data_A1D9X
# 
_chem_comp.id                                    A1D9X 
_chem_comp.name                                  "~{N}-[(3~{R})-1,1-bis(oxidanylidene)thiolan-3-yl]-2-chloranyl-~{N}-(2,2-dimethylpropyl)-5-nitro-pyrimidin-4-amine" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C13 H19 Cl N4 O4 S" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2024-07-09 
_chem_comp.pdbx_modified_date                    2025-05-09 
_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                        362.832 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A1D9X 
_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        9INP 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBC 
_chem_comp.pdbx_pcm                              Y 
# 
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 
A1D9X N3  N1  N  0  1 Y N N N N N 7.611  -6.550 23.439 1.720  -2.229 -1.452 N3  A1D9X 1  
A1D9X C4  C1  C  0  1 Y N N N N N 8.632  -6.202 24.225 1.607  -2.201 -0.138 C4  A1D9X 2  
A1D9X C5  C2  C  0  1 Y N N N N N 6.390  -6.464 23.980 1.346  -1.194 -2.191 C5  A1D9X 3  
A1D9X C6  C3  C  0  1 Y N N N N N 6.173  -6.041 25.269 0.832  -0.073 -1.570 C6  A1D9X 4  
A1D9X C7  C4  C  0  1 Y N N N N N 7.329  -5.689 26.034 0.726  -0.076 -0.177 C7  A1D9X 5  
A1D9X C8  C5  C  0  1 N N R N N N 8.585  -4.524 27.696 -1.189 0.813  0.862  C8  A1D9X 6  
A1D9X C10 C6  C  0  1 N N N N N N 10.668 -4.246 28.728 -2.822 -0.859 1.756  C10 A1D9X 7  
A1D9X C13 C7  C  0  1 N N N N N N 6.239  -6.767 29.101 2.306  2.067  1.234  C13 A1D9X 8  
A1D9X C15 C8  C  0  1 N N N N N N 7.094  -7.851 28.446 3.175  1.111  0.414  C15 A1D9X 9  
A1D9X C11 C9  C  0  1 N N N N N N 9.428  -5.123 28.838 -1.329 -0.484 1.676  C11 A1D9X 10 
A1D9X C12 C10 C  0  1 N N N N N N 6.276  -5.437 28.316 1.030  1.346  1.673  C12 A1D9X 11 
A1D9X C14 C11 C  0  1 N N N N N N 6.729  -6.533 30.530 3.081  2.529  2.469  C14 A1D9X 12 
A1D9X C16 C12 C  0  1 N N N N N N 4.784  -7.233 29.151 1.937  3.281  0.379  C16 A1D9X 13 
A1D9X C9  C13 C  0  1 N N N N N N 8.387  -3.057 28.121 -2.052 0.632  -0.414 C9  A1D9X 14 
A1D9X N2  N2  N  0  1 Y N N N N N 8.546  -5.779 25.480 1.122  -1.152 0.496  N2  A1D9X 15 
A1D9X N4  N3  N  0  1 N N N N N N 7.346  -5.247 27.323 0.217  1.026  0.492  N4  A1D9X 16 
A1D9X N5  N4  N  1  1 N N N N N N 4.804  -5.969 25.777 0.405  1.103  -2.360 N5  A1D9X 17 
A1D9X O2  O1  O  0  1 N N N N N N 9.900  -2.108 30.076 -3.963 -1.213 -0.623 O2  A1D9X 18 
A1D9X O3  O2  O  0  1 N N N N N N 10.693 -1.783 27.769 -4.506 0.850  0.603  O3  A1D9X 19 
A1D9X O4  O3  O  -1 1 N N N N N N 4.367  -4.881 26.122 -0.079 2.070  -1.800 O4  A1D9X 20 
A1D9X O5  O4  O  0  1 N N N N N N 4.141  -6.995 25.793 0.536  1.103  -3.571 O5  A1D9X 21 
