data_Y9Z # _chem_comp.id Y9Z _chem_comp.name "5'-O-[(S)-{[(S)-[2-(acetylamino)ethoxy](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]guanosine" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C14 H22 N6 O12 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2013-12-27 _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 528.305 _chem_comp.one_letter_code ? _chem_comp.three_letter_code Y9Z _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 4NMM _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB _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 Y9Z N N N 0 1 N N N N N N 39.595 34.090 11.767 7.496 -2.549 -0.200 N Y9Z 1 Y9Z C C C 0 1 N N N N N N 40.765 34.642 11.469 6.900 -2.191 -1.360 C Y9Z 2 Y9Z O O O 0 1 N N N N N N 40.876 35.626 10.677 7.336 -2.577 -2.431 O Y9Z 3 Y9Z P P P 0 1 N N N N N N 47.906 32.902 14.876 -2.168 1.996 -0.500 P Y9Z 4 Y9Z P1 P1 P 0 1 N N N N N N 49.480 34.891 16.242 -4.429 0.334 -1.454 P1 Y9Z 5 Y9Z C1 C1 C 0 1 N N N N N N 39.476 33.028 12.609 7.001 -2.112 0.992 C1 Y9Z 6 Y9Z N1 N1 N 0 1 N N N N N N 38.260 32.512 12.807 7.623 -2.495 2.153 N1 Y9Z 7 Y9Z O1 O1 O 0 1 N N N N N N 43.783 29.688 13.281 4.686 1.826 2.278 O1 Y9Z 8 Y9Z C2 C2 C 0 1 Y N N N N N 41.723 32.975 13.085 5.304 -0.935 -0.045 C2 Y9Z 9 Y9Z N2 N2 N 0 1 N N N N N N 40.485 32.493 13.310 5.944 -1.334 1.061 N2 Y9Z 10 Y9Z O2 O2 O 0 1 N N N N N N 44.187 29.214 15.891 2.601 3.248 2.624 O2 Y9Z 11 Y9Z C3 C3 C 0 1 Y N N N N N 41.930 34.104 12.161 5.758 -1.360 -1.299 C3 Y9Z 12 Y9Z N3 N3 N 0 1 Y N N N N N 43.231 34.406 12.170 4.931 -0.822 -2.229 N3 Y9Z 13 Y9Z O3 O3 O 0 1 N N N N N N 46.373 32.592 15.096 -0.783 1.581 0.207 O3 Y9Z 14 Y9Z C4 C4 C 0 1 Y N N N N N 43.830 33.540 13.021 4.013 -0.118 -1.633 C4 Y9Z 15 Y9Z N4 N4 N 0 1 Y N N N N N 42.934 32.682 13.515 4.199 -0.164 -0.282 N4 Y9Z 16 Y9Z O4 O4 O 0 1 N N N N N N 48.104 34.099 15.978 -3.142 0.716 -0.565 O4 Y9Z 17 Y9Z C5 C5 C 0 1 N N R N N N 43.180 31.629 14.505 3.358 0.479 0.730 C5 Y9Z 18 Y9Z N5 N5 N 0 1 N N N N N N 53.133 34.820 18.816 -7.333 -1.824 1.047 N5 Y9Z 19 Y9Z O5 O5 O 0 1 N N N N N N 49.981 34.397 17.633 -5.267 -0.825 -0.715 O5 Y9Z 20 Y9Z C6 C6 C 0 1 N N R N N N 44.313 30.733 14.076 3.911 1.879 1.079 C6 Y9Z 21 Y9Z O6 O6 O 0 1 N N N N N N 52.486 36.920 19.399 -7.992 -3.789 1.841 O6 Y9Z 22 Y9Z C7 C7 C 0 1 N N S N N N 44.910 30.300 15.395 2.646 2.741 1.289 C7 Y9Z 23 Y9Z O7 O7 O 0 1 N N N N N N 49.140 36.419 16.422 -3.946 -0.190 -2.898 O7 Y9Z 24 Y9Z C8 C8 C 0 1 N N R N N N 44.635 31.489 16.301 1.478 1.761 1.042 C8 Y9Z 25 Y9Z O8 O8 O 0 1 N N N N N N 50.508 34.689 15.224 -5.284 1.530 -1.624 O8 Y9Z 26 Y9Z C9 C9 C 0 1 N N N N N N 45.892 32.342 16.423 0.330 2.470 0.322 C9 Y9Z 27 Y9Z O9 O9 O 0 1 N N N N N