data_XG5 # _chem_comp.id XG5 _chem_comp.name "(2R,3R,4R,5S)-1-(2-{6-[2-(4-azido-2-nitroanilino)ethyl]pyrazin-2-yl}ethyl)-2-(hydroxymethyl)piperidine-3,4,5-triol" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C20 H26 N8 O6" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2022-11-15 _chem_comp.pdbx_modified_date 2023-02-17 _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 474.470 _chem_comp.one_letter_code ? _chem_comp.three_letter_code XG5 _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 8ER4 _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 XG5 N1 N1 N 0 1 N N N -36.383 -30.290 -68.865 -4.997 -0.139 0.217 N1 XG5 1 XG5 N3 N2 N 0 1 N N N -43.197 -30.560 -69.513 3.831 0.695 -0.876 N3 XG5 2 XG5 C4 C1 C 0 1 N N R -33.995 -30.765 -69.242 -7.370 -0.561 -0.219 C4 XG5 3 XG5 C5 C2 C 0 1 N N R -35.058 -30.003 -68.412 -6.191 0.384 -0.459 C5 XG5 4 XG5 C6 C3 C 0 1 N N N -34.769 -28.476 -68.475 -6.526 1.770 0.097 C6 XG5 5 XG5 C7 C4 C 0 1 N N N -37.301 -29.654 -68.274 -3.880 0.811 0.124 C7 XG5 6 XG5 C8 C5 C 0 1 N N N -37.377 -29.881 -66.731 -2.763 0.380 1.076 C8 XG5 7 XG5 C10 C6 C 0 1 Y N N -41.111 -29.404 -66.445 0.414 1.946 0.110 C10 XG5 8 XG5 C13 C7 C 0 1 Y N N -43.124 -32.005 -69.347 4.949 0.094 -0.376 C13 XG5 9 XG5 C15 C8 C 0 1 Y N N -44.069 -34.267 -69.615 7.205 -0.637 -0.744 C15 XG5 10 XG5 C17 C9 C 0 1 Y N N -41.941 -33.953 -68.551 6.035 -0.961 1.485 C17 XG5 11 XG5 C20 C10 C 0 1 Y N N -38.837 -28.546 -65.041 -1.632 2.514 1.735 C20 XG5 12 XG5 C1 C11 C 0 1 N N R -34.307 -32.197 -69.378 -7.023 -1.951 -0.760 C1 XG5 13 XG5 C11 C12 C 0 1 N N N -42.414 -29.862 -67.148 1.581 1.651 -0.798 C11 XG5 14 XG5 C12 C13 C 0 1 N N N -42.384 -29.618 -68.684 2.697 0.981 0.007 C12 XG5 15 XG5 C14 C14 C 0 1 Y N N -44.131 -32.830 -69.770 6.080 -0.048 -1.204 C14 XG5 16 XG5 C16 C15 C 0 1 Y N N -42.961 -34.801 -68.988 7.239 -1.134 0.647 C16 XG5 17 XG5 C18 C16 C 0 1 Y N N -42.025 -32.562 -68.726 4.946 -0.362 0.956 C18 XG5 18 XG5 C19 C17 C 0 1 Y N N -41.159 -28.543 -65.288 0.395 3.111 0.856 C19 XG5 19 XG5 C2 C18 C 0 1 N N S -35.617 -32.361 -69.944 -5.748 -2.452 -0.074 C2 XG5 20 XG5 C3 C19 C 0 1 N N N -36.617 -31.770 -68.927 -4.616 -1.452 -0.319 C3 XG5 21 XG5 C9 C20 C 0 1 Y N N -38.763 -29.451 -66.204 -1.618 1.355 0.981 C9 XG5 22 XG5 N2 N3 N 0 1 Y N N -39.879 -29.820 -66.864 -0.592 1.094 0.189 N2 XG5 23 XG5 N4 N4 N 1 1 N N N -45.308 -32.236 -70.418 6.034 0.454 -2.596 N4 XG5 24 XG5 N5 N5 N 0 1 N N N -42.783 -36.248 -68.769 8.307 -1.713 1.123 N5 XG5 25 XG5 N6 N6 N 1 1 N N N -41.475 -36.781 -68.465 8.319 -2.086 2.183 N6 XG5 26 XG5 N7 N7 N -1 1 N N N -41.217 -38.073 -69.001 8.330 -2.460 3.243 N7 XG5 27 XG5 N8 N8 N 0 1 Y N N -40.032 -28.139 -64.620 -0.627 3.369 