data_XKO # _chem_comp.id XKO _chem_comp.name ;5'-O-[N-(3-Indolepropionic acid)sulfamoyl] N2-methyl-2-aminoethenoadenosine ; _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C24 H26 N8 O7 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "[(2~{R},3~{S},4~{R},5~{R})-5-[5-(methylamino)imidazo[2,1-f]purin-3-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-[3-(1~{H}-indol-3-yl)propanoyl]sulfamate" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2023-06-07 _chem_comp.pdbx_modified_date 2023-06-09 _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 570.578 _chem_comp.one_letter_code ? _chem_comp.three_letter_code XKO _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 8PAI _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 XKO "O5'" O1 O 0 1 N N N 5.908 5.162 7.007 -1.811 -3.694 -0.608 "O5'" XKO 1 XKO "C5'" C1 C 0 1 N N N 5.787 4.673 5.654 -0.978 -3.692 0.554 "C5'" XKO 2 XKO "C4'" C2 C 0 1 N N R 6.703 5.461 4.785 0.486 -3.549 0.131 "C4'" XKO 3 XKO "O4'" O2 O 0 1 N N N 6.506 4.930 3.465 0.703 -2.251 -0.447 "O4'" XKO 4 XKO "C3'" C3 C 0 1 N N S 6.436 6.977 4.740 1.401 -3.664 1.365 "C3'" XKO 5 XKO "O3'" O3 O 0 1 N N N 7.518 7.695 5.337 2.300 -4.765 1.221 "O3'" XKO 6 XKO "C2'" C4 C 0 1 N N R 6.234 7.261 3.252 2.181 -2.327 1.385 "C2'" XKO 7 XKO "O2'" O4 O 0 1 N N N 6.889 8.432 2.787 3.552 -2.541 1.726 "O2'" XKO 8 XKO N9 N1 N 0 1 Y N N 6.086 5.736 1.275 2.186 -0.393 -0.173 N9 XKO 9 XKO C8 C5 C 0 1 Y N N 4.704 5.804 1.081 1.172 0.518 -0.176 C8 XKO 10 XKO N7 N2 N 0 1 Y N N 4.343 5.660 -0.184 1.663 1.722 -0.263 N7 XKO 11 XKO C5 C6 C 0 1 Y N N 5.544 5.512 -0.871 3.012 1.653 -0.321 C5 XKO 12 XKO C6 C7 C 0 1 Y N N 5.835 5.283 -2.234 4.087 2.639 -0.424 C6 XKO 13 XKO N6 N3 N 0 1 Y N N 5.074 5.173 -3.324 4.120 3.954 -0.497 N6 XKO 14 XKO N1 N4 N 0 1 Y N N 7.196 5.155 -2.549 5.381 2.174 -0.459 N1 XKO 15 XKO C2 C8 C 0 1 Y N N 8.212 5.241 -1.575 5.622 0.830 -0.398 C2 XKO 16 XKO N3 N5 N 0 1 Y N N 7.926 5.445 -0.301 4.657 -0.051 -0.306 N3 XKO 17 XKO C4 C9 C 0 1 Y N N 6.623 5.562 0.017 3.365 0.303 -0.259 C4 XKO 18 XKO C9 C10 C 0 1 Y N N 5.978 4.978 -4.358 5.393 4.360 -0.577 C9 XKO 19 XKO C10 C11 C 0 1 Y N N 7.256 4.967 -3.931 6.194 3.275 -0.556 C10 XKO 20 XKO N2 N6 N 0 1 N N N 9.495 5.111 -1.947 6.924 0.387 -0.435 N2 XKO 21 XKO S1 S1 S 0 1 N N N 4.738 4.772 8.004 -3.296 -3.832 -0.304 S1 XKO 22 XKO O2 O5 O 0 1 N N N 3.933 3.775 7.355 -3.945 -4.017 -1.554 O2 XKO 23 XKO O3 O6 O 0 1 N N N 5.324 4.476 9.250 -3.402 -4.754 0.772 O3 XKO 24 XKO N4 N7 N 0 1 N N N 3.744 6.138 8.005 -3.814 -2.371 0.280 N4 XKO 25 XKO C7 C12 C 0 1 N N N 3.937 7.447 7.780 -3.799 -1.283 -0.515 C7 XKO 26 XKO C11 C13 C 0 1 N N N 2.734 8.332 7.987 -4.271 0.045 0.016 C11 XKO 27 XKO C12 C14 C 0 1 N N N 2.896 9.069 9.311 -4.151 1.105 -1.081 C12 XKO 28 XKO C13 C15 C 0 1 Y N N 1.846 10.106 9.592 -4.623 2.434 -0.549 C13 XKO 29 XKO C14 C16 C 0 1 Y N N 1.552 11.275 8.789 -3.823 3.407 0.199 C14 XKO 30 XKO C15 C17 C 0 1 Y N N 0.530 11.987 