data_A1LX0
# 
_chem_comp.id                                    A1LX0 
_chem_comp.name                                  "2-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-2-[(~{R})-cyclobutyl(oxidanyl)methyl]-4-methyl-1,3-thiazol-5-yl]ethyl phosphono hydrogen phosphate" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C17 H27 N4 O8 P2 S" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    1 
_chem_comp.pdbx_initial_date                     2024-02-07 
_chem_comp.pdbx_modified_date                    2024-12-27 
_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                        509.431 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A1LX0 
_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        8XOD 
_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 
A1LX0 C5    C1  C 0 1 Y N N N N N 20.193 -18.872 -2.309 -0.474 -0.305 -0.261 C5    A1LX0 1  
A1LX0 CM4   C2  C 0 1 N N N N N N 22.396 -17.768 -2.713 -0.962 1.911  0.783  CM4   A1LX0 2  
A1LX0 C8    C3  C 0 1 N N R N N N 18.563 -18.609 -6.068 -3.773 -2.178 0.858  C8    A1LX0 3  
A1LX0 C7    C4  C 0 1 N N N N N N 19.412 -18.980 0.226  1.964  -0.195 0.179  C7    A1LX0 4  
A1LX0 "C2'" C5  C 0 1 Y N N N N N 21.690 -13.346 -4.769 -5.076 3.658  -0.691 "C2'" A1LX0 5  
A1LX0 "C4'" C6  C 0 1 Y N N N N N 20.413 -15.129 -5.226 -5.127 1.465  0.002  "C4'" A1LX0 6  
A1LX0 "C5'" C7  C 0 1 Y N N N N N 21.494 -15.943 -5.240 -4.010 1.708  0.806  "C5'" A1LX0 7  
A1LX0 "C6'" C8  C 0 1 Y N N N N N 22.739 -15.360 -5.020 -3.476 2.981  0.817  "C6'" A1LX0 8  
A1LX0 CM2   C9  C 0 1 N N N N N N 21.756 -11.834 -4.509 -5.670 4.759  -1.531 CM2   A1LX0 9  
A1LX0 "C7'" C10 C 0 1 N N N N N N 21.375 -17.449 -5.505 -3.404 0.608  1.639  "C7'" A1LX0 10 
A1LX0 C2    C11 C 0 1 Y N N N N N 19.373 -18.595 -4.716 -2.571 -1.341 0.503  C2    A1LX0 11 
A1LX0 C4    C12 C 0 1 Y N N N N N 21.035 -18.249 -3.221 -1.289 0.477  0.453  C4    A1LX0 12 
A1LX0 C6    C13 C 0 1 N N N N N N 20.533 -19.144 -0.814 0.859  0.097  -0.838 C6    A1LX0 13 
A1LX0 C9    C14 C 0 1 N N N N N N 18.837 -19.823 -6.841 -4.696 -2.285 -0.357 C9    A1LX0 14 
A1LX0 C10   C15 C 0 1 N N N N N N 18.396 -21.029 -6.088 -6.015 -3.020 -0.066 C10   A1LX0 15 
A1LX0 C12   C16 C 0 1 N N N N N N 19.793 -21.587 -6.132 -5.858 -3.684 -1.444 C12   A1LX0 16 
A1LX0 C11   C17 C 0 1 N N N N N N 20.257 -20.339 -6.816 -4.345 -3.451 -1.297 C11   A1LX0 17 
A1LX0 "N1'" N1  N 0 1 Y N N N N N 22.791 -14.091 -4.785 -4.026 3.920  0.060  "N1'" A1LX0 18 
A1LX0 "N3'" N2  N 0 1 Y N N N N N 20.538 -13.847 -4.989 -5.625 2.460  -0.725 "N3'" A1LX0 19 
