data_9QV # _chem_comp.id 9QV _chem_comp.name ;uridine 2',5'-bis(dihydrogen phosphate) ; _chem_comp.type "RNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C9 H14 N2 O12 P2" _chem_comp.mon_nstd_parent_comp_id U _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2017-05-31 _chem_comp.pdbx_modified_date 2018-05-04 _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 404.161 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 9QV _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 5VSU _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 9QV "O5'" O1 O 0 1 N N N 23.539 -7.362 -21.222 -3.678 -0.191 -0.496 "O5'" 9QV 1 9QV "C5'" C1 C 0 1 N N N 24.514 -7.718 -22.179 -2.700 -0.815 0.338 "C5'" 9QV 2 9QV "C4'" C2 C 0 1 N N R 24.073 -8.929 -22.946 -1.372 -0.910 -0.416 "C4'" 9QV 3 9QV "O4'" O2 O 0 1 N N N 24.627 -8.898 -24.277 -0.795 0.404 -0.584 "O4'" 9QV 4 9QV "C1'" C3 C 0 1 N N R 24.882 -10.207 -24.707 0.609 0.173 -0.831 "C1'" 9QV 5 9QV N1 N1 N 0 1 N N N 26.329 -10.304 -24.891 1.383 1.382 -0.537 N1 9QV 6 9QV C6 C4 C 0 1 N N N 27.121 -10.652 -23.834 2.224 1.895 -1.486 C6 9QV 7 9QV C5 C5 C 0 1 N N N 28.438 -10.746 -23.974 2.938 3.009 -1.215 C5 9QV 8 9QV C4 C6 C 0 1 N N N 29.042 -10.486 -25.249 2.799 3.625 0.052 C4 9QV 9 9QV O4 O3 O 0 1 N N N 30.254 -10.546 -25.481 3.432 4.630 0.319 O4 9QV 10 9QV N3 N2 N 0 1 N N N 28.162 -10.137 -26.260 1.960 3.087 0.960 N3 9QV 11 9QV C2 C7 C 0 1 N N N 26.800 -10.030 -26.151 1.257 1.979 0.662 C2 9QV 12 9QV O2 O4 O 0 1 N N N 26.065 -9.706 -27.074 0.503 1.506 1.491 O2 9QV 13 9QV "C2'" C8 C 0 1 N N R 24.402 -11.157 -23.608 0.999 -0.964 0.139 "C2'" 9QV 14 9QV "O2'" O5 O 0 1 N N N 23.034 -11.457 -23.828 1.934 -1.851 -0.479 "O2'" 9QV 15 9QV P P1 P 0 1 N N N 23.358 -5.851 -20.817 -5.195 0.072 -0.023 P 9QV 16 9QV O3P O6 O 0 1 N N N 22.697 -13.482 -22.145 4.133 -3.264 -0.761 O1P 9QV 17 9QV O2P O7 O 0 1 N N N 20.977 -13.168 -23.665 4.271 -0.762 0.037 O2P 9QV 18 9QV O1P O8 O 0 1 N N N 23.034 -14.083 -24.279 3.303 -2.563 1.518 O3P 9QV 19 9QV "C3'" C9 C 0 1 N N R 24.512 -10.268 -22.396 -0.335 -1.693 0.418 "C3'" 9QV 20 9QV "O3'" O9 O 0 1 N N N 23.684 -10.701 -21.341 -0.264 -3.052 -0.019 "O3'" 9QV 21 9QV P1 P2 P 0 1 N N N 22.472 -12.910 -23.513 3.408 -2.120 0.110 P1 9QV 22 9QV OP1 O10 O 0 1 N N N 24.744 -5.326 -20.991 -5.801 -1.202 0.422 OP1 9QV 23 9QV OP2 O11 O 0 1 N N N 22.178 -5.441 -21.612 -5.202 1.125 1.195 OP2 9QV 24 9QV H1 H1 H 0 1 N N N 25.462 -7.939 -21.666 -2.563 -0.223 1.243 H1 9QV 25 9QV H2 H2 H 0 1 N N N 24.661 -6.880 -22.877 -3.038 -1.816 0.606 H2 9QV 26 9QV H3 H3 H 0 1 N N N 22.975 -8.923 -23.009 -1.520 -1.388 -1.385 H3 9QV 27 9QV H4 H4 H 0 1 N N N 24.356 -10.433 -25.647 0.767 -0.138 -1.863 H4 9QV 28 9QV H5 H5 H 0 1 N N N 26.671 -10.853 -22.873 2.318 1.412 -2.447 H5 9QV 29 9QV H6 H6 H 0 1 N N N 29.054 -11.018 -23.129 3.606 3.425 -1.955 H6 9QV 30 9QV H7 H7 H 0 1 N N N 28.559 -9.944 -27.157 1.856 3.506 1.829 H7 9QV 31 9QV H8 H8 H 0 1 N N N 25.042 -12.048 -23.529 1.411 -0.556 1.061 H8 9QV 32 9QV H9 H9 H 0 1 N N N 23.095 -14.341 -22.222 5.027 -3.478 -0.461 H9 9QV 33 9QV H10 H10 H 0 1 N N N 20.842 -13.958 -24.175 4.380 -0.414 -0.858 H10 9QV 34 9QV H11 H11 H 0 1 N N N 25.563 -10.208 -22.075 -0.582 -1.645 1.478 H11 9QV 35 9QV H12 H12 H 0 1 N N N 23.783 -10.116 -20.599 -1.093 -3.540 0.077 H12 9QV 36 9QV H14 H14 H 0 1 N N N 22.438 -4.790 -22.253 -4.819 1.985 0.974 H14 9QV 37 9QV OP3 OP3 O 0 1 N Y N 22.926 -5.875 -19.261 -6.045 0.669 -1.253 OP3 9QV 38 9QV H16 H16 H 0 1 N Y N 23.641 -5.546 -18.728 -6.970 0.853 -1.040 H16 9QV 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 9QV O2 C2 DOUB N N 1 9QV N3 C2 SING N N 2 9QV N3 C4 SING N N 3 9QV C2 N1 SING N N 4 9QV O4 C4 DOUB N N 5 9QV C4 C5 SING N N 6 9QV N1 "C1'" SING N N 7 9QV N1 C6 SING N N 8 9QV "C1'" "O4'" SING N N 9 9QV "C1'" "C2'" SING N N 10 9QV O1P P1 DOUB N N 11 9QV "O4'" "C4'" SING N N 12 9QV C5 C6 DOUB N N 13 9QV "O2'" "C2'" SING N N 14 9QV "O2'" P1 SING N N 15 9QV O2P P1 SING N N 16 9QV "C2'" "C3'" SING N N 17 9QV P1 O3P SING N N 18 9QV "C4'" "C3'" SING N N 19 9QV "C4'" "C5'" SING N N 20 9QV "C3'" "O3'" SING N N 21 9QV "C5'" "O5'" SING N N 22 9QV OP2 P SING N N 23 9QV "O5'" P SING N N 24 9QV OP1 P DOUB N N 25 9QV "C5'" H1 SING N N 26 9QV "C5'" H2 SING N N 27 9QV "C4'" H3 SING N N 28 9QV "C1'" H4 SING N N 29 9QV C6 H5 SING N N 30 9QV C5 H6 SING N N 31 9QV N3 H7 SING N N 32 9QV "C2'" H8 SING N N 33 9QV O3P H9 SING N N 34 9QV O2P H10 SING N N 35 9QV "C3'" H11 SING N N 36 9QV "O3'" H12 SING N N 37 9QV OP2 H14 SING N N 38 9QV P OP3 SING N N 39 9QV OP3 H16 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 9QV SMILES ACDLabs 12.01 "O(P(O)(=O)O)CC1C(C(C(O1)N2C=CC(=O)NC2=O)OP(O)(O)=O)O" 9QV InChI InChI 1.03 "InChI=1S/C9H14N2O12P2/c12-5-1-2-11(9(14)10-5)8-7(23-25(18,19)20)6(13)4(22-8)3-21-24(15,16)17/h1-2,4,6-8,13H,3H2,(H,10,12,14)(H2,15,16,17)(H2,18,19,20)/t4-,6-,7-,8-/m1/s1" 9QV InChIKey InChI 1.03 HQYLGYLPRPXVMN-XVFCMESISA-N 9QV SMILES_CANONICAL CACTVS 3.385 "O[C@@H]1[C@@H](CO[P](O)(O)=O)O[C@H]([C@@H]1O[P](O)(O)=O)N2C=CC(=O)NC2=O" 9QV SMILES CACTVS 3.385 "O[CH]1[CH](CO[P](O)(O)=O)O[CH]([CH]1O[P](O)(O)=O)N2C=CC(=O)NC2=O" 9QV SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)OP(=O)(O)O" 9QV SMILES "OpenEye OEToolkits" 2.0.6 "C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)OP(=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 9QV "SYSTEMATIC NAME" ACDLabs 12.01 ;uridine 2',5'-bis(dihydrogen phosphate) ; 9QV "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[(2~{R},3~{R},4~{R},5~{R})-2-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-4-oxidanyl-5-(phosphonooxymethyl)oxolan-3-yl] 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 9QV "Create component" 2017-05-31 RCSB 9QV "Initial release" 2018-05-09 RCSB #