data_A1IT4
# 
_chem_comp.id                                    A1IT4 
_chem_comp.name                                  
;1-(beta-D-Ribofuranosyl)cyanuric acid-5'-monophosphate
;
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C8 H12 N3 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-[2,4,6-tris(oxidanylidene)-1,3,5-triazinan-1-yl]oxolan-2-yl]methyl dihydrogen phosphate; ((2R,3S,4R,5R)-3,4-dihydroxy-5-(2,4,6-trioxo-1,3,5-triazinan-1-yl)tetrahydrofuran-2-yl)methyl dihydrogen phosphate" 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2024-11-13 
_chem_comp.pdbx_modified_date                    2025-10-17 
_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                        341.169 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A1IT4 
_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        9HDV 
_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 
A1IT4 P      P1  P 0 1 N N N N N N 12.129 13.424 42.200 4.367  -0.948 -0.159 P      A1IT4 1  
A1IT4 O1P    O1  O 0 1 N N N N N N 12.561 14.825 41.850 5.375  0.025  0.319  O1P    A1IT4 2  
A1IT4 O2P    O2  O 0 1 N N N N N N 13.257 12.673 42.856 4.095  -2.046 0.987  O2P    A1IT4 3  
A1IT4 "O5'"  O3  O 0 1 N N N N N N 11.769 12.678 40.851 2.996  -0.177 -0.500 "O5'"  A1IT4 4  
A1IT4 "C5'"  C1  C 0 1 N N N N N N 12.733 12.445 39.839 2.316  0.655  0.442  "C5'"  A1IT4 5  
A1IT4 "C4'"  C2  C 0 1 N N R N N N 12.006 11.930 38.626 1.054  1.231  -0.203 "C4'"  A1IT4 6  
A1IT4 "O4'"  O4  O 0 1 N N N N N N 12.882 11.793 37.484 0.075  0.189  -0.409 "O4'"  A1IT4 7  
A1IT4 "C1'"  C3  C 0 1 N N R N N N 13.143 10.447 37.263 -1.190 0.875  -0.535 "C1'"  A1IT4 8  
A1IT4 "C2'"  C4  C 0 1 N N R N N N 12.384 9.599  38.275 -1.140 1.993  0.531  "C2'"  A1IT4 9  
A1IT4 "C3'"  C5  C 0 1 N N S N N N 11.350 10.570 38.830 0.370  2.232  0.754  "C3'"  A1IT4 10 
A1IT4 "O3'"  O5  O 0 1 N N N N N N 10.174 10.461 38.040 0.720  3.574  0.410  "O3'"  A1IT4 11 
A1IT4 "O2'"  O6  O 0 1 N N N N N N 11.789 8.442  37.687 -1.768 3.180  0.041  "O2'"  A1IT4 12 
A1IT4 C4     C6  C 0 1 N N N N N N 17.118 9.775  36.569 -4.336 -1.732 0.246  C4     A1IT4 13 
A1IT4 N3     N1  N 0 1 N N N N N N 16.279 9.672  35.536 -3.340 -1.591 1.142  N3     A1IT4 14 
A1IT4 N1     N2  N 0 1 N N N N N N 14.514 10.188 36.977 -2.298 -0.043 -0.260 N1     A1IT4 15 
A1IT4 C2     C7  C 0 1 N N N N N N 14.976 9.915  35.694 -2.320 -0.747 0.889  C2     A1IT4 16 
A1IT4 C7     C8  C 0 1 N N N N N N 15.416 10.329 38.034 -3.295 -0.183 -1.156 C7     A1IT4 17 
A1IT4 N2     N3  N 0 1 N N N N N N 16.695 10.096 37.811 -4.314 -1.028 -0.903 N2     A1IT4 18 
A1IT4 O2     O7  O 0 1 N N N N N N 14.182 9.861  34.763 -1.421 -0.621 1.697  O2     A1IT4 19 
A1IT4 O3P    O8  O 0 1 N N N N N N 10.930 13.351 43.044 4.915  -1.680 -1.485 O3P    A1IT4 20 
A1IT4 O4     O9  O 0 1 N N N N N N 18.340 9.591  36.393 -5.253 -2.497 0.472  O4     A1IT4 21 
A1IT4 O71    O10 O 0 1 N N N N N N 15.024 10.617 39.181 -3.275 0.452  -2.191 O71    A1IT4 22 
A1IT4 H1     H1  H 0 1 N N N N N N 14.019 13.236 42.918 3.444  -2.717 0.742  H1     A1IT4 23 
A1IT4 "H5'2" H2  H 0 0 N N N N N N 13.464 11.699 40.183 2.041  0.065  1.316  "H5'2" A1IT4 24 
A1IT4 "H5'1" H3  H 0 0 N N N N N N 13.253 13.383 39.594 2.973  1.470  0.747  "H5'1" A1IT4 25 
A1IT4 "H4'"  H4  H 0 1 N N N N N N 11.212 12.650 38.377 1.299  1.716  -1.148 "H4'"  A1IT4 26 
A1IT4 "H1'"  H5  H 0 1 N N N N N N 12.629 10.223 36.317 -1.291 1.305  -1.531 "H1'"  A1IT4 27 
A1IT4 "H2'"  H6  H 0 1 N N N N N N 13.070 9.306  39.083 -1.615 1.661  1.454  "H2'"  A1IT4 28 
A1IT4 "H3'"  H7  H 0 1 N N N N N N 11.162 10.379 39.897 0.641  2.019  1.788  "H3'"  A1IT4 29 
A1IT4 "HO3'" H8  H 0 0 N N N N N N 9.514  11.060 38.369 0.318  4.244  0.979  "HO3'" A1IT4 30 
