data_A1IXU # _chem_comp.id A1IXU _chem_comp.name "[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)-6-prop-1-en-2-yl-pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C12 H17 N2 O9 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "6-Isopropenyl UMP" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2025-01-02 _chem_comp.pdbx_modified_date 2026-07-10 _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 364.245 _chem_comp.one_letter_code ? _chem_comp.three_letter_code A1IXU _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 9HVU _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBE _chem_comp.pdbx_pcm ? # 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.pdbx_n_terminal_atom_flag _chem_comp_atom.pdbx_backbone_atom_flag _chem_comp_atom.pdbx_c_terminal_atom_flag _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 A1IXU C1 C1 C 0 1 N N N N N N -13.121 -5.442 14.668 -3.523 -0.921 1.522 C1 A1IXU 1 A1IXU N1 N1 N 0 1 N N N N N N -13.115 -7.939 14.526 -2.016 0.273 -0.032 N1 A1IXU 2 A1IXU C2 C2 C 0 1 N N N N N N -13.466 -8.984 13.696 -1.732 1.319 -0.830 C2 A1IXU 3 A1IXU C3 C3 C 0 1 N N N N N N -14.003 -4.271 15.020 -2.693 -1.184 2.752 C3 A1IXU 4 A1IXU C4 C4 C 0 1 N N N N N N -15.150 -7.648 12.620 -3.774 2.339 -0.314 C4 A1IXU 5 A1IXU C5 C5 C 0 1 N N N N N N -14.812 -6.554 13.379 -4.102 1.254 0.524 C5 A1IXU 6 A1IXU C6 C6 C 0 1 N N N N N N -13.804 -6.700 14.314 -3.211 0.225 0.656 C6 A1IXU 7 A1IXU "C1'" C7 C 0 1 N N R N N N -12.101 -8.094 15.613 -1.054 -0.823 0.102 "C1'" A1IXU 8 A1IXU "C2'" C8 C 0 1 N N R N N N -12.372 -9.181 16.649 -0.870 -1.556 -1.252 "C2'" A1IXU 9 A1IXU "C3'" C9 C 0 1 N N S N N N -10.977 -9.680 17.015 0.541 -2.174 -1.097 "C3'" A1IXU 10 A1IXU "C4'" C10 C 0 1 N N R N N N -10.176 -9.474 15.730 1.203 -1.331 0.010 "C4'" A1IXU 11 A1IXU "C5'" C11 C 0 1 N N N N N N -10.095 -10.708 14.836 2.486 -0.689 -0.524 "C5'" A1IXU 12 A1IXU C7 C12 C 0 1 N N N N N N -11.818 -5.278 14.509 -4.536 -1.729 1.217 C7 A1IXU 13 A1IXU N3 N2 N 0 1 N N N N N N -14.423 -8.790 12.759 -2.597 2.340 -0.971 N3 A1IXU 14 A1IXU O1P O1 O 0 1 N N N N N N -8.231 -13.705 16.036 5.703 -0.257 -0.052 O1P A1IXU 15 A1IXU O2 O2 O 0 1 N N N N N N -12.907 -10.070 13.769 -0.676 1.342 -1.432 O2 A1IXU 16 A1IXU "O2'" O3 O 0 1 N N N N N N -13.024 -8.644 17.778 -1.858 -2.574 -1.419 "O2'" A1IXU 17 A1IXU O2P O4 O 0 1 N N N N N N -10.168 -13.763 14.277 4.932 1.541 1.704 O2P A1IXU 18 A1IXU "O3'" O5 O 0 1 N N N N N N -10.434 -8.948 18.153 0.445 -3.542 -0.693 "O3'" A1IXU 19 A1IXU O3P O6 O 0 1 N N N N N N -7.906 -12.668 13.731 4.387 1.782 -0.748 O3P A1IXU 20 A1IXU O4 O7 O 0 1 N N N N N N -16.112 -7.649 11.789 -4.551 3.267 -0.448 O4 A1IXU 21 A1IXU "O4'" O8 O 0 1 N N N N N N -10.848 -8.407 15.004 0.264 -0.311 0.389 "O4'" A1IXU 22 A1IXU "O5'" O9 O 0 1 N N N N N N -9.359 -11.744 15.489 3.154 -0.005 0.539 "O5'" A1IXU 23 A1IXU P P1 P 0 1 N N N N N N -8.906 -13.133 14.809 4.541 0.787 0.337 P A1IXU 24 A1IXU H1 H1 H 0 1 N N N N N N -13.377 -3.400 15.263 -3.126 -0.657 3.602 H1 A1IXU 25 A1IXU H2 H2 H 0 1 N N N N N N -14.651 -4.030 14.164 -2.678 -2.255 2.957 H2 A1IXU 26 A1IXU H3 H3 H 0 1 N N N N N N -14.625 -4.529 15.890 -1.675 -0.832 2.585 H3 A1IXU 27 A1IXU H4 H4 H 0 1 N N N N N N -15.318 -5.609 13.249 -5.041 1.238 1.057 H4 A1IXU 28 A1IXU H7 H7 H 0 1 N N N N N N -12.015 -7.135 16.144 -1.375 -1.521 0.875 H7 A1IXU 29 A1IXU H8 H8 H 0 1 N N N N N N -12.954 -9.996 16.194 -0.896 -0.850 -2.083 H8 A1IXU 30 A1IXU H9 H9 H 0 1 N N N N N N -11.025 -10.755 17.243 1.099 -2.091 -2.029 H9 A1IXU 31 A1IXU H10 H10 H 0 1 N N N N N N -9.156 -9.159 15.995 1.434 -1.961 0.869 H10 A1IXU 32 A1IXU H11 H11 H 0 1 N N N N N N -9.591 -10.442 13.895 3.140 -1.463 -0.925 H11 A1IXU 33 A1IXU H12 H12 H 0 1 N N N N N N -11.112 -11.067 14.619 2.236 0.021 -1.312 H12 A1IXU 34 A1IXU H13 H13 H 0 1 N N N N N N -11.378 -4.299 14.631 -4.814 -2.524 1.892 H13 A1IXU 35 A1IXU H14 H14 H 0 1 N N N N N N -11.194 -6.123 14.257 -5.078 -1.589 0.294 H14 A1IXU 36 A1IXU H15 H15 H 0 1 N N N N N N -14.609 -9.539 12.123 -2.370 3.086 -1.548 H15 A1IXU 37 A1IXU H16 H16 H 0 1 N N N N N N -7.288 -13.676 15.922 5.858 -0.939 0.615 H16 A1IXU 38 A1IXU H17 H17 H 0 1 N N N N N N -13.184 -9.335 18.410 -1.784 -3.061 -2.252 H17 A1IXU 39 A1IXU H18 H18 H 0 1 N N N N N N -10.142 -13.772 13.327 5.759 2.040 1.656 H18 A1IXU 40 A1IXU H19 H19 H 0 1 N N N N N N -10.969 -9.113 18.920 -0.016 -4.108 -1.327 H19 A1IXU 41 # 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 A1IXU O4 C4 DOUB N N 1 A1IXU C4 N3 SING N N 2 A1IXU C4 C5 SING N N 3 A1IXU N3 C2 SING N N 4 A1IXU C5 C6 DOUB N N 5 A1IXU C2 O2 DOUB N N 6 A1IXU C2 N1 SING N N 7 A1IXU O3P P DOUB N N 8 A1IXU O2P P SING N N 9 A1IXU C6 N1 SING N N 10 A1IXU C6 C1 SING N N 11 A1IXU C7 C1 DOUB N N 12 A1IXU N1 "C1'" SING N N 13 A1IXU C1 C3 SING N N 14 A1IXU P "O5'" SING N N 15 A1IXU P O1P SING N N 16 A1IXU "C5'" "O5'" SING N N 17 A1IXU "C5'" "C4'" SING N N 18 A1IXU "O4'" "C1'" SING N N 19 A1IXU "O4'" "C4'" SING N N 20 A1IXU "C1'" "C2'" SING N N 21 A1IXU "C4'" "C3'" SING N N 22 A1IXU "C2'" "C3'" SING N N 23 A1IXU "C2'" "O2'" SING N N 24 A1IXU "C3'" "O3'" SING N N 25 A1IXU C3 H1 SING N N 26 A1IXU C3 H2 SING N N 27 A1IXU C3 H3 SING N N 28 A1IXU C5 H4 SING N N 29 A1IXU "C1'" H7 SING N N 30 A1IXU "C2'" H8 SING N N 31 A1IXU "C3'" H9 SING N N 32 A1IXU "C4'" H10 SING N N 33 A1IXU "C5'" H11 SING N N 34 A1IXU "C5'" H12 SING N N 35 A1IXU C7 H13 SING N N 36 A1IXU C7 H14 SING N N 37 A1IXU N3 H15 SING N N 38 A1IXU O1P H16 SING N N 39 A1IXU "O2'" H17 SING N N 40 A1IXU O2P H18 SING N N 41 A1IXU "O3'" H19 SING N N 42 # 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 A1IXU InChI InChI 1.06 "InChI=1S/C12H17N2O9P/c1-5(2)6-3-8(15)13-12(18)14(6)11-10(17)9(16)7(23-11)4-22-24(19,20)21/h3,7,9-11,16-17H,1,4H2,2H3,(H,13,15,18)(H2,19,20,21)/t7-,9-,10-,11-/m1/s1" A1IXU InChIKey InChI 1.06 SVRBGGUJOXQNTQ-QCNRFFRDSA-N A1IXU SMILES_CANONICAL CACTVS 3.385 "CC(=C)C1=CC(=O)NC(=O)N1[C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O" A1IXU SMILES CACTVS 3.385 "CC(=C)C1=CC(=O)NC(=O)N1[CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O" A1IXU SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC(=C)C1=CC(=O)NC(=O)N1[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O" A1IXU SMILES "OpenEye OEToolkits" 2.0.7 "CC(=C)C1=CC(=O)NC(=O)N1C2C(C(C(O2)COP(=O)(O)O)O)O" # _pdbx_chem_comp_identifier.comp_id A1IXU _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.7 _pdbx_chem_comp_identifier.identifier "[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)-6-prop-1-en-2-yl-pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-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 A1IXU "Create component" 2025-01-02 PDBE A1IXU "Modify synonyms" 2025-01-02 PDBE A1IXU "Initial release" 2026-07-15 RCSB # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id A1IXU _pdbx_chem_comp_synonyms.name "6-Isopropenyl UMP" _pdbx_chem_comp_synonyms.provenance AUTHOR _pdbx_chem_comp_synonyms.type ? #