data_U23 # _chem_comp.id U23 _chem_comp.name "URIDINE-5'-MONOPHOSPHATE-2',3'-CYCLIC PHOSPHATE" _chem_comp.type "RNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C9 H12 N2 O11 P2" _chem_comp.mon_nstd_parent_comp_id U _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2020-07-31 _chem_comp.pdbx_modified_date 2020-09-04 _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 386.146 _chem_comp.one_letter_code U _chem_comp.three_letter_code U23 _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 7JJU _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 U23 N1 N1 N 0 1 N N N 64.028 46.229 76.004 -2.231 -1.048 -0.222 N1 U23 1 U23 C2 C1 C 0 1 N N N 64.697 45.492 75.077 -3.245 -1.390 -1.038 C2 U23 2 U23 O2 O1 O 0 1 N N N 65.790 45.026 75.348 -3.322 -0.887 -2.142 O2 U23 3 U23 N3 N2 N 0 1 N N N 64.153 45.270 73.845 -4.175 -2.281 -0.649 N3 U23 4 U23 C4 C2 C 0 1 N N N 62.921 45.809 73.571 -4.105 -2.849 0.572 C4 U23 5 U23 O4 O2 O 0 1 N N N 62.413 45.622 72.467 -4.946 -3.656 0.925 O4 U23 6 U23 C5 C3 C 0 1 N N N 62.226 46.576 74.535 -3.043 -2.497 1.441 C5 U23 7 U23 C6 C4 C 0 1 N N N 62.798 46.770 75.734 -2.124 -1.600 1.025 C6 U23 8 U23 "C1'" C5 C 0 1 N N R 64.649 46.450 77.331 -1.230 -0.079 -0.675 "C1'" U23 9 U23 "C2'" C6 C 0 1 N N R 65.698 47.566 77.240 -1.305 1.197 0.190 "C2'" U23 10 U23 "C3'" C7 C 0 1 N N R 65.416 48.474 78.430 0.115 1.321 0.795 "C3'" U23 11 U23 "O3'" O3 O 0 1 N N N 66.634 48.582 79.153 0.553 2.684 0.754 "O3'" U23 12 U23 "C4'" C8 C 0 1 N N R 64.380 47.712 79.233 0.964 0.468 -0.176 "C4'" U23 13 U23 "O4'" O4 O 0 1 N N N 63.675 46.885 78.263 0.088 -0.628 -0.516 "O4'" U23 14 U23 "C5'" C9 C 0 1 N N N 63.427 48.655 79.907 2.226 -0.046 0.521 "C5'" U23 15 U23 "O5'" O5 O 0 1 N N N 62.448 49.090 78.964 3.048 -0.730 -0.426 "O5'" U23 16 U23 "O2'" O6 O 0 1 N N N 67.013 47.067 77.411 -1.495 2.324 -0.700 "O2'" U23 17 U23 OP1 O7 O 0 1 N N N 61.170 50.590 80.519 4.262 -2.349 1.083 OP1 U23 18 U23 OP2 O8 O 0 1 N N N 60.158 49.965 78.411 5.043 -2.194 -1.312 OP2 U23 19 U23 OP5 O9 O 0 1 N N N 68.607 47.253 79.150 -0.179 4.519 -0.875 OP5 U23 20 U23 OP4 O10 O 0 1 N N N 68.344 49.015 77.540 -1.601 4.189 1.209 OP4 U23 21 U23 P P1 P 0 1 N N N 61.033 49.540 79.506 4.458 -1.403 -0.038 P U23 22 U23 P2 P2 P 0 1 N N N 67.650 47.975 78.308 -0.680 3.505 0.079 P2 U23 23 U23 H1 H1 H 0 1 N N N 64.640 44.728 73.160 -4.900 -2.516 -1.249 H1 U23 24 U23 H2 H2 H 0 1 N N N 61.257 46.996 74.311 -2.970 -2.941 2.423 H2 U23 25 U23 H3 H3 H 0 1 N N N 62.288 47.353 76.487 -1.307 -1.321 1.674 H3 U23 26 U23 H4 H4 H 0 1 N N N 65.135 45.525 77.675 -1.405 0.172 -1.721 H4 U23 27 U23 H5 H5 H 0 1 N N N 64.881 47.084 79.985 1.223 1.043 -1.066 H5 U23 28 U23 H6 H6 H 0 1 N N N 62.930 48.140 80.742 2.777 0.796 0.940 H6 U23 29 U23 H7 H7 H 0 1 N N N 63.980 49.525 80.290 1.945 -0.731 1.321 H7 U23 30 U23 H9 H9 H 0 1 N N N 59.849 50.848 78.577 5.894 -2.626 -1.151 H9 U23 31 U23 H11 H11 H 0 1 N N N 69.270 49.001 77.751 -2.349 4.690 0.857 H11 U23 32 U23 OP3 OP3 O 0 1 N Y N 60.424 48.220 80.189 5.497 -0.255 