data_XNY # _chem_comp.id XNY _chem_comp.name "[(2~{R},3~{S},4~{R},5~{R})-5-(4-azanyl-3~{H}-imidazo[4,5-c]pyridin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate" _chem_comp.type "RNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C11 H15 N4 O7 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2020-12-22 _chem_comp.pdbx_modified_date 2021-04-30 _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 346.233 _chem_comp.one_letter_code ? _chem_comp.three_letter_code XNY _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 7L3R _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 XNY C2 C1 C 0 1 Y N N -14.473 -0.316 -4.432 5.234 -0.559 -1.259 C2 XNY 1 XNY C5 C2 C 0 1 Y N N -15.442 -0.178 -1.897 3.792 1.180 0.277 C5 XNY 2 XNY C3 C3 C 0 1 Y N N -15.615 0.464 -4.269 3.896 -0.788 -1.105 C3 XNY 3 XNY C8 C4 C 0 1 Y N N -17.225 0.902 -1.098 1.696 1.279 0.835 C8 XNY 4 XNY N7 N1 N 0 1 Y N N -16.193 0.094 -0.743 2.850 1.866 0.970 N7 XNY 5 XNY "C1'" C5 C 0 1 N N R -18.110 1.989 -3.190 0.751 -0.744 -0.341 "C1'" XNY 6 XNY "C2'" C6 C 0 1 N N R -19.082 1.104 -3.963 0.661 -1.915 0.663 "C2'" XNY 7 XNY "C3'" C7 C 0 1 N N S -20.197 0.976 -2.947 -0.855 -2.189 0.785 "C3'" XNY 8 XNY C4 C8 C 0 1 Y N N -16.076 0.501 -2.968 3.144 0.088 -0.326 C4 XNY 9 XNY "C4'" C9 C 0 1 N N R -20.264 2.388 -2.404 -1.501 -1.152 -0.159 "C4'" XNY 10 XNY "C5'" C10 C 0 1 N N N -20.968 2.568 -1.092 -2.809 -0.629 0.438 "C5'" XNY 11 XNY C6 C11 C 0 1 Y N N -14.286 -0.918 -2.145 5.170 1.341 0.066 C6 XNY 12 XNY N1 N2 N 0 1 Y N N -13.850 -0.967 -3.431 5.829 0.475 -0.685 N1 XNY 13 XNY N6 N3 N 0 1 N N N -13.638 -1.603 -1.148 5.842 2.409 0.647 N6 XNY 14 XNY N9 N4 N 0 1 Y N N -17.158 1.169 -2.441 1.823 0.177 0.044 N9 XNY 15 XNY "O2'" O1 O 0 1 N N N -19.533 1.804 -5.110 1.338 -3.065 0.154 "O2'" XNY 16 XNY "O3'" O2 O 0 1 N N N -21.419 0.546 -3.507 -1.160 -3.517 0.355 "O3'" XNY 17 XNY "O4'" O3 O 0 1 N N N -18.869 2.760 -2.287 -0.532 -0.086 -0.255 "O4'" XNY 18 XNY "O5'" O4 O 0 1 N N N -20.377 1.768 -0.088 -3.449 0.238 -0.500 "O5'" XNY 19 XNY OP1 O5 O 0 1 N N N -22.143 2.339 1.571 -5.867 -0.042 0.166 OP1 XNY 20 XNY OP2 O6 O 0 1 N N N -20.051 0.998 2.251 -4.668 2.012 1.010 OP2 XNY 21 XNY P P1 P 0 1 N N N -20.688 2.062 1.433 -4.852 0.970 -0.203 P XNY 22 XNY H2 H1 H 0 1 N N N -14.060 -0.405 -5.426 5.820 -1.239 -1.859 H2 XNY 23 XNY H3 H2 H 0 1 N N N -16.094 0.989 -5.082 3.428 -1.636 -1.582 H3 XNY 24 XNY H8 H3 H 0 1 N N N -17.982 1.277 -0.425 0.774 1.617 1.283 H8 XNY 25 XNY "H1'" H5 H 0 1 N N N -17.572 2.636 -3.898 0.918 -1.120 -1.350 "H1'" XNY 26 XNY "H2'" H6 H 0 1 N N N -18.635 0.127 -4.200 1.075 -1.623 1.628 "H2'" XNY 27 XNY "H3'" H7 H 0 1 N N N -19.878 0.295 -2.144 -1.190 -2.033 1.811 "H3'" XNY 28 XNY "H4'" H8 H 0 1 N N N -20.750 3.028 -3.155 -1.680 -1.592 -1.140 "H4'" XNY 29 XNY "H5'" H9 H 0 1 N N N -20.907 3.625 -0.793 -3.467 -1.469 0.663 "H5'" XNY 