data_A1AEK
# 
_chem_comp.id                                    A1AEK 
_chem_comp.name                                  "3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-2-(hydroxymethyl)-5-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3-thiazol-3-ium" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C13 H21 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                     2024-02-12 
_chem_comp.pdbx_modified_date                    2024-09-27 
_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                        455.340 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A1AEK 
_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        8VZE 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
# 
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 
A1AEK C2     C1  C 0 1 Y N N N N N 6.250 44.335 17.005 3.184  -2.031 -0.560 C2     A1AEK 1  
A1AEK "C2'"  C2  C 0 1 Y N N N N N 4.302 46.542 21.934 4.834  3.085  -0.731 "C2'"  A1AEK 2  
A1AEK C27    C3  C 0 1 N N N N N N 5.879 45.625 15.876 4.454  -2.300 -1.326 C27    A1AEK 3  
A1AEK C4     C4  C 0 1 Y N N N N N 6.648 42.998 18.784 1.913  -1.169 1.051  C4     A1AEK 4  
A1AEK "C4'"  C5  C 0 1 Y N N N N N 4.879 46.311 19.683 5.618  1.459  0.696  "C4'"  A1AEK 5  
A1AEK C5     C6  C 0 1 Y N N N N N 6.119 41.997 17.828 0.933  -1.814 0.410  C5     A1AEK 6  
A1AEK "C5'"  C7  C 0 1 Y N N N N N 6.119 45.811 20.052 4.482  0.693  0.425  "C5'"  A1AEK 7  
A1AEK C6     C8  C 0 1 N N N N N N 5.883 40.520 17.910 -0.522 -1.832 0.803  C6     A1AEK 8  
A1AEK "C6'"  C9  C 0 1 Y N N N N N 6.398 45.695 21.403 3.550  1.194  -0.462 "C6'"  A1AEK 9  
A1AEK C7     C10 C 0 1 N N N N N N 6.467 39.836 16.686 -1.249 -0.671 0.121  C7     A1AEK 10 
A1AEK "C7'"  C11 C 0 1 N N N N N N 7.173 45.392 19.042 4.285  -0.652 1.075  "C7'"  A1AEK 11 
A1AEK CM2    C12 C 0 1 N N N N N N 3.305 46.932 22.951 5.025  4.429  -1.385 CM2    A1AEK 12 
A1AEK CM4    C13 C 0 1 N N N N N N 7.086 42.616 20.164 1.674  -0.350 2.293  CM4    A1AEK 13 
A1AEK "N1'"  N1  N 0 1 Y N N N N N 5.497 46.061 22.309 3.754  2.383  -1.012 "N1'"  A1AEK 14 
A1AEK N3     N2  N 1 1 Y N N N N N 6.696 44.252 18.271 3.104  -1.303 0.502  N3     A1AEK 15 
A1AEK "N3'"  N3  N 0 1 Y N N N N N 3.998 46.659 20.636 5.754  2.641  0.101  "N3'"  A1AEK 16 
A1AEK "N4'"  N4  N 0 1 N N N N N N 4.517 46.474 18.401 6.582  1.001  1.579  "N4'"  A1AEK 17 
A1AEK O1A    O1  O 0 1 N N N N N N 4.295 37.877 17.396 -3.677 0.415  -1.520 O1A    A1AEK 18 
A1AEK O1B    O2  O 0 1 N N N N N N 5.480 35.703 13.304 -6.709 1.806  -0.373 O1B    A1AEK 19 
A1AEK O28    O3  O 0 1 N N N N N N 6.426 46.901 16.153 5.085  -3.472 -0.806 O28    A1AEK 20 
A1AEK O2A    O4  O 0 1 N N N N N N 6.006 36.106 17.350 -3.305 1.853  0.521  O2A    A1AEK 21 
A1AEK O2B    O5  O 0 1 N N N N N N 7.438 36.045 14.807 -7.060 -0.526 -1.273 O2B    A1AEK 22 
A1AEK O3A    O6  O 0 1 N N N N N N 5.281 37.336 15.182 -5.167 -0.003 0.475  O3A    A1AEK 23 
A1AEK O3B    O7  O 0 1 N N N N N N 6.783 37.765 13.224 -7.691 0.096  1.202  O3B    A1AEK 24 
