data_A1D9W # _chem_comp.id A1D9W _chem_comp.name "~{N}-[(3~{R})-1,1-bis(oxidanylidene)thiolan-3-yl]-2-chloranyl-5-nitro-pyrimidin-4-amine" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C8 H9 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 2026-01-16 _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 292.699 _chem_comp.one_letter_code ? _chem_comp.three_letter_code A1D9W _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 9INQ _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 A1D9W C1 C1 C 0 1 Y N N N N N 6.511 -5.970 25.572 -2.357 1.111 -0.019 C1 A1D9W 1 A1D9W C2 C2 C 0 1 Y N N N N N 6.697 -6.458 24.302 -3.587 0.485 -0.051 C2 A1D9W 2 A1D9W C3 C3 C 0 1 Y N N N N N 8.880 -6.001 24.443 -2.535 -1.563 -0.050 C3 A1D9W 3 A1D9W C4 C4 C 0 1 Y N N N N N 7.658 -5.472 26.261 -1.208 0.317 -0.009 C4 A1D9W 4 A1D9W C5 C5 C 0 1 N N R N N N 8.896 -4.526 28.106 1.246 0.062 -0.089 C5 A1D9W 5 A1D9W C6 C6 C 0 1 N N N N N N 9.095 -3.010 28.161 2.427 0.896 -0.650 C6 A1D9W 6 A1D9W C7 C7 C 0 1 N N N N N N 10.421 -4.438 29.969 3.102 -1.008 1.205 C7 A1D9W 7 A1D9W C8 C8 C 0 1 N N N N N N 9.082 -4.978 29.552 1.677 -0.429 1.304 C8 A1D9W 8 A1D9W N1 N1 N 1 1 N N N N N N 5.179 -5.987 26.168 -2.259 2.588 -0.002 N1 A1D9W 9 A1D9W N2 N2 N 0 1 Y N N N N N 7.886 -6.465 23.708 -3.638 -0.840 -0.065 N2 A1D9W 10 A1D9W N3 N3 N 0 1 Y N N N N N 8.849 -5.468 25.653 -1.340 -1.005 -0.031 N3 A1D9W 11 A1D9W N4 N4 N 0 1 N N N N N N 7.640 -4.961 27.513 0.049 0.899 0.022 N4 A1D9W 12 A1D9W O1 O1 O -1 1 N N N N N N 5.021 -5.404 27.228 -3.263 3.267 -0.121 O1 A1D9W 13 A1D9W O2 O2 O 0 1 N N N N N N 4.290 -6.598 25.591 -1.173 3.125 0.131 O2 A1D9W 14 A1D9W O3 O3 O 0 1 N N N N N N 10.283 -1.798 30.226 4.905 0.738 0.317 O3 A1D9W 15 A1D9W O4 O4 O 0 1 N N N N N N 11.727 -2.721 28.493 4.175 -1.030 -1.231 O4 A1D9W 16 A1D9W S1 S1 S 0 1 N N N N N N 10.506 -2.825 29.249 3.884 -0.113 -0.185 S1 A1D9W 17 A1D9W H1 H1 H 0 1 N N N N N N 5.846 -6.851 23.766 -4.497 1.067 -0.063 H1 A1D9W 18 A1D9W CL1 CL1 CL 0 0 N Y N N N N 9.859 -6.066 23.991 -2.659 -3.294 -0.069 CL1 A1D9W 19 A1D9W H2 H3 H 0 1 N N N N N N 9.724 -4.948 27.517 1.048 -0.789 -0.741 H2 A1D9W 20 A1D9W H4 H4 H 0 1 N N N N N N 9.311 -2.603 27.162 2.352 0.992 -1.734 H4 A1D9W 21 A1D9W H3 H5 H 0 1 N N N N N N 8.208 -2.510 28.577 2.468 1.877 -0.176 H3 A1D9W 22 A1D9W H6 H6 H 0 1 N N N N N N 11.232 -5.076 29.586 3.650 -0.824 2.130 H6 A1D9W 23 A1D9W H5 H7 H 0 1 N N N N N N 10.489 -4.377 31.065 3.063 -2.076 0.993 H5 A1D9W 24 A1D9W H7 H8 H 0 1 N N N N N N 8.285 -4.567 30.189 1.668 0.406 2.005 H7 A1D9W 25 A1D9W H8 H9 H 0 1 N N N N N N 9.073 -6.076 29.616 0.990 -1.202 1.648 H8 A1D9W 26 A1D9W H9 H10 H 0 1 N N N N N N 7.030 -4.168 27.499 0.136 1.860 0.116 H9 A1D9W 27 # 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 A1D9W C1 C2 DOUB Y N 1 A1D9W C1 N1 SING N N 2 A1D9W C1 C4 SING Y N 3 A1D9W C2 N2 SING Y N 4 A1D9W C3 N2 DOUB Y N 5 A1D9W C3 N3 SING Y N 6 A1D9W C4 N4 SING N N 7 A1D9W C4 N3 DOUB Y N 8 A1D9W C5 N4 SING N N 9 A1D9W C5 C6 SING N N 10 A1D9W C5 C8 SING N N 11 A1D9W C6 S1 SING N N 12 A1D9W C7 S1 SING N N 13 A1D9W C7 C8 SING N N 14 A1D9W N1 O1 SING N N 15 A1D9W N1 O2 DOUB N N 16 A1D9W O3 S1 DOUB N N 17 A1D9W O4 S1 DOUB N N 18 A1D9W C2 H1 SING N N 19 A1D9W C3 CL1 SING N N 20 A1D9W C5 H2 SING N N 21 A1D9W C6 H4 SING N N 22 A1D9W C6 H3 SING N N 23 A1D9W C7 H6 SING N N 24 A1D9W C7 H5 SING N N 25 A1D9W C8 H7 SING N N 26 A1D9W C8 H8 SING N N 27 A1D9W N4 H9 SING N N 28 # 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 A1D9W InChI InChI 1.06 "InChI=1S/C8H9ClN4O4S/c9-8-10-3-6(13(14)15)7(12-8)11-5-1-2-18(16,17)4-5/h3,5H,1-2,4H2,(H,10,11,12)/t5-/m1/s1" A1D9W InChIKey InChI 1.06 PIOPFRGKOMYGFX-RXMQYKEDSA-N A1D9W SMILES_CANONICAL CACTVS 3.385 "[O-][N+](=O)c1cnc(Cl)nc1N[C@@H]2CC[S](=O)(=O)C2" A1D9W SMILES CACTVS 3.385 "[O-][N+](=O)c1cnc(Cl)nc1N[CH]2CC[S](=O)(=O)C2" A1D9W SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1c(c(nc(n1)Cl)N[C@@H]2CCS(=O)(=O)C2)[N+](=O)[O-]" A1D9W SMILES "OpenEye OEToolkits" 2.0.7 "c1c(c(nc(n1)Cl)NC2CCS(=O)(=O)C2)[N+](=O)[O-]" # _pdbx_chem_comp_identifier.comp_id A1D9W _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-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 A1D9W "Create component" 2024-07-09 PDBC A1D9W "Modify PCM" 2024-09-27 PDBE A1D9W "Initial release" 2026-01-21 RCSB # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id A1D9W _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 C3 _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 ? #