0.404 OP3 U23 33 U23 H12 H12 H 0 1 N N N 65.585 48.121 76.297 -2.078 1.132 0.957 H12 U23 34 U23 H13 H13 H 0 1 N N N 65.028 49.450 78.102 0.147 0.928 1.811 H13 U23 35 U23 H8 H8 H 0 1 N N N 60.274 48.382 81.113 5.673 0.402 -0.283 H8 U23 36 # # 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 U23 N1 C2 SING N N 1 U23 N1 C6 SING N N 2 U23 N1 "C1'" SING N N 3 U23 C2 O2 DOUB N N 4 U23 C2 N3 SING N N 5 U23 N3 C4 SING N N 6 U23 C4 O4 DOUB N N 7 U23 C4 C5 SING N N 8 U23 C5 C6 DOUB N N 9 U23 "C1'" "C2'" SING N N 10 U23 "C1'" "O4'" SING N N 11 U23 "C2'" "C3'" SING N N 12 U23 "C2'" "O2'" SING N N 13 U23 "C3'" "O3'" SING N N 14 U23 "C3'" "C4'" SING N N 15 U23 "O3'" P2 SING N N 16 U23 "C4'" "O4'" SING N N 17 U23 "C4'" "C5'" SING N N 18 U23 "C5'" "O5'" SING N N 19 U23 "O5'" P SING N N 20 U23 "O2'" P2 SING N N 21 U23 OP1 P DOUB N N 22 U23 OP2 P SING N N 23 U23 OP5 P2 DOUB N N 24 U23 OP4 P2 SING N N 25 U23 N3 H1 SING N N 26 U23 C5 H2 SING N N 27 U23 C6 H3 SING N N 28 U23 "C1'" H4 SING N N 29 U23 "C4'" H5 SING N N 30 U23 "C5'" H6 SING N N 31 U23 "C5'" H7 SING N N 32 U23 OP2 H9 SING N N 33 U23 OP4 H11 SING N N 34 U23 P OP3 SING N N 35 U23 "C2'" H12 SING N N 36 U23 "C3'" H13 SING N N 37 U23 OP3 H8 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 U23 SMILES ACDLabs 12.01 "N1(C(=O)NC(=O)C=C1)C3C2C(OP(O2)(=O)O)C(O3)COP(=O)(O)O" U23 InChI InChI 1.03 "InChI=1S/C9H12N2O11P2/c12-5-1-2-11(9(13)10-5)8-7-6(21-24(17,18)22-7)4(20-8)3-19-23(14,15)16/h1-2,4,6-8H,3H2,(H,17,18)(H,10,12,13)(H2,14,15,16)/t4-,6-,7-,8-/m1/s1" U23 InChIKey InChI 1.03 PXHRDNPZBBFFEO-XVFCMESISA-N U23 SMILES_CANONICAL CACTVS 3.385 "O[P](O)(=O)OC[C@H]1O[C@H]([C@@H]2O[P](O)(=O)O[C@H]12)N3C=CC(=O)NC3=O" U23 SMILES CACTVS 3.385 "O[P](O)(=O)OC[CH]1O[CH]([CH]2O[P](O)(=O)O[CH]12)N3C=CC(=O)NC3=O" U23 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C1=CN(C(=O)NC1=O)[C@H]2[C@H]3[C@@H]([C@H](O2)COP(=O)(O)O)OP(=O)(O3)O" U23 SMILES "OpenEye OEToolkits" 2.0.7 "C1=CN(C(=O)NC1=O)C2C3C(C(O2)COP(=O)(O)O)OP(=O)(O3)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 U23 "SYSTEMATIC NAME" ACDLabs 12.01 "[(2S,3aR,4R,6R,6aR)-6-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-2-hydroxy-2-oxotetrahydro-2H-2lambda~5~-furo[3,4-d][1,3,2]dioxaphosphol-4-yl]methyl dihydrogen phosphate" U23 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[(3~{a}~{R},4~{R},6~{R},6~{a}~{R})-4-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-2-oxidanyl-2-oxidanylidene-3~{a},4,6,6~{a}-tetrahydrofuro[3,4-d][1,3,2]dioxaphosphol-6-yl]methyl dihydrogen phosphate" # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id U23 _pdbx_chem_comp_synonyms.name "[(2S,3aR,4R,6R,6aR)-6-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-2-hydroxy-2-oxotetrahydro-2H-2lambda~5~-furo[3,4-d][1,3,2]dioxaphosphol-4-yl]methyl dihydrogen phosphate" _pdbx_chem_comp_synonyms.provenance PDB _pdbx_chem_comp_synonyms.type ? # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site U23 "Create component" 2020-07-31 RCSB U23 "Initial release" 2020-09-09 RCSB ##