data_UVP # _chem_comp.id UVP _chem_comp.name "1-[(5E)-5,6-dideoxy-2-O-methyl-6-phosphono-beta-D-ribo-hex-5-enofuranosyl]-2,4-dihydroxypyrimidin-1-ium" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C11 H16 N2 O8 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "uridine vinyl phosphonate" _chem_comp.pdbx_formal_charge 1 _chem_comp.pdbx_initial_date 2016-11-15 _chem_comp.pdbx_modified_date 2021-03-01 _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 335.227 _chem_comp.one_letter_code ? _chem_comp.three_letter_code UVP _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 5T7B _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 UVP OP O1 O 0 1 N N N 42.517 44.337 100.560 4.858 -1.779 -0.965 OP UVP 1 UVP P P1 P 0 1 N N N 42.165 43.416 101.821 4.236 -0.980 0.115 P UVP 2 UVP OP1 O2 O 0 1 N N N 42.368 41.940 101.246 4.062 -1.895 1.428 OP1 UVP 3 UVP OP2 O3 O 0 1 N N N 40.736 43.595 102.126 5.177 0.280 0.460 OP2 UVP 4 UVP "C6'" C1 C 0 1 N N N 43.385 43.690 103.129 2.610 -0.389 -0.430 "C6'" UVP 5 UVP "C5'" C2 C 0 1 N N N 44.721 42.977 102.937 2.367 0.897 -0.490 "C5'" UVP 6 UVP "C4'" C3 C 0 1 N N R 45.738 43.208 104.053 1.016 1.388 -0.942 "C4'" UVP 7 UVP "O4'" O4 O 0 1 N N N 45.654 42.139 104.999 0.122 0.275 -1.108 "O4'" UVP 8 UVP "C3'" C4 C 0 1 N N R 47.167 43.116 103.512 0.406 2.310 0.132 "C3'" UVP 9 UVP "O3'" O5 O 0 1 N N N 47.744 44.430 103.516 0.171 3.614 -0.403 "O3'" UVP 10 UVP "C2'" C5 C 0 1 N N R 47.810 42.208 104.556 -0.932 1.626 0.503 "C2'" UVP 11 UVP "O2'" O6 O 0 1 N N N 49.154 42.626 104.887 -1.971 2.594 0.665 "O2'" UVP 12 UVP "CB'" C6 C 0 1 N N N 49.996 41.488 105.089 -2.118 3.069 2.005 "CB'" UVP 13 UVP "C1'" C7 C 0 1 N N R 46.858 42.332 105.723 -1.196 0.735 -0.737 "C1'" UVP 14 UVP N1 N1 N 1 1 Y N N 46.973 41.176 106.630 -2.056 -0.398 -0.384 N1 UVP 15 UVP C2 C8 C 0 1 Y N N 47.778 41.198 107.704 -3.371 -0.270 -0.471 C2 UVP 16 UVP O2 O7 O 0 1 N N N 48.437 42.205 107.962 -3.894 0.909 -0.886 O2 UVP 17 UVP N3 N2 N 0 1 Y N N 47.861 40.069 108.536 -4.187 -1.265 -0.164 N3 UVP 18 UVP C4 C9 C 0 1 Y N N 47.114 38.917 108.252 -3.706 -2.433 0.244 C4 UVP 19 UVP O4 O8 O 0 1 N N N 47.182 37.926 108.976 -4.545 -3.450 0.558 O4 UVP 20 UVP C5 C10 C 0 1 Y N N 46.289 38.899 107.140 -2.326 -2.599 0.347 C5 UVP 21 UVP C6 C11 C 0 1 Y N N 46.223 40.026 106.333 -1.508 -1.536 0.012 C6 UVP 22 UVP H1 H1 H 0 1 N N N 42.636 41.988 100.336 4.893 -2.247 1.775 H1 UVP 23 UVP H2 H2 H 0 1 N N N 40.355 44.210 101.510 4.831 0.849 1.161 H2 UVP 24 UVP H3 H3 H 0 1 N N N 43.182 44.315 103.986 1.843 -1.097 -0.706 H3 UVP 25 UVP H5 H5 H 0 1 N N N 44.931 42.357 102.078 3.134 1.605 -0.214 H5 UVP 26 UVP H7 H7 H 0 1 N N N 45.571 44.187 104.526 1.115 1.928 -1.884 H7 UVP 27 UVP H8 H8 H 0 1 N N N 47.184 42.650 102.516 1.061 2.368 1.001 H8 UVP 28 UVP H9 H9 H 0 1 N N N 48.632 44.387 103.182 0.970 4.065 -0.706 H9 UVP 29 UVP H10 H10 H 0 1 N N N 47.809 41.171 104.188 -0.823 1.020 1.402 H10 UVP 30 UVP H11 H11 H 0 1 N N N 51.013 41.824 105.340 -2.352 2.233 2.664 H11 UVP 31 UVP