data_7K8 # _chem_comp.id 7K8 _chem_comp.name "[(2~{R},3~{S},5~{R})-5-[(4~{E})-4-hydroxyimino-2-oxidanylidene-1,3-diazinan-1-yl]-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C9 H16 N3 O8 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2016-11-03 _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 325.212 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 7K8 _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 5M4Z _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site EBI _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_backbone_atom_flag _chem_comp_atom.pdbx_n_terminal_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 7K8 O2 O1 O 0 1 N N N N N N 44.648 26.117 15.493 1.266 -0.280 1.450 O2 7K8 1 7K8 C2 C1 C 0 1 N N N N N N 45.232 27.215 15.379 2.192 -0.026 0.705 C2 7K8 2 7K8 N3 N1 N 0 1 N N N N N N 46.564 27.254 15.221 3.208 0.726 1.166 N3 7K8 3 7K8 C4 C2 C 0 1 N N N N N N 47.193 28.371 14.826 4.257 1.047 0.313 C4 7K8 4 7K8 N4 N2 N 0 1 N N N N N N 48.406 28.323 14.436 5.422 1.362 0.770 N4 7K8 5 7K8 O4 O2 O 0 1 N N N N N N 49.058 29.477 13.977 6.470 1.683 -0.126 O4 7K8 6 7K8 C5 C3 C 0 1 N N N N N N 46.432 29.692 14.765 3.976 1.011 -1.176 C5 7K8 7 7K8 C6 C4 C 0 1 N N N N N N 45.158 29.705 15.623 3.272 -0.318 -1.482 C6 7K8 8 7K8 N1 N3 N 0 1 N N N N N N 44.559 28.383 15.359 2.167 -0.512 -0.544 N1 7K8 9 7K8 "C1'" C5 C 0 1 N N R N N N 43.117 28.371 15.096 0.987 -1.259 -0.988 "C1'" 7K8 10 7K8 "C2'" C6 C 0 1 N N N N N N 42.340 28.313 16.416 0.855 -2.561 -0.175 "C2'" 7K8 11 7K8 "C3'" C7 C 0 1 N N S N N N 41.053 28.983 16.024 -0.539 -2.453 0.491 "C3'" 7K8 12 7K8 "O3'" O3 O 0 1 N N N N N N 40.180 28.090 15.297 -1.218 -3.710 0.459 "O3'" 7K8 13 7K8 "O4'" O4 O 0 1 N N N N N N 42.659 29.564 14.437 -0.200 -0.484 -0.750 "O4'" 7K8 14 7K8 "C4'" C8 C 0 1 N N R N N N 41.504 30.096 15.088 -1.251 -1.416 -0.414 "C4'" 7K8 15 7K8 "C5'" C9 C 0 1 N N N N N N 41.911 31.370 15.812 -2.371 -0.710 0.354 "C5'" 7K8 16 7K8 "O5'" O5 O 0 1 N N N N N N 40.742 32.077 16.225 -3.018 0.230 -0.505 "O5'" 7K8 17 7K8 P P1 P 0 1 N N N N N N 40.652 32.744 17.679 -4.247 1.154 -0.027 P 7K8 18 7K8 OP1 O6 O 0 1 N N N N N N 41.699 33.845 17.769 -4.809 1.992 -1.282 OP1 7K8 19 7K8 OP2 O7 O 0 1 N N N N N N 39.234 33.305 17.724 -5.325 0.297 0.516 OP2 7K8 20 7K8 OP3 O8 O 0 1 N N N N N N 40.862 31.646 18.710 -3.742 2.170 1.115 OP3 7K8 21 7K8 H3 H1 H 0 1 N N N N N N 47.101 26.430 15.402 3.207 1.042 2.083 H3 7K8 22 7K8 H4 H2 H 0 1 N N N N N N 49.949 29.260 13.729 7.305 1.905 0.309 H4 7K8 23 7K8 H52 H3 H 0 1 N N N N N N 47.097 30.494 15.118 3.329 1.844 -1.450 H52 7K8 24 7K8 H51 H4 H 0 1 N N N N N N 46.150 29.883 13.719 4.912 1.070 -1.731 H51 7K8 25 7K8 H6 H5 H 0 1 N N N N N N 45.402 29.821 16.689 2.887 -0.298 -2.502 H6 7K8 26 7K8 H1 H6 H 0 1 N N N N N N 44.481 30.514 15.311 3.981 -1.138 -1.377 H1 7K8 27 7K8 H11 H7 H 0 1 N N N N N N 42.859 27.486 14.495 1.074 -1.492 -2.049 H11 7K8 28 7K8 H22 H8 H 0 1 N N N N N N 42.172 27.275 16.740 0.897 -3.428 -0.833 