data_O2Z # _chem_comp.id O2Z _chem_comp.name "[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-diazanyl-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxyphosphinic acid" _chem_comp.type "RNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H16 N7 O7 P" _chem_comp.mon_nstd_parent_comp_id A _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2020-01-21 _chem_comp.pdbx_modified_date 2020-02-14 _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 377.251 _chem_comp.one_letter_code A _chem_comp.three_letter_code O2Z _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag Y _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 6XUR _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBE # # 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 O2Z P P1 P 0 1 N N N -14.493 -5.007 7.246 5.259 1.116 0.179 P O2Z 1 O2Z OP1 O1 O 0 1 N N N -14.209 -5.543 5.919 6.496 0.112 -0.054 OP1 O2Z 2 O2Z OP2 O2 O 0 1 N N N -13.590 -4.997 8.379 5.031 1.912 -1.048 OP2 O2Z 3 O2Z "O5'" O3 O 0 1 N N N -15.269 -3.638 7.206 3.936 0.266 0.521 "O5'" O2Z 4 O2Z "C5'" C1 C 0 1 N N N -16.288 -3.410 6.260 3.320 -0.625 -0.411 "C5'" O2Z 5 O2Z "C4'" C2 C 0 1 N N R -16.804 -2.007 6.387 2.090 -1.267 0.233 "C4'" O2Z 6 O2Z "O4'" O4 O 0 1 N N N -17.374 -1.788 7.695 1.085 -0.267 0.471 "O4'" O2Z 7 O2Z "C3'" C3 C 0 1 N N S -15.783 -0.895 6.245 1.481 -2.310 -0.724 "C3'" O2Z 8 O2Z "O3'" O5 O 0 1 N N N -15.446 -0.732 4.885 1.482 -3.605 -0.120 "O3'" O2Z 9 O2Z "C2'" C4 C 0 1 N N R -16.528 0.269 6.875 0.031 -1.817 -0.948 "C2'" O2Z 10 O2Z "C1'" C5 C 0 1 N N R -17.209 -0.434 8.053 -0.197 -0.905 0.283 "C1'" O2Z 11 O2Z N9 N1 N 0 1 Y N N -16.390 -0.389 9.272 -1.232 0.092 0.003 N9 O2Z 12 O2Z C8 C6 C 0 1 Y N N -15.707 -1.501 9.818 -1.034 1.339 -0.515 C8 O2Z 13 O2Z N7 N2 N 0 1 Y N N -15.090 -1.043 10.962 -2.173 1.957 -0.634 N7 O2Z 14 O2Z C5 C7 C 0 1 Y N N -15.502 0.312 11.003 -3.172 1.149 -0.202 C5 O2Z 15 O2Z C6 C8 C 0 1 Y N N -15.149 1.176 12.043 -4.568 1.276 -0.097 C6 O2Z 16 O2Z N6 N3 N 0 1 N N N -14.376 0.936 13.202 -5.202 2.441 -0.491 N6 O2Z 17 O2Z N1 N4 N 0 1 Y N N -15.609 2.501 11.942 -5.265 0.254 0.386 N1 O2Z 18 O2Z C2 C9 C 0 1 Y N N -16.410 2.810 10.810 -4.664 -0.867 0.766 C2 O2Z 19 O2Z N3 N5 N 0 1 Y N N -16.690 1.822 9.941 -3.353 -1.029 0.684 N3 O2Z 20 O2Z C4 C10 C 0 1 Y N N -16.240 0.696 10.099 -2.581 -0.058 0.207 C4 O2Z 21 O2Z "O2'" O6 O 0 1 N N N -17.534 0.716 5.994 -0.886 -2.914 -0.947 "O2'" O2Z 22 O2Z N26 N6 N 0 1 N N N -16.871 4.138 10.691 -5.436 -1.903 1.264 N26 O2Z 23 O2Z N25 N7 N 0 1 N N N -13.838 -0.349 13.406 -6.560 2.549 -0.383 N25 O2Z 24 O2Z H2 H2 H 0 1 N N N -13.326 -5.894 5.901 6.703 -0.442 0.711 H2 O2Z 25 O2Z "H5'1" H3 H 0 0 N N N -17.112 -4.118 6.435 3.018 -0.070 -1.299 "H5'1" O2Z 26 O2Z "H5'2" H4 H 0 0 N N N -15.885 -3.559 5.248 4.030 -1.403 -0.693 "H5'2" O2Z 27 O2Z "H4'" H5 H 0 1 N N N -17.583 -1.855 5.626 2.370 -1.743 1.173 "H4'" O2Z 28 O2Z "H3'" H6 H 0 1 N N N -14.894 -1.132 6.848 2.028 -2.327 -1.667 "H3'" O2Z 29 O2Z H3 H7 H 0 1 N N N -14.806 -0.035 4.798 1.110 -4.300 -0.679 H3 O2Z 30 O2Z "H2'" H8 H 0 1 N N N -15.845 1.063 7.211 -0.048 -1.248 -1.874 "H2'" O2Z 31 O2Z H4 H9 H 0 1 N N N -18.183 0.041 8.240 -0.461 -1.499 1.158 H4 O2Z 32 O2Z H5 H10 H 0 1 N N N -15.676 -2.504 9.420 -0.073 1.752 -0.786 H5 O2Z 33 O2Z H6 H11 H 0 1 N N N -13.608 1.576 13.180 -4.683 3.181 -0.843 H6 O2Z 34 O2Z H7 H12 H 0 1 N N N -18.000 1.444 6.388 -0.726 -3.561 -1.647 H7 O2Z 35 O2Z H8 H13 H 0 1 N N N -17.432 4.224 9.867 -6.399 -1.803 1.331 H8 O2Z 36 O2Z H9 H14 H 0 1 N N N -17.419 4.374 11.493 -5.015 -2.730 1.546 H9 O2Z 37 O2Z H10 H15 H 0 1 N N N -13.320 -0.362 14.262 -6.878 3.451 -0.706 H10 O2Z 38 O2Z H11 H16 H 0 1 N N N -14.580 -1.017 13.455 -7.023 1.803 -0.880 H11 O2Z 39 O2Z OP3 OP3 O 0 1 N Y N ? ? ? 5.594 2.105 1.405 OP3 O2Z 40 O2Z H1 H1 H 0 1 N N N ? ? ? 6.382 2.649 1.268 H1 O2Z 41 # # 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 O2Z "O3'" "C3'" SING N N 1 O2Z OP1 P SING N N 2 O2Z "O2'" "C2'" SING N N 3 O2Z "C3'" "C4'" SING N N 4 O2Z "C3'" "C2'" SING N N 5 O2Z "C5'" "C4'" SING N N 6 O2Z "C5'" "O5'" SING N N 7 O2Z "C4'" "O4'" SING N N 8 O2Z "C2'" "C1'" SING N N 9 O2Z "O5'" P SING N N 10 O2Z P OP2 DOUB N N 11 O2Z "O4'" "C1'" SING N N 12 O2Z "C1'" N9 SING N N 13 O2Z N9 C8 SING Y N 14 O2Z N9 C4 SING Y N 15 O2Z C8 N7 DOUB Y N 16 O2Z N3 C4 DOUB Y N 17 O2Z N3 C2 SING Y N 18 O2Z C4 C5 SING Y N 19 O2Z N26 C2 SING N N 20 O2Z C2 N1 DOUB Y N 21 O2Z N7 C5 SING Y N 22 O2Z C5 C6 DOUB Y N 23 O2Z N1 C6 SING Y N 24 O2Z C6 N6 SING N N 25 O2Z N6 N25 SING N N 26 O2Z OP1 H2 SING N N 27 O2Z "C5'" "H5'1" SING N N 28 O2Z "C5'" "H5'2" SING N N 29 O2Z "C4'" "H4'" SING N N 30 O2Z "C3'" "H3'" SING N N 31 O2Z "O3'" H3 SING N N 32 O2Z "C2'" "H2'" SING N N 33 O2Z "C1'" H4 SING N N 34 O2Z C8 H5 SING N N 35 O2Z N6 H6 SING N N 36 O2Z "O2'" H7 SING N N 37 O2Z N26 H8 SING N N 38 O2Z N26 H9 SING N N 39 O2Z N25 H10 SING N N 40 O2Z N25 H11 SING N N 41 O2Z P OP3 SING N N 42 O2Z OP3 H1 SING N N 43 # # 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 O2Z InChI InChI 1.03 "InChI=1S/C10H16N7O7P/c11-10-14-7(16-12)4-8(15-10)17(2-13-4)9-6(19)5(18)3(24-9)1-23-25(20,21)22/h2-3,5-6,9,18-19H,1,12H2,(H2,20,21,22)(H3,11,14,15,16)/t3-,5-,6-,9-/m1/s1" O2Z InChIKey InChI 1.03 QHLBVSKMFFHOCN-UUOKFMHZSA-N O2Z SMILES_CANONICAL CACTVS 3.385 "NNc1nc(N)nc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O" O2Z SMILES CACTVS 3.385 "NNc1nc(N)nc2n(cnc12)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O" O2Z SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1nc2c(nc(nc2n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N)NN" O2Z SMILES "OpenEye OEToolkits" 2.0.7 "c1nc2c(nc(nc2n1C3C(C(C(O3)COP(=O)(O)O)O)O)N)NN" # _pdbx_chem_comp_identifier.comp_id O2Z _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 "[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-diazanyl-purin-9-yl)-3,4-bis(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 O2Z "Create component" 2020-01-21 PDBE O2Z "Initial release" 2020-02-19 RCSB ##