data_A1BIK
# 
_chem_comp.id                                    A1BIK 
_chem_comp.name                                  "1-(5-amino-3,7-anhydro-5-deoxy-2-O-phosphono-D-threo-beta-D-allo-octofuranuronosyl)pyrimidine-2,4(1H,3H)-dione" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C12 H16 N3 O11 P" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2024-11-26 
_chem_comp.pdbx_modified_date                    2025-08-15 
_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                        409.243 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A1BIK 
_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        9EI7 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
_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 
A1BIK C01 C1  C 0 1 N N R N N N -16.810 15.337 -15.339 -1.852 2.557  -0.720 C01 A1BIK 1  
A1BIK C02 C2  C 0 1 N N R N N N -18.277 15.496 -14.944 -0.900 1.401  -0.966 C02 A1BIK 2  
A1BIK C03 C3  C 0 1 N N R N N N -19.144 16.006 -16.085 -0.888 0.547  0.333  C03 A1BIK 3  
A1BIK C04 C4  C 0 1 N N R N N N -20.396 16.484 -15.360 0.306  -0.371 0.062  C04 A1BIK 4  
A1BIK C05 C5  C 0 1 N N R N N N -19.817 16.964 -13.993 1.184  0.470  -0.901 C05 A1BIK 5  
A1BIK C06 C6  C 0 1 N N N N N N -19.232 19.262 -14.703 3.602  0.234  -0.821 C06 A1BIK 6  
A1BIK C07 C7  C 0 1 N N N N N N -19.790 21.172 -13.336 4.910  1.235  0.836  C07 A1BIK 7  
A1BIK C08 C8  C 0 1 N N N N N N -20.401 20.235 -12.377 3.739  1.781  1.415  C08 A1BIK 8  
A1BIK C09 C9  C 0 1 N N N N N N -20.401 18.879 -12.601 2.543  1.525  0.843  C09 A1BIK 9  
A1BIK C10 C10 C 0 1 N N S N N N -17.893 14.535 -17.564 -3.192 0.908  0.652  C10 A1BIK 10 
A1BIK C11 C11 C 0 1 N N N N N N -17.980 13.342 -18.495 -4.523 0.205  0.730  C11 A1BIK 11 
A1BIK C12 C12 C 0 1 N N R N N N -16.809 14.285 -16.474 -3.241 1.944  -0.468 C12 A1BIK 12 
A1BIK N01 N1  N 0 1 N N N N N N -16.193 16.614 -15.753 -1.417 3.322  0.457  N01 A1BIK 13 
A1BIK N02 N2  N 0 1 N N N N N N -19.822 18.444 -13.797 2.481  0.747  -0.281 N02 A1BIK 14 
A1BIK N03 N3  N 0 1 N N N N N N -19.257 20.576 -14.406 4.807  0.473  -0.271 N03 A1BIK 15 
A1BIK O01 O1  O 0 1 N N N N N N -21.190 15.336 -15.087 -0.120 -1.581 -0.568 O01 A1BIK 16 
A1BIK O02 O2  O 0 1 N N N N N N -23.502 15.872 -14.357 -0.371 -4.169 -0.958 O02 A1BIK 17 
A1BIK O03 O3  O 0 1 N N N N N N -22.937 16.120 -16.725 1.553  -3.220 0.371  O03 A1BIK 18 
A1BIK O04 O4  O 0 1 N N N N N N -23.106 13.922 -15.786 -0.731 -3.160 1.443  O04 A1BIK 19 
A1BIK O05 O5  O 0 1 N N N N N N -19.721 22.378 -13.244 6.000  1.451  1.334  O05 A1BIK 20 
A1BIK O06 O6  O 0 1 N N N N N N -18.721 18.888 -15.762 3.524  -0.459 -1.817 O06 A1BIK 21 
A1BIK O07 O7  O 0 1 N N N N N N -18.424 16.519 -13.933 0.477  1.712  -1.145 O07 A1BIK 22 