A1LX0 "N4'" N3  N 0 1 N N N N N N 19.270 -15.568 -5.411 -5.699 0.204  -0.045 "N4'" A1LX0 20 
A1LX0 N3    N4  N 1 1 Y N N N N N 20.581 -18.113 -4.468 -2.402 -0.109 0.847  N3    A1LX0 21 
A1LX0 O8    O1  O 0 1 N N N N N N 17.177 -18.700 -5.882 -3.346 -3.484 1.248  O8    A1LX0 22 
A1LX0 "O7'" O2  O 0 1 N N N N N N 19.975 -18.912 1.490  3.228  0.186  -0.368 "O7'" A1LX0 23 
A1LX0 O1A   O3  O 0 1 N N N N N N 18.804 -17.022 2.583  4.771  -1.388 0.863  O1A   A1LX0 24 
A1LX0 O2A   O4  O 0 1 N N N N N N 19.442 -18.873 3.887  4.608  0.979  1.725  O2A   A1LX0 25 
A1LX0 O2B   O5  O 0 1 N N N N N N 16.262 -21.194 2.759  8.048  0.474  -1.958 O2B   A1LX0 26 
A1LX0 O1B   O6  O 0 1 N N N N N N 18.216 -21.102 3.695  7.640  -1.320 -0.230 O1B   A1LX0 27 
A1LX0 O3B   O7  O 0 1 N N N N N N 18.081 -21.763 1.319  8.135  1.006  0.615  O3B   A1LX0 28 
A1LX0 O3A   O8  O 0 1 N N N N N N 17.678 -19.211 2.257  5.841  0.425  -0.530 O3A   A1LX0 29 
A1LX0 PA    P1  P 0 1 N N N N N N 18.995 -18.419 2.622  4.615  0.020  0.432  PA    A1LX0 30 
A1LX0 PB    P2  P 0 1 N N N N N N 17.611 -20.803 2.503  7.421  0.115  -0.519 PB    A1LX0 31 
A1LX0 S1    S1  S 0 1 Y N N N N N 18.882 -19.210 -3.233 -1.230 -1.890 -0.404 S1    A1LX0 32 
A1LX0 H152  H1  H 0 0 N N N N N N 23.139 -18.570 -2.838 -1.348 2.561  -0.002 H152  A1LX0 33 
A1LX0 H151  H2  H 0 0 N N N N N N 22.710 -16.884 -3.287 -1.420 2.179  1.735  H151  A1LX0 34 
A1LX0 H153  H3  H 0 0 N N N N N N 22.317 -17.504 -1.648 0.119  2.030  0.854  H153  A1LX0 35 
A1LX0 H171  H4  H 0 0 N N N N N N 18.830 -17.716 -6.652 -4.311 -1.710 1.683  H171  A1LX0 36 
A1LX0 H202  H5  H 0 0 N N N N N N 18.852 -18.056 0.022  1.777  0.372  1.091  H202  A1LX0 37 
A1LX0 H201  H6  H 0 0 N N N N N N 18.730 -19.841 0.172  1.974  -1.260 0.410  H201  A1LX0 38 
A1LX0 H061  H7  H 0 0 N N N N N N 23.640 -15.955 -5.045 -2.614 3.207  1.427  H061  A1LX0 39 
A1LX0 H073  H8  H 0 0 N N N N N N 22.803 -11.533 -4.355 -6.431 5.286  -0.954 H073  A1LX0 40 
A1LX0 H072  H9  H 0 0 N N N N N N 21.343 -11.295 -5.374 -4.886 5.458  -1.821 H072  A1LX0 41 
A1LX0 H071  H10 H 0 0 N N N N N N 21.169 -11.590 -3.611 -6.124 4.331  -2.425 H071  A1LX0 42 
A1LX0 H092  H11 H 0 0 N N N N N N 20.891 -17.604 -6.480 -2.930 1.040  2.520  H092  A1LX0 43 
A1LX0 H091  H12 H 0 0 N N N N N N 22.383 -17.890 -5.522 -4.185 -0.085 1.950  H091  A1LX0 44 
A1LX0 H161  H13 H 0 0 N N N N N N 20.894 -20.181 -0.745 1.046  -0.470 -1.750 H161  A1LX0 45 
A1LX0 H162  H14 H 0 0 N N N N N N 21.343 -18.455 -0.533 0.850  1.162  -1.068 H162  A1LX0 46 