A1D9X S2  S1  S  0  1 N N N N N N 10.007 -2.606 28.731 -3.571 -0.157 0.242  S2  A1D9X 22 
A1D9X CL1 CL1 CL 0  0 N Y N N N N 9.578  -6.268 23.818 2.111  -3.585 0.783  CL1 A1D9X 23 
A1D9X H16 H2  H  0  1 N N N N N N 5.538  -6.739 23.377 1.443  -1.227 -3.266 H16 A1D9X 24 
A1D9X H17 H3  H  0  1 N N N N N N 9.231  -4.507 26.806 -1.554 1.661  1.442  H17 A1D9X 25 
A1D9X H2  H4  H  0  1 N N N N N N 11.213 -4.450 27.795 -2.941 -1.942 1.769  H2  A1D9X 26 
A1D9X H1  H5  H  0  1 N N N N N N 11.339 -4.402 29.586 -3.277 -0.417 2.643  H1  A1D9X 27 
A1D9X H10 H6  H  0  1 N N N N N N 7.035  -8.775 29.040 4.156  1.558  0.255  H10 A1D9X 28 
A1D9X H12 H7  H  0  1 N N N N N N 6.723  -8.045 27.429 3.287  0.170  0.952  H12 A1D9X 29 
A1D9X H11 H8  H  0  1 N N N N N N 8.140  -7.513 28.397 2.701  0.924  -0.550 H11 A1D9X 30 
A1D9X H4  H9  H  0  1 N N N N N N 9.660  -6.184 28.663 -0.776 -1.286 1.187  H4  A1D9X 31 
A1D9X H3  H10 H  0  1 N N N N N N 8.933  -5.012 29.814 -0.936 -0.331 2.681  H3  A1D9X 32 
A1D9X H6  H11 H  0  1 N N N N N N 5.317  -5.345 27.785 1.293  0.425  2.193  H6  A1D9X 33 
A1D9X H5  H12 H  0  1 N N N N N N 6.366  -4.625 29.053 0.460  1.991  2.342  H5  A1D9X 34 
A1D9X H8  H13 H  0  1 N N N N N N 6.702  -7.481 31.087 2.462  3.210  3.053  H8  A1D9X 35 
A1D9X H7  H14 H  0  1 N N N N N N 7.760  -6.151 30.506 3.344  1.664  3.078  H7  A1D9X 36 
A1D9X H9  H15 H  0  1 N N N N N N 6.077  -5.798 31.025 3.990  3.043  2.156  H9  A1D9X 37 
A1D9X H13 H16 H  0  1 N N N N N N 4.721  -8.181 29.705 1.468  2.945  -0.546 H13 A1D9X 38 
A1D9X H14 H17 H  0  1 N N N N N N 4.172  -6.472 29.657 1.242  3.915  0.929  H14 A1D9X 39 
A1D9X H15 H18 H  0  1 N N N N N N 4.411  -7.381 28.127 2.838  3.848  0.145  H15 A1D9X 40 
A1D9X H19 H19 H  0  1 N N N N N N 8.097  -2.431 27.264 -2.281 1.597  -0.866 H19 A1D9X 41 
A1D9X H18 H20 H  0  1 N N N N N N 7.627  -2.972 28.912 -1.553 -0.022 -1.128 H18 A1D9X 42 
# 
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 
A1D9X C10 S2  SING N N 1  
A1D9X C10 C11 SING N N 2  
A1D9X C11 C8  SING N N 3  
A1D9X C12 C13 SING N N 4  
A1D9X C12 N4  SING N N 5  
A1D9X C13 C16 SING N N 6  
A1D9X C13 C15 SING N N 7  
A1D9X C13 C14 SING N N 8  
A1D9X C4  N2  DOUB Y N 9  
A1D9X C4  N3  SING Y N 10 
A1D9X C5  C6  SING Y N 11 
A1D9X C5  N3  DOUB Y N 12 
A1D9X C6  N5  SING N N 13 
A1D9X C6  C7  DOUB Y N 14 
A1D9X C7  N4  SING N N 15 
A1D9X C7  N2  SING Y N 16 
A1D9X C8  C9  SING N N 17 
A1D9X C8  N4  SING N N 18 
A1D9X C9  S2  SING N N 19 
A1D9X N5  O5  DOUB N N 20 
A1D9X N5  O4  SING N N 21 
A1D9X O2  S2  DOUB N N 22 
A1D9X O3  S2  DOUB N N 23 
A1D9X C4  CL1 SING N N 24 
A1D9X C5  H16 SING N N 25 
A1D9X C8  H17 SING N N 26 