N 48.144 33.437 13.423 -1.896 2.480 -1.872 O9 Y9Z 28 Y9Z C10 C10 C 0 1 N N N N N N 51.247 33.733 17.724 -6.520 -1.310 -1.202 C10 Y9Z 29 Y9Z O10 O10 O 0 1 N N N N N N 48.769 31.786 15.250 -2.875 3.166 0.351 O10 Y9Z 30 Y9Z C11 C11 C 0 1 N N N N N N 52.453 34.639 17.537 -7.042 -2.403 -0.267 C11 Y9Z 31 Y9Z O11 O11 O 0 1 N N N N N N 43.560 32.251 15.719 2.036 0.726 0.203 O11 Y9Z 32 Y9Z C12 C12 C 0 1 N N N N N N 52.922 35.831 19.679 -7.807 -2.606 2.038 C12 Y9Z 33 Y9Z C13 C13 C 0 1 N N N N N N 53.132 35.472 21.147 -8.106 -2.011 3.389 C13 Y9Z 34 Y9Z H1 H1 H 0 1 N N N N N N 38.767 34.471 11.356 8.279 -3.122 -0.217 H1 Y9Z 35 Y9Z H2 H2 H 0 1 N N N N N N 38.135 31.761 13.455 8.405 -3.069 2.118 H2 Y9Z 36 Y9Z H3 H3 H 0 1 N N N N N N 37.474 32.877 12.307 7.282 -2.192 3.009 H3 Y9Z 37 Y9Z H4 H4 H 0 1 N N N N N N 44.486 29.114 13.002 5.058 2.679 2.544 H4 Y9Z 38 Y9Z H5 H5 H 0 1 N N N N N N 44.559 28.938 16.721 3.345 3.822 2.852 H5 Y9Z 39 Y9Z H6 H6 H 0 1 N N N N N N 44.882 33.543 13.265 3.223 0.422 -2.134 H6 Y9Z 40 Y9Z H7 H7 H 0 1 N N N N N N 42.271 31.026 14.645 3.299 -0.141 1.625 H7 Y9Z 41 Y9Z H8 H8 H 0 1 N N N N N N 53.814 34.134 19.073 -7.185 -0.879 1.204 H8 Y9Z 42 Y9Z H9 H9 H 0 1 N N N N N N 45.053 31.319 13.512 4.509 2.269 0.255 H9 Y9Z 43 Y9Z H10 H10 H 0 1 N N N N N N 45.989 30.104 15.306 2.618 3.560 0.570 H10 Y9Z 44 Y9Z H11 H11 H 0 1 N N N N N N 49.673 36.935 15.828 -3.380 -0.974 -2.863 H11 Y9Z 45 Y9Z H12 H12 H 0 1 N N N N N N 44.348 31.125 17.299 1.130 1.340 1.986 H12 Y9Z 46 Y9Z H13 H13 H 0 1 N N N N N N 46.656 31.805 17.004 0.657 2.773 -0.673 H13 Y9Z 47 Y9Z H14 H14 H 0 1 N N N N N N 45.654 33.293 16.922 0.034 3.352 0.890 H14 Y9Z 48 Y9Z H15 H15 H 0 1 N N N N N N 51.281 32.952 16.950 -7.238 -0.490 -1.237 H15 Y9Z 49 Y9Z H16 H16 H 0 1 N N N N N N 51.319 33.267 18.718 -6.388 -1.720 -2.203 H16 Y9Z 50 Y9Z H17 H17 H 0 1 N N N N N N 49.343 31.572 14.524 -3.083 2.919 1.263 H17 Y9Z 51 Y9Z H18 H18 H 0 1 N N N N N N 53.146 34.182 16.816 -6.286 -3.182 -0.161 H18 Y9Z 52 Y9Z H19 H19 H 0 1 N N N N N N 52.121 35.617 17.157 -7.951 -2.834 -0.684 H19 Y9Z 53 Y9Z H20 H20 H 0 1 N N N N N N 52.833 36.321 21.779 -7.880 -0.945 3.375 H20 Y9Z 54 Y9Z H21 H21 H 0 1 N N N N N N 52.521 34.593 21.401 -9.161 -2.155 3.624 H21 Y9Z 55 Y9Z H22 H22 H 0 1 N N N N N N 54.194 35.242 21.320 -7.495 -2.502 4.146 H22 Y9Z 56 # 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 Y9Z O C DOUB N N 1 Y9Z C N SING N N 2 Y9Z C C3 SING N N 3 Y9Z N C1 SING N N 4 Y9Z C3 N3 SING Y N 5 Y9Z C3 C2 DOUB Y N 6 Y9Z N3 C4 DOUB Y N 7 Y9Z C1 N1 SING N N 8 Y9Z C1 N2 DOUB N N 9 Y9Z C4 N4 SING Y N 10 Y9Z C2 N2 SING N N 11 Y9Z C2 N4 SING Y N 12 Y9Z O1 C6 SING N N 13 Y9Z O9 P DOUB N N 14 Y9Z N4 C5 SING N N 15 Y9Z C6 C5 SING N N 16 