1.652 N8 XG5 28 XG5 O1 O1 O 0 1 N N N -33.286 -32.826 -70.271 -8.099 -2.851 -0.488 O1 XG5 29 XG5 O2 O2 O 0 1 N N N -35.879 -33.764 -70.237 -5.386 -3.725 -0.614 O2 XG5 30 XG5 O3 O3 O 0 1 N N N -32.679 -30.640 -68.708 -8.527 -0.062 -0.894 O3 XG5 31 XG5 O4 O4 O 0 1 N N N -34.771 -27.919 -69.819 -6.879 1.656 1.477 O4 XG5 32 XG5 O5 O5 O -1 1 N N N -45.475 -30.809 -70.627 6.615 -0.228 -3.561 O5 XG5 33 XG5 O6 O6 O 0 1 N N N -46.256 -33.133 -70.815 5.412 1.583 -2.869 O6 XG5 34 XG5 H2 H2 H 0 1 N N N -42.951 -30.376 -70.465 3.786 0.932 -1.815 H2 XG5 35 XG5 H3 H3 H 0 1 N N N -34.002 -30.324 -70.250 -7.572 -0.626 0.850 H3 XG5 36 XG5 H4 H4 H 0 1 N N N -34.955 -30.320 -67.364 -5.998 0.460 -1.530 H4 XG5 37 XG5 H5 H5 H 0 1 N N N -33.780 -28.294 -68.029 -5.657 2.421 -0.003 H5 XG5 38 XG5 H6 H6 H 0 1 N N N -35.538 -27.956 -67.886 -7.363 2.192 -0.458 H6 XG5 39 XG5 H7 H7 H 0 1 N N N -37.141 -28.580 -68.453 -3.501 0.827 -0.898 H7 XG5 40 XG5 H8 H8 H 0 1 N N N -38.263 -29.960 -68.711 -4.227 1.807 0.398 H8 XG5 41 XG5 H9 H9 H 0 1 N N N -37.218 -30.947 -66.511 -3.143 0.364 2.098 H9 XG5 42 XG5 H10 H10 H 0 1 N N N -36.597 -29.284 -66.236 -2.416 -0.616 0.802 H10 XG5 43 XG5 H11 H11 H 0 1 N N N -44.864 -34.902 -69.978 8.067 -0.746 -1.386 H11 XG5 44 XG5 H12 H12 H 0 1 N N N -41.071 -34.375 -68.069 6.024 -1.313 2.506 H12 XG5 45 XG5 H13 H13 H 0 1 N N N -37.937 -28.220 -64.540 -2.468 2.725 2.386 H13 XG5 46 XG5 H14 H14 H 0 1 N N N -34.264 -32.676 -68.389 -6.859 -1.892 -1.836 H14 XG5 47 XG5 H15 H15 H 0 1 N N N -43.260 -29.305 -66.719 1.259 0.985 -1.598 H15 XG5 48 XG5 H16 H16 H 0 1 N N N -42.553 -30.938 -66.965 1.951 2.582 -1.227 H16 XG5 49 XG5 H17 H17 H 0 1 N N N -41.338 -29.694 -69.016 2.326 0.050 0.436 H17 XG5 50 XG5 H18 H18 H 0 1 N N N -42.755 -28.599 -68.870 3.018 1.648 0.807 H18 XG5 51 XG5 H19 H19 H 0 1 N N N -41.227 -31.926 -68.373 4.062 -0.232 1.562 H19 XG5 52 XG5 H20 H20 H 0 1 N N N -42.121 -28.203 -64.934 1.216 3.809 0.788 H20 XG5 53 XG5 H21 H21 H 0 1 N N N -35.691 -31.778 -70.874 -5.925 -2.547 0.997 H21 XG5 54 XG5 H22 H22 H 0 1 N N N -37.648 -31.973 -69.254 -4.431 -1.368 -1.390 H22 XG5 55 XG5 H23 H23 H 0 1 N N N -36.452 -32.217 -67.936 -3.711 -1.799 0.180 H23 XG5 56 XG5 H28 H28 H 0 1 N N N -32.422 -32.715 -69.892 -7.946 -3.752 -0.804 H28 XG5 57 XG5 H29 H29 H 0 1 N N N -36.748 -33.853 -70.610 -4.586 -4.103 -0.225 H29 XG5 58 XG5 H30 H30 H 0 1 N N N -32.461 -29.720 -68.614 -9.314 -0.612 -0.785 H30 XG5 59 XG5 H31 H31 H 0 1 N N N -34.588 -26.988 -69.777 -7.104 2.497 1.896 H31 XG5 60 # 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 XG5 O6 N4 DOUB N N 1 XG5 O5 N4 SING N N 2 XG5 N4 C14 SING N N 3 XG5 O1 C1 SING N N 4 XG5 O2 C2 SING N N 5 XG5 C2 C1 SING N N 6 XG5 C2 C3 SING