A1D9X C10 H2  SING N N 27 
A1D9X C10 H1  SING N N 28 
A1D9X C15 H10 SING N N 29 
A1D9X C15 H12 SING N N 30 
A1D9X C15 H11 SING N N 31 
A1D9X C11 H4  SING N N 32 
A1D9X C11 H3  SING N N 33 
A1D9X C12 H6  SING N N 34 
A1D9X C12 H5  SING N N 35 
A1D9X C14 H8  SING N N 36 
A1D9X C14 H7  SING N N 37 
A1D9X C14 H9  SING N N 38 
A1D9X C16 H13 SING N N 39 
A1D9X C16 H14 SING N N 40 
A1D9X C16 H15 SING N N 41 
A1D9X C9  H19 SING N N 42 
A1D9X C9  H18 SING N N 43 
# 
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 
A1D9X InChI            InChI                1.06  "InChI=1S/C13H19ClN4O4S/c1-13(2,3)8-17(9-4-5-23(21,22)7-9)11-10(18(19)20)6-15-12(14)16-11/h6,9H,4-5,7-8H2,1-3H3/t9-/m1/s1" 
A1D9X InChIKey         InChI                1.06  FDTNEVLKLGWAGU-SECBINFHSA-N                                                                                                
A1D9X SMILES_CANONICAL CACTVS               3.385 "CC(C)(C)CN([C@@H]1CC[S](=O)(=O)C1)c2nc(Cl)ncc2[N+]([O-])=O"                                                               
A1D9X SMILES           CACTVS               3.385 "CC(C)(C)CN([CH]1CC[S](=O)(=O)C1)c2nc(Cl)ncc2[N+]([O-])=O"                                                                 
A1D9X SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC(C)(C)CN(c1c(cnc(n1)Cl)[N+](=O)[O-])[C@@H]2CCS(=O)(=O)C2"                                                               
A1D9X SMILES           "OpenEye OEToolkits" 2.0.7 "CC(C)(C)CN(c1c(cnc(n1)Cl)[N+](=O)[O-])C2CCS(=O)(=O)C2"                                                                    
# 
_pdbx_chem_comp_identifier.comp_id           A1D9X 
_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        "~{N}-[(3~{R})-1,1-bis(oxidanylidene)thiolan-3-yl]-2-chloranyl-~{N}-(2,2-dimethylpropyl)-5-nitro-pyrimidin-4-amine" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
A1D9X "Create component" 2024-07-09 PDBC 
A1D9X "Modify PCM"       2024-09-27 PDBE 
A1D9X "Initial release"  2025-05-14 RCSB 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            A1D9X 
_pdbx_chem_comp_pcm.modified_residue_id                CYS 
_pdbx_chem_comp_pcm.type                               None 
_pdbx_chem_comp_pcm.category                           "Covalent chemical modification" 
_pdbx_chem_comp_pcm.position                           "Amino-acid side chain" 
_pdbx_chem_comp_pcm.polypeptide_position               "Any position" 
_pdbx_chem_comp_pcm.comp_id_linking_atom               C4 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom   SG 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession     ? 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession      ? 
# 