Y9Z C6 C7 SING N N 17 Y9Z C5 O11 SING N N 18 Y9Z P O3 SING N N 19 Y9Z P O10 SING N N 20 Y9Z P O4 SING N N 21 Y9Z O3 C9 SING N N 22 Y9Z O8 P1 DOUB N N 23 Y9Z C7 O2 SING N N 24 Y9Z C7 C8 SING N N 25 Y9Z O11 C8 SING N N 26 Y9Z O4 P1 SING N N 27 Y9Z P1 O7 SING N N 28 Y9Z P1 O5 SING N N 29 Y9Z C8 C9 SING N N 30 Y9Z C11 C10 SING N N 31 Y9Z C11 N5 SING N N 32 Y9Z O5 C10 SING N N 33 Y9Z N5 C12 SING N N 34 Y9Z O6 C12 DOUB N N 35 Y9Z C12 C13 SING N N 36 Y9Z N H1 SING N N 37 Y9Z N1 H2 SING N N 38 Y9Z N1 H3 SING N N 39 Y9Z O1 H4 SING N N 40 Y9Z O2 H5 SING N N 41 Y9Z C4 H6 SING N N 42 Y9Z C5 H7 SING N N 43 Y9Z N5 H8 SING N N 44 Y9Z C6 H9 SING N N 45 Y9Z C7 H10 SING N N 46 Y9Z O7 H11 SING N N 47 Y9Z C8 H12 SING N N 48 Y9Z C9 H13 SING N N 49 Y9Z C9 H14 SING N N 50 Y9Z C10 H15 SING N N 51 Y9Z C10 H16 SING N N 52 Y9Z O10 H17 SING N N 53 Y9Z C11 H18 SING N N 54 Y9Z C11 H19 SING N N 55 Y9Z C13 H20 SING N N 56 Y9Z C13 H21 SING N N 57 Y9Z C13 H22 SING N N 58 # 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 Y9Z SMILES ACDLabs 12.01 "O=P(OCCNC(=O)C)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O" Y9Z InChI InChI 1.03 "InChI=1S/C14H22N6O12P2/c1-6(21)16-2-3-29-33(25,26)32-34(27,28)30-4-7-9(22)10(23)13(31-7)20-5-17-8-11(20)18-14(15)19-12(8)24/h5,7,9-10,13,22-23H,2-4H2,1H3,(H,16,21)(H,25,26)(H,27,28)(H3,15,18,19,24)/t7-,9-,10-,13-/m1/s1" Y9Z InChIKey InChI 1.03 TYLRZOMDDNITEE-QYVSTXNMSA-N Y9Z SMILES_CANONICAL CACTVS 3.385 "CC(=O)NCCO[P](O)(=O)O[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3C(=O)NC(=Nc23)N" Y9Z SMILES CACTVS 3.385 "CC(=O)NCCO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3C(=O)NC(=Nc23)N" Y9Z SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "CC(=O)NCCOP(=O)(O)OP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2N=C(NC3=O)N)O)O" Y9Z SMILES "OpenEye OEToolkits" 1.7.6 "CC(=O)NCCOP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2N=C(NC3=O)N)O)O" # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version _pdbx_chem_comp_identifier.identifier Y9Z "SYSTEMATIC NAME" ACDLabs 12.01 "5'-O-[(S)-{[(S)-[2-(acetylamino)ethoxy](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]guanosine" Y9Z "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[2-acetamidoethoxy(oxidanyl)phosphoryl] [(2R,3S,4R,5R)-5-(2-azanyl-6-oxidanylidene-1H-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen 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 Y9Z "Create component" 2013-12-27 RCSB Y9Z "Other modification" 2014-01-21 RCSB Y9Z "Initial release" 2014-06-04 RCSB Y9Z "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id Y9Z _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 C13 _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 ? #