A1LX0 H191  H15 H 0 0 N N N N N N 18.425 -19.786 -7.860 -4.831 -1.334 -0.872 H191  A1LX0 47 
A1LX0 H302  H16 H 0 0 N N N N N N 18.033 -20.813 -5.072 -5.950 -3.721 0.766  H302  A1LX0 48 
A1LX0 H301  H17 H 0 0 N N N N N N 17.653 -21.641 -6.621 -6.878 -2.358 0.003  H301  A1LX0 49 
A1LX0 H312  H18 H 0 0 N N N N N N 20.244 -21.753 -5.142 -6.138 -4.738 -1.456 H312  A1LX0 50 
A1LX0 H311  H19 H 0 0 N N N N N N 19.895 -22.499 -6.739 -6.310 -3.116 -2.257 H311  A1LX0 51 
A1LX0 H322  H20 H 0 0 N N N N N N 20.946 -19.728 -6.215 -3.860 -3.136 -2.221 H322  A1LX0 52 
A1LX0 H321  H21 H 0 0 N N N N N N 20.691 -20.508 -7.813 -3.823 -4.269 -0.801 H321  A1LX0 53 
A1LX0 H081  H23 H 0 0 N N N N N N 18.610 -14.820 -5.342 -5.508 -0.441 0.654  H081  A1LX0 54 
A1LX0 H181  H24 H 0 0 N N N N N N 16.743 -18.704 -6.727 -2.859 -3.960 0.561  H181  A1LX0 55 
A1LX0 H1    H25 H 0 1 N N N N N N 19.529 -18.133 4.477  4.510  1.918  1.518  H1    A1LX0 56 
A1LX0 H281  H22 H 0 0 N N N N N N 18.713 -22.390 1.651  8.032  1.959  0.489  H281  A1LX0 57 
A1LX0 H2    H26 H 0 1 N N N N N N 16.192 -21.531 3.645  8.999  0.312  -2.024 H2    A1LX0 58 
A1LX0 H5    H27 H 0 1 N N N N N N 19.214 -15.979 -6.321 -6.290 -0.034 -0.776 H5    A1LX0 59 
# 
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 
A1LX0 "N1'" "C2'" DOUB Y N 1  
A1LX0 "C2'" "N3'" SING Y N 2  
A1LX0 "N3'" "C4'" DOUB Y N 3  
A1LX0 "C4'" "C5'" SING Y N 4  
A1LX0 "C5'" "C6'" DOUB Y N 5  
A1LX0 "C6'" "N1'" SING Y N 6  
A1LX0 "C2'" CM2   SING N N 7  
A1LX0 "C4'" "N4'" SING N N 8  
A1LX0 "C5'" "C7'" SING N N 9  
A1LX0 "C7'" N3    SING N N 10 
A1LX0 N3    C2    DOUB Y N 11 
A1LX0 C2    S1    SING Y N 12 
A1LX0 S1    C5    SING Y N 13 
A1LX0 C5    C4    DOUB Y N 14 
A1LX0 C4    N3    SING Y N 15 
A1LX0 C4    CM4   SING N N 16 
A1LX0 C5    C6    SING N N 17 
A1LX0 C2    C8    SING N N 18 
A1LX0 C8    O8    SING N N 19 
A1LX0 C8    C9    SING N N 20 
A1LX0 C6    C7    SING N N 21 
A1LX0 C7    "O7'" SING N N 22 
A1LX0 "O7'" PA    SING N N 23 
A1LX0 PA    O1A   DOUB N N 24 
A1LX0 PA    O2A   SING N N 25 
A1LX0 PB    O2B   SING N N 26 
A1LX0 PB    O1B   DOUB N N 27 
A1LX0 PB    O3B   SING N N 28 
A1LX0 PA    O3A   SING N N 29 
A1LX0 PB    O3A   SING N N 30 
A1LX0 C9    C10   SING N N 31 
A1LX0 C10   C12   SING N N 32 
A1LX0 C12   C11   SING N N 33 
A1LX0 C11   C9    SING N N 34 
A1LX0 CM4   H152  SING N N 35 
A1LX0 CM4   H151  SING N N 36 
A1LX0 CM4   H153  SING N N 37 
A1LX0 C8    H171  SING N N 38 
A1LX0 C7    H202  SING N N 39 
A1LX0 C7    H201  SING N N 40 
A1LX0 "C6'" H061  SING N N 41 