A1AEK O7     O8  O 0 1 N N N N N N 6.716 38.478 16.991 -2.628 -0.687 0.494  O7     A1AEK 25 
A1AEK PA     P1  P 0 1 N N N N N N 5.560 37.400 16.762 -3.694 0.395  -0.040 PA     A1AEK 26 
A1AEK PB     P2  P 0 1 N N N N N N 6.281 36.680 14.109 -6.658 0.375  -0.001 PB     A1AEK 27 
A1AEK S1     S1  S 0 1 Y N N N N N 5.719 42.816 16.374 1.642  -2.639 -0.976 S1     A1AEK 28 
A1AEK H272   H1  H 0 0 N N N N N N 6.246 45.315 14.886 4.217  -2.452 -2.379 H272   A1AEK 29 
A1AEK H271   H2  H 0 0 N N N N N N 4.785 45.733 15.844 5.127  -1.449 -1.225 H271   A1AEK 30 
A1AEK H61    H3  H 0 1 N N N N N N 6.366 40.123 18.815 -0.971 -2.774 0.492  H61    A1AEK 31 
A1AEK H62    H4  H 0 1 N N N N N N 4.801 40.325 17.956 -0.607 -1.728 1.885  H62    A1AEK 32 
A1AEK "H6'"  H5  H 0 1 N N N N N N 7.353 45.305 21.723 2.660  0.629  -0.696 "H6'"  A1AEK 33 
A1AEK H72    H6  H 0 1 N N N N N N 5.753 39.901 15.852 -0.799 0.272  0.433  H72    A1AEK 34 
A1AEK H71    H7  H 0 1 N N N N N N 7.409 40.329 16.403 -1.164 -0.774 -0.961 H71    A1AEK 35 
A1AEK "H7'1" H8  H 0 0 N N N N N N 7.380 46.231 18.362 5.163  -1.273 0.898  "H7'1" A1AEK 36 
A1AEK "H7'2" H9  H 0 0 N N N N N N 8.096 45.113 19.572 4.143  -0.520 2.147  "H7'2" A1AEK 37 
A1AEK HM22   H10 H 0 0 N N N N N N 3.718 46.758 23.956 5.561  4.302  -2.325 HM22   A1AEK 38 
A1AEK HM21   H11 H 0 0 N N N N N N 3.060 47.998 22.835 4.051  4.879  -1.580 HM21   A1AEK 39 
A1AEK H1     H12 H 0 1 N N N N N N 2.393 46.330 22.820 5.599  5.077  -0.723 H1     A1AEK 40 
A1AEK HM43   H13 H 0 0 N N N N N N 6.234 42.698 20.855 1.717  -0.997 3.169  HM43   A1AEK 41 
A1AEK HM41   H14 H 0 0 N N N N N N 7.454 41.580 20.158 2.440  0.421  2.372  HM41   A1AEK 42 
A1AEK HM42   H15 H 0 0 N N N N N N 7.891 43.289 20.493 0.691  0.118  2.236  HM42   A1AEK 43 
A1AEK H2     H16 H 0 1 N N N N N N 3.592 46.852 18.361 6.509  0.111  1.958  H2     A1AEK 44 
A1AEK "HN4'" H17 H 0 0 N N N N N N 5.153 47.102 17.952 7.330  1.570  1.819  "HN4'" A1AEK 45 
A1AEK HO28   H18 H 0 0 N N N N N N 6.159 47.514 15.478 5.910  -3.706 -1.254 HO28   A1AEK 46 
A1AEK H3     H19 H 0 1 N N N N N N 5.391 35.834 18.021 -3.296 1.914  1.486  H3     A1AEK 47 
A1AEK H4     H20 H 0 1 N N N N N N 7.457 35.116 14.609 -7.047 -1.477 -1.102 H4     A1AEK 48 
A1AEK H5     H21 H 0 1 N N N N N N 6.490 37.610 12.334 -8.611 0.301  0.986  H5     A1AEK 49 
# 
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 
A1AEK "N1'" "C2'"  DOUB Y N 1  
A1AEK "C6'" "N1'"  SING Y N 2  
A1AEK CM2   "C2'"  SING N N 3  
A1AEK "C2'" "N3'"  SING Y N 4  
A1AEK "N3'" "C4'"  DOUB Y N 5  
A1AEK "N4'" "C4'"  SING N N 6  
A1AEK "C4'" "C5'"  SING Y N 7  
A1AEK "C5'" "C6'"  DOUB Y N 8  
A1AEK "C5'" "C7'"  SING N N 9  
A1AEK "C7'" N3     SING N N 10 
A1AEK C2    N3     DOUB Y N 11 
A1AEK N3    C4     SING Y N 12 
A1AEK S1    C2     SING Y N 13 
A1AEK C5    S1     SING Y N 14 
A1AEK C4    C5     DOUB Y N 15 
A1AEK C5    C6     SING N N 16 
A1AEK CM4   C4     SING N N 17 
A1AEK C6    C7     SING N N 18 
