data_8Y9 # _chem_comp.id 8Y9 _chem_comp.name ;[(2~{R},3~{S},5~{R})-5-[(5~{S})-5-carbamimidamido-2,4-bis(oxidanylidene)imidazolidin-1-yl]-3-oxidanyl-oxolan-2-yl]methy l dihydrogen phosphate ; _chem_comp.type "DNA linking" _chem_comp.pdbx_type HETAIN _chem_comp.formula "C9 H16 N5 O8 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "(S)-Gh" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2017-11-07 _chem_comp.pdbx_modified_date 2021-06-04 _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 353.226 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 8Y9 _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 5YMG _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.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 8Y9 P P1 P 0 1 N N N -78.493 302.362 104.730 -4.769 -0.388 0.653 P 8Y9 1 8Y9 C2 C1 C 0 1 N N N -75.425 304.640 108.757 4.421 1.180 1.343 C2 8Y9 2 8Y9 N3 N1 N 0 1 N N N -75.316 305.642 107.870 4.092 0.357 0.292 N3 8Y9 3 8Y9 C4 C2 C 0 1 N N S -74.064 306.229 107.493 3.133 -0.733 0.488 C4 8Y9 4 8Y9 C5 C3 C 0 1 N N N -73.981 307.479 108.246 3.634 -2.007 -0.162 C5 8Y9 5 8Y9 O5 O1 O 0 1 N N N -74.038 307.404 109.529 4.646 -2.617 0.107 O5 8Y9 6 8Y9 N7 N2 N 0 1 N N N -73.862 308.679 107.647 2.718 -2.322 -1.100 N7 8Y9 7 8Y9 C8 C4 C 0 1 N N N -73.860 308.276 106.359 1.719 -1.432 -1.133 C8 8Y9 8 8Y9 O8 O2 O 0 1 N N N -73.742 309.060 105.334 0.776 -1.504 -1.896 O8 8Y9 9 8Y9 N9 N3 N 0 1 N N N -73.982 306.945 106.241 1.876 -0.451 -0.227 N9 8Y9 10 8Y9 "C1'" C5 C 0 1 N N R -74.028 306.166 104.998 0.972 0.679 0.005 "C1'" 8Y9 11 8Y9 N11 N4 N 0 1 N N N -74.365 304.033 109.325 5.239 2.266 1.136 N11 8Y9 12 8Y9 N12 N5 N 0 1 N N N -76.606 304.245 109.018 3.957 0.932 2.535 N12 8Y9 13 8Y9 "C2'" C6 C 0 1 N N N -73.497 304.749 104.957 0.934 1.584 -1.242 "C2'" 8Y9 14 8Y9 "C3'" C7 C 0 1 N N S -74.357 304.230 103.813 -0.557 1.598 -1.656 "C3'" 8Y9 15 8Y9 "O3'" O3 O 0 1 N N N -73.885 304.784 102.554 -0.965 2.908 -2.056 "O3'" 8Y9 16 8Y9 "C4'" C8 C 0 1 N N R -75.712 304.792 104.145 -1.263 1.177 -0.342 "C4'" 8Y9 17 8Y9 "O4'" O4 O 0 1 N N N -75.410 306.092 104.650 -0.364 0.198 0.228 "O4'" 8Y9 18 8Y9 "C5'" C9 C 0 1 N N N -76.469 303.995 105.203 -2.626 0.548 -0.640 "C5'" 8Y9 19 8Y9 "O5'" O5 O 0 1 N N N -76.915 302.783 104.625 -3.304 0.276 0.588 "O5'" 8Y9 20 8Y9 OP2 O6 O 0 1 N N N -78.626 300.943 104.232 -5.274 -0.427 2.181 OP2 8Y9 21 8Y9 OP1 O7 O 0 1 N N N -79.343 303.391 104.054 -5.711 0.416 -0.158 OP1 8Y9 22 8Y9 O1 O8 O 0 1 N Y N -78.823 302.406 106.305 -4.705 -1.887 0.070 O1 8Y9 23 8Y9 H1 H1 H 0 1 N N N -76.152 305.997 107.451 4.496 0.497 -0.579 H1 8Y9 24 8Y9 H2 H2 H 0 1 N N N -73.203 305.567 107.669 2.946 -0.891 1.550 H2 8Y9 25 8Y9 H3 H3 H 0 1 N N N -73.795 309.596 108.040 2.777 -3.097 -1.680 H3 8Y9 26 8Y9 H4 H4 H 0 1 N N N -73.502 306.738 104.219 1.308 1.252 0.869 H4 8Y9 27 8Y9 H5 H5 H 0 1 N N N -74.505 303.269 109.955 5.413 2.887 1.860 H5 8Y9 28 8Y9 H6 H6 H 0 1 N N N -73.439 304.347 109.117 5.643 2.410 0.266 H6 8Y9 29 8Y9 H7 H7 H 0 1 N N N -76.611 303.477 109.658 4.189 1.513 