A1BIK O08 O8  O 0 1 N N N N N N -19.203 14.866 -17.008 -2.159 -0.067 0.431  O08 A1BIK 23 
A1BIK O09 O9  O 0 1 N N N N N N -18.941 12.594 -18.439 -5.632 0.898  1.032  O09 A1BIK 24 
A1BIK O10 O10 O 0 1 N N N N N N -17.062 13.238 -19.247 -4.592 -0.983 0.519  O10 A1BIK 25 
A1BIK O11 O11 O 0 1 N N N N N N -17.062 13.018 -15.870 -3.701 1.316  -1.666 O11 A1BIK 26 
A1BIK P01 P1  P 0 1 N N N N N N -22.741 15.322 -15.519 0.114  -3.036 0.078  P01 A1BIK 27 
A1BIK H1  H1  H 0 1 N N N N N N -16.257 14.925 -14.482 -1.884 3.206  -1.595 H1  A1BIK 28 
A1BIK H2  H2  H 0 1 N N N N N N -18.668 14.533 -14.584 -1.256 0.802  -1.805 H2  A1BIK 29 
A1BIK H3  H3  H 0 1 N N N N N N -18.650 16.862 -16.568 -0.693 1.177  1.201  H3  A1BIK 30 
A1BIK H4  H4  H 0 1 N N N N N N -20.921 17.288 -15.897 0.843  -0.588 0.986  H4  A1BIK 31 
A1BIK H5  H5  H 0 1 N N N N N N -20.393 16.489 -13.185 1.325  -0.067 -1.839 H5  A1BIK 32 
A1BIK H6  H6  H 0 1 N N N N N N -20.859 20.622 -11.479 3.802  2.394  2.302  H6  A1BIK 33 
A1BIK H7  H7  H 0 1 N N N N N N -20.826 18.186 -11.890 1.639  1.933  1.270  H7  A1BIK 34 
A1BIK H8  H8  H 0 1 N N N N N N -17.551 15.393 -18.162 -3.005 1.416  1.598  H8  A1BIK 35 
A1BIK H9  H9  H 0 1 N N N N N N -15.820 14.288 -16.956 -3.936 2.737  -0.191 H9  A1BIK 36 
A1BIK H10 H10 H 0 1 N N N N N N -16.217 17.259 -14.989 -2.040 4.096  0.635  H10 A1BIK 37 
A1BIK H11 H11 H 0 1 N N N N N N -15.244 16.453 -16.024 -1.340 2.726  1.267  H11 A1BIK 38 
A1BIK H13 H13 H 0 1 N N N N N N -18.821 21.182 -15.071 5.605  0.095  -0.674 H13 A1BIK 39 
A1BIK H14 H14 H 0 1 N N N N N N -23.977 16.649 -14.628 -0.259 -5.073 -0.634 H14 A1BIK 40 
A1BIK H15 H15 H 0 1 N N N N N N -23.392 13.835 -16.688 -1.685 -3.050 1.326  H15 A1BIK 41 
A1BIK H16 H16 H 0 1 N N N N N N -18.848 11.909 -19.091 -6.462 0.404  1.070  H16 A1BIK 42 
A1BIK H17 H17 H 0 1 N N N N N N -16.409 12.849 -15.201 -4.583 0.929  -1.594 H17 A1BIK 43 
# 
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 
A1BIK O10 C11 DOUB N N 1  
A1BIK C11 O09 SING N N 2  
A1BIK C11 C10 SING N N 3  
A1BIK C10 O08 SING N N 4  
A1BIK C10 C12 SING N N 5  
A1BIK O08 C03 SING N N 6  
A1BIK O03 P01 DOUB N N 7  
A1BIK C12 O11 SING N N 8  
A1BIK C12 C01 SING N N 9  
A1BIK C03 C04 SING N N 10 
A1BIK C03 C02 SING N N 11 
A1BIK O04 P01 SING N N 12 
A1BIK O06 C06 DOUB N N 13 
A1BIK N01 C01 SING N N 14 
A1BIK P01 O01 SING N N 15 
A1BIK P01 O02 SING N N 16 
A1BIK C04 O01 SING N N 17 
A1BIK C04 C05 SING N N 18 
A1BIK C01 C02 SING N N 19 
A1BIK C02 O07 SING N N 20 
A1BIK C06 N03 SING N N 21 
A1BIK C06 N02 SING N N 22 
A1BIK N03 C07 SING N N 23 
A1BIK C05 O07 SING N N 24 
A1BIK C05 N02 SING N N 25 
A1BIK N02 C09 SING N N 26 
A1BIK C07 O05 DOUB N N 27 
A1BIK C07 C08 SING N N 28 
A1BIK C09 C08 DOUB N N 29 
A1BIK C01 H1  SING N N 30 
