data_NYZ # _chem_comp.id NYZ _chem_comp.name "[[(2~{R},3~{S},4~{R},5~{R})-5-(6-azanyl-2-oxidanylidene-3~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]methylphosphonic acid" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C11 H17 N5 O10 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2020-01-13 _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 441.228 _chem_comp.one_letter_code ? _chem_comp.three_letter_code NYZ _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 6TW0 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site EBI # # 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 NYZ C8 C1 C 0 1 Y N N -14.509 22.053 -33.875 2.314 -1.416 -0.648 C8 NYZ 1 NYZ C5 C2 C 0 1 Y N N -13.884 23.479 -35.347 4.430 -1.755 -0.336 C5 NYZ 2 NYZ C6 C3 C 0 1 N N N -13.337 24.554 -36.105 5.765 -2.219 -0.254 C6 NYZ 3 NYZ PB P1 P 0 1 N N N -17.369 20.174 -28.884 -6.154 -1.257 0.378 PB NYZ 4 NYZ O1B O1 O 0 1 N N N -16.065 20.723 -29.362 -6.042 -1.924 -0.939 O1B NYZ 5 NYZ O2B O2 O 0 1 N N N -18.570 21.058 -29.278 -7.076 0.055 0.238 O2B NYZ 6 NYZ O3B O3 O 0 1 N N N -17.440 19.993 -27.360 -6.819 -2.270 1.437 O3B NYZ 7 NYZ PA P2 P 0 1 N N N -19.002 18.304 -30.623 -3.741 0.373 -0.243 PA NYZ 8 NYZ O1A O4 O 0 1 N N N -20.390 18.851 -30.354 -4.664 1.685 -0.382 O1A NYZ 9 NYZ O2A O5 O 0 1 N N N -19.100 16.757 -30.809 -3.629 -0.294 -1.559 O2A NYZ 10 NYZ C3A C4 C 0 1 N N N -17.676 18.498 -29.436 -4.494 -0.774 0.957 C3A NYZ 11 NYZ "O5'" O6 O 0 1 N N N -18.365 18.955 -31.907 -2.276 0.799 0.269 "O5'" NYZ 12 NYZ "C5'" C5 C 0 1 N N N -17.028 18.634 -32.352 -1.387 1.610 -0.502 "C5'" NYZ 13 NYZ "C4'" C6 C 0 1 N N R -16.844 18.892 -33.827 -0.086 1.823 0.275 "C4'" NYZ 14 NYZ "O4'" O7 O 0 1 N N N -16.792 20.311 -34.075 0.616 0.575 0.406 "O4'" NYZ 15 NYZ "C3'" C7 C 0 1 N N S -15.534 18.366 -34.392 0.832 2.791 -0.495 "C3'" NYZ 16 NYZ "O3'" O8 O 0 1 N N N -15.609 16.972 -34.673 1.106 3.953 0.290 "O3'" NYZ 17 NYZ "C2'" C8 C 0 1 N N R -15.339 19.237 -35.638 2.127 1.976 -0.734 "C2'" NYZ 18 NYZ "O2'" O9 O 0 1 N N N -15.954 18.693 -36.801 3.286 2.789 -0.537 "O2'" NYZ 19 NYZ "C1'" C9 C 0 1 N N R -16.043 20.549 -35.255 2.026 0.879 0.362 "C1'" NYZ 20 NYZ N9 N1 N 0 1 Y N N -15.127 21.688 -35.034 2.799 -0.305 -0.022 N9 NYZ 21 NYZ N7 N2 N 0 1 Y N N -13.741 23.113 -34.016 3.278 -2.271 -0.829 N7 NYZ 22 NYZ N6 N3 N 0 1 N N N -12.500 25.450 -35.569 6.102 -3.455 -0.751 N6 NYZ 23 NYZ N1 N4 N 0 1 N N N -13.627 24.684 -37.411 6.688 -1.447 0.306 N1 NYZ 24 NYZ C2 C10 C 0 1 N N N -14.482 23.810 -38.023 6.387 -0.246 0.794 C2 NYZ 25 NYZ N3 N5 N 0 1 N N N -15.043 22.787 -37.300 5.133 0.244 0.748 N3 NYZ 26 NYZ C4 C11 C 0 1 Y N N -14.737 22.598 -35.979 4.130 -0.498 0.182 C4 NYZ 27 NYZ O O10 O 0 1 N N N -14.779 23.918 -39.220 7.269 0.427 1.300 O NYZ 28 NYZ H8 H1 H 0 1 N N N -14.636 21.528 -32.940 1.286 -1.565 -0.944 H8 NYZ 29 NYZ H1 H2 H 0 1 N N N -18.262 21.813 -29.766 -7.194 0.543 1.064 H1 NYZ 30 NYZ H2 H3 H 0 1 N N N -16.619 20.269 -26.969 -7.706 -2.569 1.193 H2 NYZ 31 NYZ H4 H4 H 0 1 N N N -21.018 18.138 -30.356 -4.781 2.173 0.444 H4 NYZ 32 NYZ H3A2 H5 H 0 0 N N N -17.921 17.890 -28.552 -4.577 -0.283 1.927 H3A2 NYZ 33 NYZ H3A1 H6 H 0 0 N N N -16.752 18.119 -29.896 -3.870 -1.663 1.052 