data_A1L3O # _chem_comp.id A1L3O _chem_comp.name ;5-Hydroxyuridine 5'-phosphate ; _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C9 H13 N2 O10 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "[(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-[5-oxidanyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]oxolan-2-yl]methyl dihydrogen phosphate" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2024-08-16 _chem_comp.pdbx_modified_date 2025-09-19 _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 340.181 _chem_comp.one_letter_code ? _chem_comp.three_letter_code A1L3O _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 ? _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ _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 A1L3O C2 C1 C 0 1 N N N N N N ? ? ? 2.265 -0.511 -0.933 C2 A1L3O 1 A1L3O C4 C2 C 0 1 N N N N N N ? ? ? 4.334 -1.471 -0.426 C4 A1L3O 2 A1L3O C5 C3 C 0 1 N N N N N N ? ? ? 4.308 -0.834 0.842 C5 A1L3O 3 A1L3O C6 C4 C 0 1 N N N N N N ? ? ? 3.249 -0.058 1.165 C6 A1L3O 4 A1L3O "C1'" C5 C 0 1 N N R N N N ? ? ? 1.076 0.941 0.613 "C1'" A1L3O 5 A1L3O "C2'" C6 C 0 1 N N R N N N ? ? ? 0.966 2.131 -0.366 "C2'" A1L3O 6 A1L3O "C3'" C7 C 0 1 N N S N N N ? ? ? -0.555 2.314 -0.564 "C3'" A1L3O 7 A1L3O "C4'" C8 C 0 1 N N R N N N ? ? ? -1.184 1.212 0.317 "C4'" A1L3O 8 A1L3O "C5'" C9 C 0 1 N N N N N N ? ? ? -2.423 0.627 -0.364 "C5'" A1L3O 9 A1L3O N1 N1 N 0 1 N N N N N N ? ? ? 2.224 0.100 0.265 N1 A1L3O 10 A1L3O N3 N2 N 0 1 N N N N N N ? ? ? 3.306 -1.289 -1.279 N3 A1L3O 11 A1L3O O1 O1 O 0 1 N N N N N N ? ? ? 5.334 -1.003 1.721 O1 A1L3O 12 A1L3O O2 O2 O 0 1 N N N N N N ? ? ? 1.343 -0.362 -1.712 O2 A1L3O 13 A1L3O "O2'" O3 O 0 1 N N N N N N ? ? ? 1.543 3.306 0.207 "O2'" A1L3O 14 A1L3O "O3'" O4 O 0 1 N N N N N N ? ? ? -0.967 3.608 -0.119 "O3'" A1L3O 15 A1L3O O4 O5 O 0 1 N N N N N N ? ? ? 5.276 -2.176 -0.740 O4 A1L3O 16 A1L3O "O4'" O6 O 0 1 N N N N N N ? ? ? -0.155 0.206 0.441 "O4'" A1L3O 17 A1L3O "O5'" O7 O 0 1 N N N N N N ? ? ? -3.055 -0.305 0.516 "O5'" A1L3O 18 A1L3O OP1 O8 O 0 1 N N N N N N ? ? ? -4.172 -1.843 -1.144 OP1 A1L3O 19 A1L3O OP2 O9 O 0 1 N N N N N N ? ? ? -4.745 -2.163 1.293 OP2 A1L3O 20 A1L3O P P1 P 0 1 N N N N N N ? ? ? -4.391 -1.114 0.124 P A1L3O 21 A1L3O O3P O10 O 0 1 N Y N N N N ? ? ? -5.611 -0.079 -0.055 O3P A1L3O 22 A1L3O H1 H1 H 0 1 N N N N N N ? ? ? 3.210 0.436 2.125 H1 A1L3O 23 A1L3O H2 H2 H 0 1 N N N N N N ? ? ? 1.165 1.298 1.639 H2 A1L3O 24 A1L3O H3 H3 H 0 1 N N N N N N ? ? ? 1.449 1.893 -1.313 H3 A1L3O 25 A1L3O H4 H4 H 0 1 N N N N N N ? ? ? -0.825 2.166 -1.610 H4 A1L3O 26 A1L3O H5 H5 H 0 1 N N N N N N ? ? ? -1.443 1.613 1.298 H5 A1L3O 27 A1L3O H6 H6 H 0 1 N N N N N N ? ? ? -3.119 1.430 -0.604 H6 A1L3O 28 A1L3O H7 H7 H 0 1 N N N N N N ? ? ? -2.126 0.117 -1.281 H7 A1L3O 29 A1L3O H8 H8 H 0 1 N N N N N N ? ? ? 