H12 H12 H 0 1 N N N 49.597 40.879 105.914 -1.189 3.538 2.328 H12 UVP 32 UVP H13 H13 H 0 1 N N N 50.025 40.886 104.169 -2.926 3.800 2.045 H13 UVP 33 UVP H14 H14 H 0 1 N N N 46.932 43.302 106.236 -1.640 1.319 -1.543 H14 UVP 34 UVP H16 H16 H 0 1 N N N 45.706 38.021 106.904 -1.905 -3.537 0.677 H16 UVP 35 UVP H17 H17 H 0 1 N N N 45.584 40.019 105.462 -0.434 -1.632 0.075 H17 UVP 36 UVP H4 H4 H 0 1 N N N 48.946 42.057 108.750 -4.017 0.970 -1.843 H4 UVP 37 UVP H6 H6 H 0 1 N N N 47.785 38.096 109.690 -4.760 -4.027 -0.189 H6 UVP 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 UVP OP P DOUB N N 1 UVP OP1 P SING N N 2 UVP P OP2 SING N N 3 UVP P "C6'" SING N N 4 UVP "C5'" "C6'" DOUB N E 5 UVP "C5'" "C4'" SING N N 6 UVP "C3'" "O3'" SING N N 7 UVP "C3'" "C4'" SING N N 8 UVP "C3'" "C2'" SING N N 9 UVP "C4'" "O4'" SING N N 10 UVP "C2'" "O2'" SING N N 11 UVP "C2'" "C1'" SING N N 12 UVP "O2'" "CB'" SING N N 13 UVP "O4'" "C1'" SING N N 14 UVP "C1'" N1 SING N N 15 UVP C6 N1 DOUB Y N 16 UVP C6 C5 SING Y N 17 UVP N1 C2 SING Y N 18 UVP C5 C4 DOUB Y N 19 UVP C2 O2 SING N N 20 UVP C2 N3 DOUB Y N 21 UVP C4 N3 SING Y N 22 UVP C4 O4 SING N N 23 UVP OP1 H1 SING N N 24 UVP OP2 H2 SING N N 25 UVP "C6'" H3 SING N N 26 UVP "C5'" H5 SING N N 27 UVP "C4'" H7 SING N N 28 UVP "C3'" H8 SING N N 29 UVP "O3'" H9 SING N N 30 UVP "C2'" H10 SING N N 31 UVP "CB'" H11 SING N N 32 UVP "CB'" H12 SING N N 33 UVP "CB'" H13 SING N N 34 UVP "C1'" H14 SING N N 35 UVP C5 H16 SING N N 36 UVP C6 H17 SING N N 37 UVP O2 H4 SING N N 38 UVP O4 H6 SING N N 39 # # 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 UVP SMILES ACDLabs 12.01 "O=P(O)([C@H]=CC1OC(C(C1O)OC)[n+]2c(O)nc(O)cc2)O" UVP InChI InChI 1.03 "InChI=1S/C11H15N2O8P/c1-20-9-8(15)6(3-5-22(17,18)19)21-10(9)13-4-2-7(14)12-11(13)16/h2-6,8-10,15H,1H3,(H3,12,14,16,17,18,19)/p+1/b5-3+/t6-,8-,9-,10-/m1/s1" UVP InChIKey InChI 1.03 XBCZHNUNHZIGAE-JKXAUABFSA-O UVP SMILES_CANONICAL CACTVS 3.385 "CO[C@@H]1[C@H](O)[C@H](O[C@H]1[n+]2ccc(O)nc2O)\C=C\[P](O)(O)=O" UVP SMILES CACTVS 3.385 "CO[CH]1[CH](O)[CH](O[CH]1[n+]2ccc(O)nc2O)C=C[P](O)(O)=O" UVP SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "CO[C@@H]1[C@@H]([C@H](O[C@H]1[n+]2ccc(nc2O)O)/C=C/P(=O)(O)O)O" UVP SMILES "OpenEye OEToolkits" 2.0.6 "COC1C(C(OC1[n+]2ccc(nc2O)O)C=CP(=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 UVP "SYSTEMATIC NAME" ACDLabs 12.01 "1-[(5E)-5,6-dideoxy-2-O-methyl-6-phosphono-beta-D-ribo-hex-5-enofuranosyl]-2,4-dihydroxypyrimidin-1-ium" UVP "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[(~{E})-2-[(2~{R},3~{R},4~{R},5~{R})-5-[2,4-bis(oxidanyl)pyrimidin-1-ium-1-yl]-4-methoxy-3-oxidanyl-oxolan-2-yl]ethenyl]phosphonic 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 UVP "Create component" 2016-11-15 RCSB UVP "Initial release" 2016-12-14 RCSB UVP "Modify synonyms" 2021-03-01 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id UVP _pdbx_chem_comp_synonyms.name "uridine vinyl phosphonate" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##