9.462 -4.683 4.484 0.479 C15 XKO 31 XKO N16 N8 N 0 1 Y N N 0.235 11.296 10.611 -5.910 4.176 -0.064 N16 XKO 32 XKO C17 C18 C 0 1 Y N N 1.029 10.183 10.681 -5.854 2.954 -0.677 C17 XKO 33 XKO O24 O7 O 0 1 N N N 4.989 7.920 7.455 -3.406 -1.374 -1.659 O24 XKO 34 XKO C25 C19 C 0 1 Y N N 2.035 11.783 7.575 -2.497 3.443 0.634 C25 XKO 35 XKO C26 C20 C 0 1 Y N N 1.500 12.952 7.077 -2.041 4.526 1.331 C26 XKO 36 XKO C27 C21 C 0 1 Y N N 0.489 13.634 7.759 -2.885 5.592 1.609 C27 XKO 37 XKO C28 C22 C 0 1 Y N N -0.011 13.170 8.955 -4.197 5.577 1.189 C28 XKO 38 XKO C16 C23 C 0 1 N N R 6.775 5.983 2.564 2.043 -1.849 -0.087 C16 XKO 39 XKO C1 C24 C 0 1 N N N 10.597 5.246 -1.026 7.211 -1.048 -0.371 C1 XKO 40 XKO H1 H1 H 0 1 N N N 4.750 4.794 5.307 -1.253 -2.856 1.197 H1 XKO 41 XKO H2 H2 H 0 1 N N N 6.064 3.609 5.617 -1.110 -4.628 1.097 H2 XKO 42 XKO H3 H3 H 0 1 N N N 7.742 5.296 5.107 0.740 -4.324 -0.592 H3 XKO 43 XKO H4 H4 H 0 1 N N N 5.498 7.187 5.274 0.807 -3.774 2.272 H4 XKO 44 XKO H5 H5 H 0 1 N N N 7.580 7.467 6.257 2.900 -4.884 1.970 H5 XKO 45 XKO H6 H6 H 0 1 N N N 5.154 7.329 3.053 1.719 -1.616 2.070 H6 XKO 46 XKO H7 H7 H 0 1 N N N 6.532 9.192 3.230 3.684 -2.925 2.603 H7 XKO 47 XKO H8 H8 H 0 1 N N N 3.999 5.959 1.885 0.121 0.278 -0.115 H8 XKO 48 XKO H9 H9 H 0 1 N N N 5.689 4.849 -5.391 5.724 5.385 -0.648 H9 XKO 49 XKO H10 H10 H 0 1 N N N 8.143 4.839 -4.533 7.273 3.273 -0.605 H10 XKO 50 XKO H11 H11 H 0 1 N N N 9.576 4.196 -2.342 7.651 1.024 -0.503 H11 XKO 51 XKO H12 H12 H 0 1 N N N 2.793 5.921 8.224 -4.128 -2.299 1.195 H12 XKO 52 XKO H13 H13 H 0 1 N N N 2.662 9.059 7.164 -5.311 -0.037 0.330 H13 XKO 53 XKO H14 H14 H 0 1 N N N 1.822 7.718 8.014 -3.656 0.335 0.869 H14 XKO 54 XKO H15 H15 H 0 1 N N N 2.867 8.326 10.121 -3.111 1.188 -1.395 H15 XKO 55 XKO H16 H16 H 0 1 N N N 3.876 9.568 9.306 -4.766 0.816 -1.934 H16 XKO 56 XKO H17 H17 H 0 1 N N N -0.450 11.563 11.289 -6.696 4.742 -0.022 H17 XKO 57 XKO H18 H18 H 0 1 N N N 1.011 9.465 11.488 -6.678 2.477 -1.186 H18 XKO 58 XKO H19 H19 H 0 1 N N N 2.816 11.266 7.037 -1.834 2.617 0.421 H19 XKO 59 XKO H20 H20 H 0 1 N N N 1.869 13.348 6.142 -1.015 4.554 1.667 H20 XKO 60 XKO H21 H21 H 0 1 N N N 0.091 14.546 7.339 -2.510 6.441 2.161 H21 XKO 61 XKO H22 H22 H 0 1 N N N -0.791 13.700 9.480 -4.847 6.411 1.411 H22 XKO 62 XKO H23 H23 H 0 1 N N N 7.857 6.094 2.397 2.777 -2.344 -0.723 H23 XKO 63 XKO H24 H24 H 0 1 N N N 11.545 5.098 -1.564 6.820 -1.456 0.562 H24 XKO 64 XKO H25 H25 H 0 1 N N N 10.582 6.252 -0.581 6.738 -1.552 -1.214 H25 XKO 65 XKO H26 H26 H 0 1 N N N 10.505 4.492 -0.231 8.289 -1.205 -0.412 H26 XKO 66 # 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 XKO C9 C10 DOUB Y N 1 XKO C9 N6 SING Y N 2 XKO C10 N1 SING Y N 3 XKO N6 C6 DOUB Y N 4 XKO N1 C6 SING Y N 5 XKO N1 C2 SING Y N 6 XKO C6 C5 SING Y N 7 XKO N2 C2 SING N N 8 XKO N2 C1 SING N N 9 XKO C2 N3 DOUB Y N 10 XKO C5 N7 SING Y N 11 XKO C5 C4 DOUB Y N 12 XKO N3 C4 SING Y N 13 XKO N7 C8 DOUB Y N 14 XKO C4 N9 