3.318 -1.722 -2.148 H8 A1L3O 30 A1L3O H9 H9 H 0 1 N N N N N N ? ? ? 6.042 -1.576 1.395 H9 A1L3O 31 A1L3O H10 H10 H 0 1 N N N N N N ? ? ? 1.501 4.084 -0.365 H10 A1L3O 32 A1L3O H11 H11 H 0 1 N N N N N N ? ? ? -0.555 4.339 -0.599 H11 A1L3O 33 A1L3O H12 H12 H 0 1 N N N N N N ? ? ? -5.540 -2.687 1.124 H12 A1L3O 34 A1L3O H13 H13 H 0 1 N N N N N N ? ? ? -5.811 0.435 0.739 H13 A1L3O 35 # 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 A1L3O "O3'" "C3'" SING N N 1 A1L3O "O2'" "C2'" SING N N 2 A1L3O "C3'" "C2'" SING N N 3 A1L3O "C3'" "C4'" SING N N 4 A1L3O O2 C2 DOUB N N 5 A1L3O "C2'" "C1'" SING N N 6 A1L3O "C4'" "O4'" SING N N 7 A1L3O "C4'" "C5'" SING N N 8 A1L3O "C1'" "O4'" SING N N 9 A1L3O "C1'" N1 SING N N 10 A1L3O "C5'" "O5'" SING N N 11 A1L3O C2 N1 SING N N 12 A1L3O C2 N3 SING N N 13 A1L3O "O5'" P SING N N 14 A1L3O N1 C6 SING N N 15 A1L3O P OP1 DOUB N N 16 A1L3O P OP2 SING N N 17 A1L3O N3 C4 SING N N 18 A1L3O C6 C5 DOUB N N 19 A1L3O C4 C5 SING N N 20 A1L3O C4 O4 DOUB N N 21 A1L3O C5 O1 SING N N 22 A1L3O P O3P SING N N 23 A1L3O C6 H1 SING N N 24 A1L3O "C1'" H2 SING N N 25 A1L3O "C2'" H3 SING N N 26 A1L3O "C3'" H4 SING N N 27 A1L3O "C4'" H5 SING N N 28 A1L3O "C5'" H6 SING N N 29 A1L3O "C5'" H7 SING N N 30 A1L3O N3 H8 SING N N 31 A1L3O O1 H9 SING N N 32 A1L3O "O2'" H10 SING N N 33 A1L3O "O3'" H11 SING N N 34 A1L3O OP2 H12 SING N N 35 A1L3O O3P H13 SING N N 36 # 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 A1L3O InChI InChI 1.06 "InChI=1S/C9H13N2O10P/c12-3-1-11(9(16)10-7(3)15)8-6(14)5(13)4(21-8)2-20-22(17,18)19/h1,4-6,8,12-14H,2H2,(H,10,15,16)(H2,17,18,19)/t4-,5-,6-,8-/m1/s1" A1L3O InChIKey InChI 1.06 YGRIIPJUCYYPFJ-UAKXSSHOSA-N A1L3O SMILES_CANONICAL CACTVS 3.385 "O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=C(O)C(=O)NC2=O" A1L3O SMILES CACTVS 3.385 "O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)N2C=C(O)C(=O)NC2=O" A1L3O SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C1=C(C(=O)NC(=O)N1[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O)O" A1L3O SMILES "OpenEye OEToolkits" 2.0.7 "C1=C(C(=O)NC(=O)N1C2C(C(C(O2)COP(=O)(O)O)O)O)O" # _pdbx_chem_comp_identifier.comp_id A1L3O _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})-3,4-bis(oxidanyl)-5-[5-oxidanyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]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 A1L3O "Create component" 2024-08-16 PDBJ A1L3O "Modify coordinates" 2025-09-15 RCSB A1L3O "Initial release" 2025-09-24 RCSB # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id A1L3O _pdbx_chem_comp_synonyms.name "[(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-[5-oxidanyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]oxolan-2-yl]methyl dihydrogen phosphate" _pdbx_chem_comp_synonyms.provenance PDB _pdbx_chem_comp_synonyms.type ? #