A1BIK C02 H2  SING N N 31 
A1BIK C03 H3  SING N N 32 
A1BIK C04 H4  SING N N 33 
A1BIK C05 H5  SING N N 34 
A1BIK C08 H6  SING N N 35 
A1BIK C09 H7  SING N N 36 
A1BIK C10 H8  SING N N 37 
A1BIK C12 H9  SING N N 38 
A1BIK N01 H10 SING N N 39 
A1BIK N01 H11 SING N N 40 
A1BIK N03 H13 SING N N 41 
A1BIK O02 H14 SING N N 42 
A1BIK O04 H15 SING N N 43 
A1BIK O09 H16 SING N N 44 
A1BIK O11 H17 SING N N 45 
# 
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 
A1BIK SMILES           ACDLabs              14.52   "O=C(O)C1OC2C(OC(C2OP(=O)(O)O)N2C=CC(=O)NC2=O)C(N)C1O"                                                                                                                                     
A1BIK InChI            InChI                1.06    "InChI=1S/C12H16N3O11P/c13-4-5(17)7(11(18)19)24-8-6(4)25-10(9(8)26-27(21,22)23)15-2-1-3(16)14-12(15)20/h1-2,4-10,17H,13H2,(H,18,19)(H,14,16,20)(H2,21,22,23)/t4-,5-,6-,7+,8-,9-,10-/m1/s1" 
A1BIK InChIKey         InChI                1.06    WKDVCFXFVRNMOM-OLYSFKJBSA-N                                                                                                                                                                
A1BIK SMILES_CANONICAL CACTVS               3.385   "N[C@@H]1[C@@H](O)[C@H](O[C@@H]2[C@@H]1O[C@H]([C@@H]2O[P](O)(O)=O)N3C=CC(=O)NC3=O)C(O)=O"                                                                                                  
A1BIK SMILES           CACTVS               3.385   "N[CH]1[CH](O)[CH](O[CH]2[CH]1O[CH]([CH]2O[P](O)(O)=O)N3C=CC(=O)NC3=O)C(O)=O"                                                                                                              
A1BIK SMILES_CANONICAL "OpenEye OEToolkits" 3.1.0.0 "C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@H]3[C@H](O2)[C@@H]([C@H]([C@H](O3)C(=O)O)O)N)OP(=O)(O)O"                                                                                                 
A1BIK SMILES           "OpenEye OEToolkits" 3.1.0.0 "C1=CN(C(=O)NC1=O)C2C(C3C(O2)C(C(C(O3)C(=O)O)O)N)OP(=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 
A1BIK "SYSTEMATIC NAME" ACDLabs              14.52   "1-(5-amino-3,7-anhydro-5-deoxy-2-O-phosphono-D-threo-beta-D-allo-octofuranuronosyl)pyrimidine-2,4(1H,3H)-dione"                                                                                         
A1BIK "SYSTEMATIC NAME" "OpenEye OEToolkits" 3.1.0.0 "(2~{R},3~{R},3~{a}~{R},5~{S},6~{R},7~{R},7~{a}~{R})-7-azanyl-2-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-6-oxidanyl-3-phosphonooxy-3,3~{a},5,6,7,7~{a}-hexahydro-2~{H}-furo[3,2-b]pyran-5-carboxylic 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 
A1BIK "Create component" 2024-11-26 RCSB 
A1BIK "Initial release"  2025-08-20 RCSB 
# 
