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 
# 