30 XNY "H5''" H10 H 0 0 N N N -22.023 2.280 -1.207 -2.596 -0.080 1.355 "H5''" XNY 31 XNY H61 H11 H 0 1 N N N -12.857 -2.094 -1.534 5.358 3.044 1.198 H61 XNY 32 XNY H62 H12 H 0 1 N N N -13.316 -0.958 -0.455 6.794 2.520 0.501 H62 XNY 33 XNY "HO2'" H13 H 0 0 N N N -20.139 1.258 -5.597 1.313 -3.830 0.744 "HO2'" XNY 34 XNY "HO3'" H14 H 0 0 N Y N -22.077 0.485 -2.824 -0.730 -4.208 0.877 "HO3'" XNY 35 XNY HOP2 H16 H 0 0 N N N -20.705 0.592 2.808 -4.016 2.705 0.837 HOP2 XNY 36 XNY OP3 OP3 O 0 1 N Y N -19.979 3.471 1.710 -5.335 1.759 -1.520 OP3 XNY 37 XNY HOP3 H15 H 0 0 N Y N -20.640 4.129 1.891 -6.176 2.224 -1.414 HOP3 XNY 38 # # 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 XNY "O2'" "C2'" SING N N 1 XNY C2 C3 DOUB Y N 2 XNY C2 N1 SING Y N 3 XNY C3 C4 SING Y N 4 XNY "C2'" "C1'" SING N N 5 XNY "C2'" "C3'" SING N N 6 XNY "O3'" "C3'" SING N N 7 XNY N1 C6 DOUB Y N 8 XNY "C1'" N9 SING N N 9 XNY "C1'" "O4'" SING N N 10 XNY C4 N9 SING Y N 11 XNY C4 C5 DOUB Y N 12 XNY "C3'" "C4'" SING N N 13 XNY N9 C8 SING Y N 14 XNY "C4'" "O4'" SING N N 15 XNY "C4'" "C5'" SING N N 16 XNY C6 C5 SING Y N 17 XNY C6 N6 SING N N 18 XNY C5 N7 SING Y N 19 XNY C8 N7 DOUB Y N 20 XNY "C5'" "O5'" SING N N 21 XNY "O5'" P SING N N 22 XNY P OP1 DOUB N N 23 XNY P OP2 SING N N 24 XNY C2 H2 SING N N 25 XNY C3 H3 SING N N 26 XNY C8 H8 SING N N 27 XNY "C1'" "H1'" SING N N 28 XNY "C2'" "H2'" SING N N 29 XNY "C3'" "H3'" SING N N 30 XNY "C4'" "H4'" SING N N 31 XNY "C5'" "H5'" SING N N 32 XNY "C5'" "H5''" SING N N 33 XNY N6 H61 SING N N 34 XNY N6 H62 SING N N 35 XNY "O2'" "HO2'" SING N N 36 XNY "O3'" "HO3'" SING N N 37 XNY OP2 HOP2 SING N N 38 XNY P OP3 SING N N 39 XNY OP3 HOP3 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 XNY SMILES ACDLabs 12.01 "c3cc2c(ncn2C1OC(C(C1O)O)COP(=O)(O)O)c(N)n3" XNY InChI InChI 1.03 "InChI=1S/C11H15N4O7P/c12-10-7-5(1-2-13-10)15(4-14-7)11-9(17)8(16)6(22-11)3-21-23(18,19)20/h1-2,4,6,8-9,11,16-17H,3H2,(H2,12,13)(H2,18,19,20)/t6-,8-,9-,11-/m1/s1" XNY InChIKey InChI 1.03 YZVSCCUSJPOQJU-PNHWDRBUSA-N XNY SMILES_CANONICAL CACTVS 3.385 "Nc1nccc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O" XNY SMILES CACTVS 3.385 "Nc1nccc2n(cnc12)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O" XNY SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1cnc(c2c1n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N" XNY SMILES "OpenEye OEToolkits" 2.0.7 "c1cnc(c2c1n(cn2)C3C(C(C(O3)COP(=O)(O)O)O)O)N" # # 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 XNY "SYSTEMATIC NAME" ACDLabs 12.01 "1-(5-O-phosphono-beta-D-ribofuranosyl)-1H-imidazo[4,5-c]pyridin-4-amine" XNY "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[(2~{R},3~{S},4~{R},5~{R})-5-(4-azanylimidazo[4,5-c]pyridin-1-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 XNY "Create component" 2020-12-22 RCSB XNY "Initial release" 2021-05-05 RCSB ##