SING Y N 15 XKO C8 N9 SING Y N 16 XKO N9 C16 SING N N 17 XKO C16 "C2'" SING N N 18 XKO C16 "O4'" SING N N 19 XKO "O2'" "C2'" SING N N 20 XKO "C2'" "C3'" SING N N 21 XKO "O4'" "C4'" SING N N 22 XKO "C3'" "C4'" SING N N 23 XKO "C3'" "O3'" SING N N 24 XKO "C4'" "C5'" SING N N 25 XKO "C5'" "O5'" SING N N 26 XKO "O5'" S1 SING N N 27 XKO C26 C25 DOUB Y N 28 XKO C26 C27 SING Y N 29 XKO O2 S1 DOUB N N 30 XKO O24 C7 DOUB N N 31 XKO C25 C14 SING Y N 32 XKO C27 C28 DOUB Y N 33 XKO C7 C11 SING N N 34 XKO C7 N4 SING N N 35 XKO C11 C12 SING N N 36 XKO S1 N4 SING N N 37 XKO S1 O3 DOUB N N 38 XKO C14 C15 DOUB Y N 39 XKO C14 C13 SING Y N 40 XKO C28 C15 SING Y N 41 XKO C12 C13 SING N N 42 XKO C15 N16 SING Y N 43 XKO C13 C17 DOUB Y N 44 XKO N16 C17 SING Y N 45 XKO "C5'" H1 SING N N 46 XKO "C5'" H2 SING N N 47 XKO "C4'" H3 SING N N 48 XKO "C3'" H4 SING N N 49 XKO "O3'" H5 SING N N 50 XKO "C2'" H6 SING N N 51 XKO "O2'" H7 SING N N 52 XKO C8 H8 SING N N 53 XKO C9 H9 SING N N 54 XKO C10 H10 SING N N 55 XKO N2 H11 SING N N 56 XKO N4 H12 SING N N 57 XKO C11 H13 SING N N 58 XKO C11 H14 SING N N 59 XKO C12 H15 SING N N 60 XKO C12 H16 SING N N 61 XKO N16 H17 SING N N 62 XKO C17 H18 SING N N 63 XKO C25 H19 SING N N 64 XKO C26 H20 SING N N 65 XKO C27 H21 SING N N 66 XKO C28 H22 SING N N 67 XKO C16 H23 SING N N 68 XKO C1 H24 SING N N 69 XKO C1 H25 SING N N 70 XKO C1 H26 SING N N 71 # 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 XKO InChI InChI 1.06 "InChI=1S/C24H26N8O7S/c1-25-24-29-22-18(21-26-8-9-31(21)24)28-12-32(22)23-20(35)19(34)16(39-23)11-38-40(36,37)30-17(33)7-6-13-10-27-15-5-3-2-4-14(13)15/h2-5,8-10,12,16,19-20,23,27,34-35H,6-7,11H2,1H3,(H,25,29)(H,30,33)/t16-,19-,20-,23-/m1/s1" XKO InChIKey InChI 1.06 MCGJNWYQNXMIEN-UGTJMOTHSA-N XKO SMILES_CANONICAL CACTVS 3.385 "CNc1nc2n(cnc2c3nccn13)[C@@H]4O[C@H](CO[S](=O)(=O)NC(=O)CCc5c[nH]c6ccccc56)[C@@H](O)[C@H]4O" XKO SMILES CACTVS 3.385 "CNc1nc2n(cnc2c3nccn13)[CH]4O[CH](CO[S](=O)(=O)NC(=O)CCc5c[nH]c6ccccc56)[CH](O)[CH]4O" XKO SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CNc1nc2c(c3n1ccn3)ncn2[C@H]4[C@@H]([C@@H]([C@H](O4)COS(=O)(=O)NC(=O)CCc5c[nH]c6c5cccc6)O)O" XKO SMILES "OpenEye OEToolkits" 2.0.7 "CNc1nc2c(c3n1ccn3)ncn2C4C(C(C(O4)COS(=O)(=O)NC(=O)CCc5c[nH]c6c5cccc6)O)O" # _pdbx_chem_comp_identifier.comp_id XKO _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-[5-(methylamino)imidazo[2,1-f]purin-3-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-[3-(1~{H}-indol-3-yl)propanoyl]sulfamate" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site XKO "Create component" 2023-06-07 PDBE XKO "Initial release" 2023-06-14 RCSB # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id XKO _pdbx_chem_comp_synonyms.name "[(2~{R},3~{S},4~{R},5~{R})-5-[5-(methylamino)imidazo[2,1-f]purin-3-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-[3-(1~{H}-indol-3-yl)propanoyl]sulfamate" _pdbx_chem_comp_synonyms.provenance AUTHOR _pdbx_chem_comp_synonyms.type ? #