H22 7K8 29 7K8 H21 H9 H 0 1 N N N N N N 42.857 28.867 17.213 1.638 -2.619 0.582 H21 7K8 30 7K8 H31 H10 H 0 1 N N N N N N 40.552 29.406 16.907 -0.454 -2.085 1.513 H31 7K8 31 7K8 H32 H11 H 0 1 N N N N N N 39.892 27.391 15.872 -0.762 -4.416 0.938 H32 7K8 32 7K8 H41 H12 H 0 1 N N N N N N 40.707 30.318 14.363 -1.644 -1.892 -1.312 H41 7K8 33 7K8 H53 H13 H 0 1 N N N N N N 42.515 31.113 16.695 -3.096 -1.448 0.697 H53 7K8 34 7K8 H54 H14 H 0 1 N N N N N N 42.502 32.004 15.135 -1.949 -0.188 1.213 H54 7K8 35 7K8 H2 H15 H 0 1 N N N N N N 41.267 34.688 17.837 -5.552 2.571 -1.066 H2 7K8 36 7K8 H5 H16 H 0 1 N N N N N N 40.058 31.511 19.198 -3.034 2.764 0.828 H5 7K8 37 # 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 7K8 O4 N4 SING N N 1 7K8 N4 C4 DOUB N E 2 7K8 "O4'" "C4'" SING N N 3 7K8 "O4'" "C1'" SING N N 4 7K8 C5 C4 SING N N 5 7K8 C5 C6 SING N N 6 7K8 C4 N3 SING N N 7 7K8 "C4'" "C5'" SING N N 8 7K8 "C4'" "C3'" SING N N 9 7K8 "C1'" N1 SING N N 10 7K8 "C1'" "C2'" SING N N 11 7K8 N3 C2 SING N N 12 7K8 "O3'" "C3'" SING N N 13 7K8 N1 C2 SING N N 14 7K8 N1 C6 SING N N 15 7K8 C2 O2 DOUB N N 16 7K8 "C5'" "O5'" SING N N 17 7K8 "C3'" "C2'" SING N N 18 7K8 "O5'" P SING N N 19 7K8 P OP2 DOUB N N 20 7K8 P OP1 SING N N 21 7K8 P OP3 SING N N 22 7K8 N3 H3 SING N N 23 7K8 O4 H4 SING N N 24 7K8 C5 H52 SING N N 25 7K8 C5 H51 SING N N 26 7K8 C6 H6 SING N N 27 7K8 C6 H1 SING N N 28 7K8 "C1'" H11 SING N N 29 7K8 "C2'" H22 SING N N 30 7K8 "C2'" H21 SING N N 31 7K8 "C3'" H31 SING N N 32 7K8 "O3'" H32 SING N N 33 7K8 "C4'" H41 SING N N 34 7K8 "C5'" H53 SING N N 35 7K8 "C5'" H54 SING N N 36 7K8 OP1 H2 SING N N 37 7K8 OP3 H5 SING N N 38 # 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 7K8 InChI InChI 1.03 "InChI=1S/C9H16N3O8P/c13-5-3-8(20-6(5)4-19-21(16,17)18)12-2-1-7(11-15)10-9(12)14/h5-6,8,13,15H,1-4H2,(H,10,11,14)(H2,16,17,18)/t5-,6+,8+/m0/s1" 7K8 InChIKey InChI 1.03 BXCKTJBMNGLVHU-SHYZEUOFSA-N 7K8 SMILES_CANONICAL CACTVS 3.385 "O\N=C\1CCN([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)C(=O)N\1" 7K8 SMILES CACTVS 3.385 "ON=C1CCN([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)C(=O)N1" 7K8 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "C\1CN(C(=O)N/C1=N/O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O" 7K8 SMILES "OpenEye OEToolkits" 2.0.6 "C1CN(C(=O)NC1=NO)C2CC(C(O2)COP(=O)(O)O)O" # _pdbx_chem_comp_identifier.comp_id 7K8 _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.6 _pdbx_chem_comp_identifier.identifier "[(2~{R},3~{S},5~{R})-5-[(4~{E})-4-hydroxyimino-2-oxidanylidene-1,3-diazinan-1-yl]-3-oxidanyl-oxolan-2-yl]methyl dihydrogen 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 7K8 "Create component" 2016-11-03 EBI 7K8 "Modify atom id" 2016-12-13 EBI 7K8 "Modify atom id" 2016-12-15 EBI 7K8 "Initial release" 2017-12-20 RCSB 7K8 "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id 7K8 _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 C6 _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 ? #