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      ? 
# 