N N 7 XG5 O4 C6 SING N N 8 XG5 C14 C15 DOUB Y N 9 XG5 C14 C13 SING Y N 10 XG5 C15 C16 SING Y N 11 XG5 N3 C13 SING N N 12 XG5 N3 C12 SING N N 13 XG5 C1 C4 SING N N 14 XG5 C13 C18 DOUB Y N 15 XG5 C4 O3 SING N N 16 XG5 C4 C5 SING N N 17 XG5 N7 N6 DOUB N N 18 XG5 C16 N5 SING N N 19 XG5 C16 C17 DOUB Y N 20 XG5 C3 N1 SING N N 21 XG5 N1 C5 SING N N 22 XG5 N1 C7 SING N N 23 XG5 N5 N6 DOUB N N 24 XG5 C18 C17 SING Y N 25 XG5 C12 C11 SING N N 26 XG5 C6 C5 SING N N 27 XG5 C7 C8 SING N N 28 XG5 C11 C10 SING N N 29 XG5 N2 C10 DOUB Y N 30 XG5 N2 C9 SING Y N 31 XG5 C8 C9 SING N N 32 XG5 C10 C19 SING Y N 33 XG5 C9 C20 DOUB Y N 34 XG5 C19 N8 DOUB Y N 35 XG5 C20 N8 SING Y N 36 XG5 N3 H2 SING N N 37 XG5 C4 H3 SING N N 38 XG5 C5 H4 SING N N 39 XG5 C6 H5 SING N N 40 XG5 C6 H6 SING N N 41 XG5 C7 H7 SING N N 42 XG5 C7 H8 SING N N 43 XG5 C8 H9 SING N N 44 XG5 C8 H10 SING N N 45 XG5 C15 H11 SING N N 46 XG5 C17 H12 SING N N 47 XG5 C20 H13 SING N N 48 XG5 C1 H14 SING N N 49 XG5 C11 H15 SING N N 50 XG5 C11 H16 SING N N 51 XG5 C12 H17 SING N N 52 XG5 C12 H18 SING N N 53 XG5 C18 H19 SING N N 54 XG5 C19 H20 SING N N 55 XG5 C2 H21 SING N N 56 XG5 C3 H22 SING N N 57 XG5 C3 H23 SING N N 58 XG5 O1 H28 SING N N 59 XG5 O2 H29 SING N N 60 XG5 O3 H30 SING N N 61 XG5 O4 H31 SING N N 62 # 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 XG5 SMILES ACDLabs 12.01 "[O-][N+](=O)c1cc(\N=[N+]=[N-])ccc1NCCc1cncc(CCN2CC(O)C(O)C(O)C2CO)n1" XG5 InChI InChI 1.06 "InChI=1S/C20H26N8O6/c21-26-25-12-1-2-15(16(7-12)28(33)34)23-5-3-13-8-22-9-14(24-13)4-6-27-10-18(30)20(32)19(31)17(27)11-29/h1-2,7-9,17-20,23,29-32H,3-6,10-11H2/t17-,18+,19-,20-/m1/s1" XG5 InChIKey InChI 1.06 VRDSVTXDIGQKQB-IYWMVGAKSA-N XG5 SMILES_CANONICAL CACTVS 3.385 "OC[C@@H]1[C@@H](O)[C@H](O)[C@@H](O)CN1CCc2cncc(CCNc3ccc(cc3[N+]([O-])=O)N=[N+]=[N-])n2" XG5 SMILES CACTVS 3.385 "OC[CH]1[CH](O)[CH](O)[CH](O)CN1CCc2cncc(CCNc3ccc(cc3[N+]([O-])=O)N=[N+]=[N-])n2" XG5 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1cc(c(cc1N=[N+]=[N-])[N+](=O)[O-])NCCc2cncc(n2)CCN3C[C@@H]([C@H]([C@@H]([C@H]3CO)O)O)O" XG5 SMILES "OpenEye OEToolkits" 2.0.7 "c1cc(c(cc1N=[N+]=[N-])[N+](=O)[O-])NCCc2cncc(n2)CCN3CC(C(C(C3CO)O)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 XG5 "SYSTEMATIC NAME" ACDLabs 12.01 "(2R,3R,4R,5S)-1-(2-{6-[2-(4-azido-2-nitroanilino)ethyl]pyrazin-2-yl}ethyl)-2-(hydroxymethyl)piperidine-3,4,5-triol" XG5 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(2~{R},3~{R},4~{R},5~{S})-1-[2-[6-[2-[(4-azido-2-nitro-phenyl)amino]ethyl]pyrazin-2-yl]ethyl]-2-(hydroxymethyl)piperidine-3,4,5-triol" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site XG5 "Create component" 2022-11-15 RCSB XG5 "Initial release" 2023-02-22 RCSB #