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 ? #