3.277 H7 8Y9 30 8Y9 H8 H8 H 0 1 N N N -73.683 304.208 105.896 1.270 2.591 -0.993 H8 8Y9 31 8Y9 H9 H9 H 0 1 N N N -72.423 304.714 104.720 1.549 1.164 -2.037 H9 8Y9 32 8Y9 H10 H10 H 0 1 N N N -74.373 303.130 103.800 -0.746 0.874 -2.448 H10 8Y9 33 8Y9 H11 H11 H 0 1 N N N -73.029 304.425 102.351 -0.550 3.216 -2.874 H11 8Y9 34 8Y9 H12 H12 H 0 1 N N N -76.321 304.858 103.231 -1.371 2.031 0.327 H12 8Y9 35 8Y9 H13 H13 H 0 1 N N N -75.802 303.778 106.050 -3.221 1.238 -1.238 H13 8Y9 36 8Y9 H14 H14 H 0 1 N N N -77.333 304.577 105.557 -2.485 -0.382 -1.191 H14 8Y9 37 8Y9 H15 H15 H 0 1 N N N -79.262 300.913 103.527 -6.152 -0.816 2.295 H15 8Y9 38 8Y9 H16 H16 H 0 1 N N N -79.482 303.070 106.473 -4.105 -2.472 0.553 H16 8Y9 39 # # 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 8Y9 "O3'" "C3'" SING N N 1 8Y9 "C3'" "C4'" SING N N 2 8Y9 "C3'" "C2'" SING N N 3 8Y9 OP1 P DOUB N N 4 8Y9 "C4'" "O4'" SING N N 5 8Y9 "C4'" "C5'" SING N N 6 8Y9 OP2 P SING N N 7 8Y9 "O5'" P SING N N 8 8Y9 "O5'" "C5'" SING N N 9 8Y9 "O4'" "C1'" SING N N 10 8Y9 "C2'" "C1'" SING N N 11 8Y9 "C1'" N9 SING N N 12 8Y9 O8 C8 DOUB N N 13 8Y9 N9 C8 SING N N 14 8Y9 N9 C4 SING N N 15 8Y9 C8 N7 SING N N 16 8Y9 C4 N3 SING N N 17 8Y9 C4 C5 SING N N 18 8Y9 N7 C5 SING N N 19 8Y9 N3 C2 SING N N 20 8Y9 C5 O5 DOUB N N 21 8Y9 C2 N12 DOUB N N 22 8Y9 C2 N11 SING N N 23 8Y9 P O1 SING N N 24 8Y9 N3 H1 SING N N 25 8Y9 C4 H2 SING N N 26 8Y9 N7 H3 SING N N 27 8Y9 "C1'" H4 SING N N 28 8Y9 N11 H5 SING N N 29 8Y9 N11 H6 SING N N 30 8Y9 N12 H7 SING N N 31 8Y9 "C2'" H8 SING N N 32 8Y9 "C2'" H9 SING N N 33 8Y9 "C3'" H10 SING N N 34 8Y9 "O3'" H11 SING N N 35 8Y9 "C4'" H12 SING N N 36 8Y9 "C5'" H13 SING N N 37 8Y9 "C5'" H14 SING N N 38 8Y9 OP2 H15 SING N N 39 8Y9 O1 H16 SING N N 40 # # 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 8Y9 InChI InChI 1.03 "InChI=1S/C9H16N5O8P/c10-8(11)12-6-7(16)13-9(17)14(6)5-1-3(15)4(22-5)2-21-23(18,19)20/h3-6,15H,1-2H2,(H4,10,11,12)(H,13,16,17)(H2,18,19,20)/t3-,4+,5+,6-/m0/s1" 8Y9 InChIKey InChI 1.03 IMJMAQUBWVPHQG-KCDKBNATSA-N 8Y9 SMILES_CANONICAL CACTVS 3.385 "NC(=N)N[C@H]1N([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)C(=O)NC1=O" 8Y9 SMILES CACTVS 3.385 "NC(=N)N[CH]1N([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)C(=O)NC1=O" 8Y9 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "[H]/N=C(/N)\N[C@@H]1C(=O)NC(=O)N1[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O" 8Y9 SMILES "OpenEye OEToolkits" 2.0.6 "C1C(C(OC1N2C(C(=O)NC2=O)NC(=N)N)COP(=O)(O)O)O" # _pdbx_chem_comp_identifier.comp_id 8Y9 _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-[(5~{S})-5-carbamimidamido-2,4-bis(oxidanylidene)imidazolidin-1-yl]-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate" # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id 8Y9 _pdbx_chem_comp_synonyms.name "(S)-Gh" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site 8Y9 "Create component" 2017-11-07 RCSB 8Y9 "Modify linking type" 2017-11-07 PDBJ 8Y9 "Modify synonyms" 2020-06-05 PDBE 8Y9 "Initial release" 2021-06-09 RCSB ##