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         ? 
# 