H3A1 NYZ 34 NYZ "H5'1" H7 H 0 0 N N N -16.833 17.570 -32.151 -1.168 1.111 -1.446 "H5'1" NYZ 35 NYZ "H5'2" H8 H 0 0 N N N -16.310 19.251 -31.792 -1.854 2.574 -0.700 "H5'2" NYZ 36 NYZ "H4'" H9 H 0 1 N N N -17.681 18.441 -34.381 -0.308 2.229 1.263 "H4'" NYZ 37 NYZ "H3'" H10 H 0 1 N N N -14.723 18.573 -33.678 0.378 3.073 -1.445 "H3'" NYZ 38 NYZ "HO3'" H11 H 0 0 N N N -15.729 16.491 -33.863 1.681 4.596 -0.147 "HO3'" NYZ 39 NYZ "H2'" H12 H 0 1 N N N -14.267 19.423 -35.800 2.129 1.533 -1.730 "H2'" NYZ 40 NYZ "HO2'" H13 H 0 0 N N N -15.520 17.882 -37.039 3.392 3.488 -1.196 "HO2'" NYZ 41 NYZ "H1'" H14 H 0 1 N N N -16.730 20.810 -36.073 2.368 1.264 1.323 "H1'" NYZ 42 NYZ H61 H15 H 0 1 N N N -12.117 26.179 -36.137 5.424 -4.015 -1.160 H61 NYZ 43 NYZ H62 H16 H 0 1 N N N -12.257 25.391 -34.601 7.019 -3.768 -0.692 H62 NYZ 44 NYZ H3 H17 H 0 1 N N N -15.688 22.167 -37.747 4.941 1.123 1.112 H3 NYZ 45 # # 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 NYZ O C2 DOUB N N 1 NYZ C2 N1 SING N N 2 NYZ C2 N3 SING N N 3 NYZ N1 C6 DOUB N N 4 NYZ N3 C4 SING N N 5 NYZ "O2'" "C2'" SING N N 6 NYZ C6 N6 SING N N 7 NYZ C6 C5 SING N N 8 NYZ C4 C5 DOUB Y N 9 NYZ C4 N9 SING Y N 10 NYZ "C2'" "C1'" SING N N 11 NYZ "C2'" "C3'" SING N N 12 NYZ C5 N7 SING Y N 13 NYZ "C1'" N9 SING N N 14 NYZ "C1'" "O4'" SING N N 15 NYZ N9 C8 SING Y N 16 NYZ "O3'" "C3'" SING N N 17 NYZ "C3'" "C4'" SING N N 18 NYZ "O4'" "C4'" SING N N 19 NYZ N7 C8 DOUB Y N 20 NYZ "C4'" "C5'" SING N N 21 NYZ "C5'" "O5'" SING N N 22 NYZ "O5'" PA SING N N 23 NYZ O2A PA DOUB N N 24 NYZ PA O1A SING N N 25 NYZ PA C3A SING N N 26 NYZ C3A PB SING N N 27 NYZ O1B PB DOUB N N 28 NYZ O2B PB SING N N 29 NYZ PB O3B SING N N 30 NYZ C8 H8 SING N N 31 NYZ O2B H1 SING N N 32 NYZ O3B H2 SING N N 33 NYZ O1A H4 SING N N 34 NYZ C3A H3A2 SING N N 35 NYZ C3A H3A1 SING N N 36 NYZ "C5'" "H5'1" SING N N 37 NYZ "C5'" "H5'2" SING N N 38 NYZ "C4'" "H4'" SING N N 39 NYZ "C3'" "H3'" SING N N 40 NYZ "O3'" "HO3'" SING N N 41 NYZ "C2'" "H2'" SING N N 42 NYZ "O2'" "HO2'" SING N N 43 NYZ "C1'" "H1'" SING N N 44 NYZ N6 H61 SING N N 45 NYZ N6 H62 SING N N 46 NYZ N3 H3 SING N N 47 # # 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 NYZ InChI InChI 1.03 "InChI=1S/C11H17N5O10P2/c12-8-5-9(15-11(19)14-8)16(2-13-5)10-7(18)6(17)4(26-10)1-25-28(23,24)3-27(20,21)22/h2,4,6-7,10,17-18H,1,3H2,(H,23,24)(H2,20,21,22)(H3,12,14,15,19)/t4-,6-,7-,10-/m1/s1" NYZ InChIKey InChI 1.03 ZFKXMQLZXNYUBT-KQYNXXCUSA-N NYZ SMILES_CANONICAL CACTVS 3.385 "NC1=NC(=O)Nc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)C[P](O)(O)=O)[C@@H](O)[C@H]3O" NYZ SMILES CACTVS 3.385 "NC1=NC(=O)Nc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)C[P](O)(O)=O)[CH](O)[CH]3O" NYZ SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(CP(=O)(O)O)O)O)O)NC(=O)N=C2N" NYZ SMILES "OpenEye OEToolkits" 2.0.7 "c1nc2c(n1C3C(C(C(O3)COP(=O)(CP(=O)(O)O)O)O)O)NC(=O)N=C2N" # _pdbx_chem_comp_identifier.comp_id NYZ _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-(6-azanyl-2-oxidanylidene-3~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]methylphosphonic acid" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site NYZ "Create component" 2020-01-13 EBI NYZ "Initial release" 2020-02-19 RCSB ##