A1AEK C7    O7     SING N N 19 
A1AEK O7    PA     SING N N 20 
A1AEK O1A   PA     DOUB N N 21 
A1AEK PA    O2A    SING N N 22 
A1AEK O3A   PA     SING N N 23 
A1AEK PB    O3A    SING N N 24 
A1AEK O1B   PB     DOUB N N 25 
A1AEK O2B   PB     SING N N 26 
A1AEK O3B   PB     SING N N 27 
A1AEK C27   C2     SING N N 28 
A1AEK O28   C27    SING N N 29 
A1AEK C27   H272   SING N N 30 
A1AEK C27   H271   SING N N 31 
A1AEK C6    H61    SING N N 32 
A1AEK C6    H62    SING N N 33 
A1AEK "C6'" "H6'"  SING N N 34 
A1AEK C7    H72    SING N N 35 
A1AEK C7    H71    SING N N 36 
A1AEK "C7'" "H7'1" SING N N 37 
A1AEK "C7'" "H7'2" SING N N 38 
A1AEK CM2   HM22   SING N N 39 
A1AEK CM2   HM21   SING N N 40 
A1AEK CM2   H1     SING N N 41 
A1AEK CM4   HM43   SING N N 42 
A1AEK CM4   HM41   SING N N 43 
A1AEK CM4   HM42   SING N N 44 
A1AEK "N4'" H2     SING N N 45 
A1AEK "N4'" "HN4'" SING N N 46 
A1AEK O28   HO28   SING N N 47 
A1AEK O2A   H3     SING N N 48 
A1AEK O2B   H4     SING N N 49 
A1AEK O3B   H5     SING N N 50 
# 
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 
A1AEK SMILES           ACDLabs              12.01 "OCc1sc(CCOP(=O)(O)OP(=O)(O)O)c(C)[n+]1Cc1cnc(C)nc1N"                                                                                                              
A1AEK InChI            InChI                1.06  "InChI=1S/C13H20N4O8P2S/c1-8-11(3-4-24-27(22,23)25-26(19,20)21)28-12(7-18)17(8)6-10-5-15-9(2)16-13(10)14/h5,18H,3-4,6-7H2,1-2H3,(H4-,14,15,16,19,20,21,22,23)/p+1" 
A1AEK InChIKey         InChI                1.06  DKVWQSZJFWOHFA-UHFFFAOYSA-O                                                                                                                                        
A1AEK SMILES_CANONICAL CACTVS               3.385 "Cc1ncc(C[n+]2c(C)c(CCO[P](O)(=O)O[P](O)(O)=O)sc2CO)c(N)n1"                                                                                                        
A1AEK SMILES           CACTVS               3.385 "Cc1ncc(C[n+]2c(C)c(CCO[P](O)(=O)O[P](O)(O)=O)sc2CO)c(N)n1"                                                                                                        
A1AEK SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "Cc1c(sc([n+]1Cc2cnc(nc2N)C)CO)CCOP(=O)(O)OP(=O)(O)O"                                                                                                              
A1AEK SMILES           "OpenEye OEToolkits" 2.0.7 "Cc1c(sc([n+]1Cc2cnc(nc2N)C)CO)CCOP(=O)(O)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 
A1AEK "SYSTEMATIC NAME" ACDLabs              12.01 "3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-2-(hydroxymethyl)-5-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3-thiazol-3-ium" 
A1AEK "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "2-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-2-(hydroxymethyl)-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 
A1AEK "Create component" 2024-02-12 RCSB 
A1AEK "Initial release"  2024-10-02 RCSB 
# 