A1IT4 "HO2'" H9  H 0 0 N N N N N N 11.329 7.948  38.355 -1.766 3.914  0.670  "HO2'" A1IT4 31 
A1IT4 HN3    H10 H 0 1 N N N N N N 16.629 9.411  34.637 -3.356 -2.098 1.969  HN3    A1IT4 32 
A1IT4 HN2    H11 H 0 1 N N N N N N 17.352 10.157 38.562 -5.031 -1.129 -1.548 HN2    A1IT4 33 
A1IT4 H2     H12 H 0 1 N N N N N N 10.621 14.229 43.232 5.740  -2.166 -1.353 H2     A1IT4 34 
# 
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 
A1IT4 O2    C2     DOUB N N 1  
A1IT4 N3    C2     SING N N 2  
A1IT4 N3    C4     SING N N 3  
A1IT4 C2    N1     SING N N 4  
A1IT4 O4    C4     DOUB N N 5  
A1IT4 C4    N2     SING N N 6  
A1IT4 N1    "C1'"  SING N N 7  
A1IT4 N1    C7     SING N N 8  
A1IT4 "C1'" "O4'"  SING N N 9  
A1IT4 "C1'" "C2'"  SING N N 10 
A1IT4 "O4'" "C4'"  SING N N 11 
A1IT4 "O2'" "C2'"  SING N N 12 
A1IT4 N2    C7     SING N N 13 
A1IT4 C7    O71    DOUB N N 14 
A1IT4 "O3'" "C3'"  SING N N 15 
A1IT4 "C2'" "C3'"  SING N N 16 
A1IT4 "C4'" "C3'"  SING N N 17 
A1IT4 "C4'" "C5'"  SING N N 18 
A1IT4 "C5'" "O5'"  SING N N 19 
A1IT4 "O5'" P      SING N N 20 
A1IT4 O1P   P      DOUB N N 21 
A1IT4 P     O2P    SING N N 22 
A1IT4 P     O3P    SING N N 23 
A1IT4 O2P   H1     SING N N 24 
A1IT4 "C5'" "H5'2" SING N N 25 
A1IT4 "C5'" "H5'1" SING N N 26 
A1IT4 "C4'" "H4'"  SING N N 27 
A1IT4 "C1'" "H1'"  SING N N 28 
A1IT4 "C2'" "H2'"  SING N N 29 
A1IT4 "C3'" "H3'"  SING N N 30 
A1IT4 "O3'" "HO3'" SING N N 31 
A1IT4 "O2'" "HO2'" SING N N 32 
A1IT4 N3    HN3    SING N N 33 
A1IT4 N2    HN2    SING N N 34 
A1IT4 O3P   H2     SING N N 35 
# 
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 
A1IT4 InChI            InChI                1.06  "InChI=1S/C8H12N3O10P/c12-3-2(1-20-22(17,18)19)21-5(4(3)13)11-7(15)9-6(14)10-8(11)16/h2-5,12-13H,1H2,(H2,17,18,19)(H2,9,10,14,15,16)/t2-,3-,4-,5-/m1/s1" 
A1IT4 InChIKey         InChI                1.06  AEXLPCNSEAEGAT-TXICZTDVSA-N                                                                                                                              
A1IT4 SMILES_CANONICAL CACTVS               3.385 "O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C(=O)NC(=O)NC2=O"                                                                                        
A1IT4 SMILES           CACTVS               3.385 "O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)N2C(=O)NC(=O)NC2=O"                                                                                               
A1IT4 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C([C@@H]1[C@H]([C@H]([C@@H](O1)N2C(=O)NC(=O)NC2=O)O)O)OP(=O)(O)O"                                                                                       
A1IT4 SMILES           "OpenEye OEToolkits" 2.0.7 "C(C1C(C(C(O1)N2C(=O)NC(=O)NC2=O)O)O)OP(=O)(O)O"                                                                                                         
# 
_pdbx_chem_comp_identifier.comp_id           A1IT4 
_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-[2,4,6-tris(oxidanylidene)-1,3,5-triazinan-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 
A1IT4 "Create component" 2024-11-13 PDBE 
A1IT4 "Initial release"  2025-10-22 RCSB 
# 
loop_
_pdbx_chem_comp_synonyms.ordinal 
_pdbx_chem_comp_synonyms.comp_id 
_pdbx_chem_comp_synonyms.name 
_pdbx_chem_comp_synonyms.provenance 
_pdbx_chem_comp_synonyms.type 
1 A1IT4 "[(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-[2,4,6-tris(oxidanylidene)-1,3,5-triazinan-1-yl]oxolan-2-yl]methyl dihydrogen phosphate" PDB    ? 
2 A1IT4 "((2R,3S,4R,5R)-3,4-dihydroxy-5-(2,4,6-trioxo-1,3,5-triazinan-1-yl)tetrahydrofuran-2-yl)methyl dihydrogen phosphate"                     AUTHOR ? 
# 
