'" "C4'" SING N N 5 9V9 "O4'" "C4'" SING N N 6 9V9 "O4'" "C1'" SING N N 7 9V9 "C6'" "C4'" SING N N 8 9V9 "C6'" "O2'" SING N N 9 9V9 "C4'" "C3'" SING N N 10 9V9 C5M C5 SING N N 11 9V9 C6 C5 DOUB N N 12 9V9 C6 N1 SING N N 13 9V9 C5 C4 SING N N 14 9V9 "C1'" N1 SING N N 15 9V9 "C1'" "C2'" SING N N 16 9V9 N1 C2 SING N N 17 9V9 C4 O4 DOUB N N 18 9V9 C4 N3 SING N N 19 9V9 "O2'" "C2'" SING N N 20 9V9 C2 N3 SING N N 21 9V9 C2 S1 DOUB N N 22 9V9 "C3'" "C2'" SING N N 23 9V9 "C3'" "O3'" SING N N 24 9V9 C6 H1 SING N N 25 9V9 OP2 H2 SING N N 26 9V9 "C5'" H4 SING N N 27 9V9 "C5'" H5 SING N N 28 9V9 "C1'" H6 SING N N 29 9V9 N3 H7 SING N N 30 9V9 C5M H8 SING N N 31 9V9 C5M H9 SING N N 32 9V9 C5M H10 SING N N 33 9V9 "C2'" H11 SING N N 34 9V9 "C6'" H12 SING N N 35 9V9 "C6'" H13 SING N N 36 9V9 "C3'" H14 SING N N 37 9V9 "O3'" H15 SING N N 38 9V9 P OP3 SING N N 39 9V9 OP3 H3 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 9V9 SMILES ACDLabs 12.01 "C1(=O)NC(N(C=C1C)C2OC3(COP(O)(O)=O)C(C2OC3)O)=S" 9V9 InChI InChI 1.03 "InChI=1S/C11H15N2O8PS/c1-5-2-13(10(23)12-8(5)15)9-6-7(14)11(21-9,3-19-6)4-20-22(16,17)18/h2,6-7,9,14H,3-4H2,1H3,(H,12,15,23)(H2,16,17,18)/t6-,7+,9-,11-/m1/s1" 9V9 InChIKey InChI 1.03 OQJRNZAUGSRQOO-YRCORFKGSA-N 9V9 SMILES_CANONICAL CACTVS 3.385 "CC1=CN([C@@H]2O[C@]3(CO[C@@H]2[C@@H]3O)CO[P](O)(O)=O)C(=S)NC1=O" 9V9 SMILES CACTVS 3.385 "CC1=CN([CH]2O[C]3(CO[CH]2[CH]3O)CO[P](O)(O)=O)C(=S)NC1=O" 9V9 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "CC1=CN(C(=S)NC1=O)[C@H]2[C@H]3[C@@H]([C@@](O2)(CO3)COP(=O)(O)O)O" 9V9 SMILES "OpenEye OEToolkits" 2.0.6 "CC1=CN(C(=S)NC1=O)C2C3C(C(O2)(CO3)COP(=O)(O)O)O" # # 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 9V9 "SYSTEMATIC NAME" ACDLabs 12.01 "1-{2,5-anhydro-4-[(phosphonooxy)methyl]-alpha-L-lyxofuranosyl}-5-methyl-2-sulfanylidene-2,3-dihydropyrimidin-4(1H)-one" 9V9 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[(1~{R},3~{R},4~{R},7~{S})-3-(5-methyl-4-oxidanylidene-2-sulfanylidene-pyrimidin-1-yl)-7-oxidanyl-2,5-dioxabicyclo[2.2.1]heptan-1-yl]methyl dihydrogen phosphate" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site 9V9 "Create component" 2018-08-16 PDBJ 9V9 "Initial release" 2019-03-27 RCSB ##