A1LX0 CM2   H073  SING N N 42 
A1LX0 CM2   H072  SING N N 43 
A1LX0 CM2   H071  SING N N 44 
A1LX0 "C7'" H092  SING N N 45 
A1LX0 "C7'" H091  SING N N 46 
A1LX0 C6    H161  SING N N 47 
A1LX0 C6    H162  SING N N 48 
A1LX0 C9    H191  SING N N 49 
A1LX0 C10   H302  SING N N 50 
A1LX0 C10   H301  SING N N 51 
A1LX0 C12   H312  SING N N 52 
A1LX0 C12   H311  SING N N 53 
A1LX0 C11   H322  SING N N 54 
A1LX0 C11   H321  SING N N 55 
A1LX0 "N4'" H081  SING N N 56 
A1LX0 O8    H181  SING N N 57 
A1LX0 O2A   H1    SING N N 58 
A1LX0 O3B   H281  SING N N 59 
A1LX0 O2B   H2    SING N N 60 
A1LX0 "N4'" H5    SING N N 61 
# 
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 
A1LX0 InChI            InChI                1.06  "InChI=1S/C17H26N4O8P2S/c1-10-14(6-7-28-31(26,27)29-30(23,24)25)32-17(15(22)12-4-3-5-12)21(10)9-13-8-19-11(2)20-16(13)18/h8,12,15,22H,3-7,9H2,1-2H3,(H4-,18,19,20,23,24,25,26,27)/p+1/t15-/m1/s1" 
A1LX0 InChIKey         InChI                1.06  FVAVQECWBZFMTG-OAHLLOKOSA-O                                                                                                                                                                       
A1LX0 SMILES_CANONICAL CACTVS               3.385 "Cc1ncc(C[n+]2c(C)c(CCO[P](O)(=O)O[P](O)(O)=O)sc2[C@H](O)C3CCC3)c(N)n1"                                                                                                                           
A1LX0 SMILES           CACTVS               3.385 "Cc1ncc(C[n+]2c(C)c(CCO[P](O)(=O)O[P](O)(O)=O)sc2[CH](O)C3CCC3)c(N)n1"                                                                                                                            
A1LX0 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "Cc1c(sc([n+]1Cc2cnc(nc2N)C)[C@@H](C3CCC3)O)CCOP(=O)(O)OP(=O)(O)O"                                                                                                                                
A1LX0 SMILES           "OpenEye OEToolkits" 2.0.7 "Cc1c(sc([n+]1Cc2cnc(nc2N)C)C(C3CCC3)O)CCOP(=O)(O)OP(=O)(O)O"                                                                                                                                     
# 
_pdbx_chem_comp_identifier.comp_id           A1LX0 
_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-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-2-[(~{R})-cyclobutyl(oxidanyl)methyl]-4-methyl-1,3-thiazol-3-ium-5-yl]ethyl phosphono hydrogen 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 
A1LX0 "Create component" 2024-02-07 PDBJ 
A1LX0 "Initial release"  2025-01-01 RCSB 
# 
