data_X8Y # _chem_comp.id X8Y _chem_comp.name "(1S,2S,3R,4S,5S)-5-({6-[(4-azido-2-nitrophenyl)amino]hexyl}amino)-1-(hydroxymethyl)cyclohexane-1,2,3,4-tetrol" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C19 H30 N6 O7" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2020-12-06 _chem_comp.pdbx_modified_date 2021-11-26 _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 454.478 _chem_comp.one_letter_code ? _chem_comp.three_letter_code X8Y _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 7KRY _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 X8Y N1 N1 N 0 1 N N N -7.286 34.921 17.192 4.327 -0.220 -0.827 N1 X8Y 1 X8Y N3 N2 N 1 1 N N N -15.548 40.049 14.697 -6.566 -2.416 -0.053 N3 X8Y 2 X8Y C4 C1 C 0 1 N N N -7.454 34.325 15.318 6.646 -0.228 -1.615 C4 X8Y 3 X8Y C5 C2 C 0 1 N N S -7.465 33.776 16.427 5.510 -1.067 -1.025 C5 X8Y 4 X8Y C6 C3 C 0 1 N N N -8.259 35.828 16.607 3.096 -1.023 -0.842 C6 X8Y 5 X8Y C7 C4 C 0 1 N N N -7.755 37.294 16.377 1.888 -0.108 -0.633 C7 X8Y 6 X8Y C8 C5 C 0 1 N N N -9.068 38.100 16.136 0.607 -0.944 -0.649 C8 X8Y 7 X8Y C10 C6 C 0 1 N N N -10.311 40.268 15.929 -1.883 -0.865 -0.456 C10 X8Y 8 X8Y C13 C7 C 0 1 Y N N -15.358 40.069 16.167 -6.685 -0.942 0.016 C13 X8Y 9 X8Y C15 C8 C 0 1 Y N N -16.350 40.162 18.385 -8.009 1.093 0.245 C15 X8Y 10 X8Y C17 C9 C 0 1 Y N N -13.938 40.030 18.128 -5.592 1.260 -0.035 C17 X8Y 11 X8Y C1 C10 C 0 1 N N S -5.753 33.450 13.779 7.430 0.330 0.691 C1 X8Y 12 X8Y C11 C11 C 0 1 N N N -11.562 40.058 16.783 -3.091 0.050 -0.248 C11 X8Y 13 X8Y C12 C12 C 0 1 Y N N -14.071 40.010 16.744 -5.530 -0.145 -0.095 C12 X8Y 14 X8Y C14 C13 C 0 1 Y N N -16.496 40.143 16.993 -7.903 -0.379 0.178 C14 X8Y 15 X8Y C16 C14 C 0 1 Y N N -15.072 40.104 18.949 -6.773 1.895 0.131 C16 X8Y 16 X8Y C18 C15 C 0 1 N N S -5.930 33.122 16.549 5.952 -1.649 0.319 C18 X8Y 17 X8Y C19 C16 C 0 1 N N R -5.119 32.722 15.146 6.295 -0.510 1.281 C19 X8Y 18 X8Y C2 C17 C 0 1 N N S -7.167 33.920 13.757 6.989 0.912 -0.653 C2 X8Y 19 X8Y C3 C18 C 0 1 N N N -8.055 33.699 12.786 8.124 1.752 -1.243 C3 X8Y 20 X8Y C9 C19 C 0 1 N N N -9.103 39.586 16.602 -0.602 -0.029 -0.441 C9 X8Y 21 X8Y N2 N3 N 0 1 N N N -12.823 39.944 15.965 -4.318 -0.750 -0.263 N2 X8Y 22 X8Y N4 N4 N 0 1 N N N -17.519 40.238 19.275 -9.168 1.672 0.406 N4 X8Y 23 X8Y N5 N5 N 1 1 N N N -18.418 41.349 19.196 -9.234 2.793 0.460 N5 X8Y 24 X8Y N6 N6 N -1 1 N N N -19.475 41.201 20.165 -9.300 3.913 0.514 N6 X8Y 25 X8Y O1 O1 O 0 1 N N N -4.910 34.224 13.729 7.751 1.394 1.589 O1 X8Y 26 X8Y O2 O2 O 0 1 N N N -8.273 32.307 12.859 8.524 2.744 -0.296 O2 X8Y 27 X8Y O3 O3 O 0 1 N N N -6.815 35.184 13.449 5.838 1.736 -0.461 O3 X8Y 28 X8Y O4 O4 O 0 1 N N N -16.810 39.734 14.181 -7.485 -3.123 -0.678 O4 X8Y 29 X8Y O5 O5 O -1 1 N N N -14.463 40.341 13.837 -5.540 -3.021 0.510 O5 X8Y 30 X8Y O6 O6 O 0 1 N N N -4.744 33.482 17.375 4.891 -2.434 0.870 O6 X8Y 31 X8Y O7 O7 O 0 1 N N N -5.649 31.824 14.921 6.707 -1.053 2.536 O7 X8Y 32 X8Y H1 H1 H 0 1 N N N -7.484 34.748 18.157 4.401 0.311 0.027 H1 X8Y 33 X8Y H3 H3 H 0 1 N N N -6.733 35.141 15.476 7.524 -0.856 -1.761 H3 X8Y 34 X8Y H4 H4 H 0 1 N N N -8.471 34.740 15.261 6.331 0.187 -2.572 H4 X8Y 35 X8Y H5 H5 H 0 1 N N N -8.258 33.073 16.722 5.266 -1.879 -1.710 H5 X8Y 36 X8Y H6 H6 H 0 1 N N N -9.130 35.870 17.277 3.006 -1.531 -1.802 H6 X8Y 37 X8Y H7 H7 H 0 1 N N N -8.564 35.417 15.633 3.135 -1.762 -0.042 H7 X8Y 38 X8Y H8 H8 H 0 1 N N N -7.094 37.349 15.500 1.979 0.400 0.326 H8 X8Y 39 X8Y H9 H9 H 0 1 N N N -7.221 37.669 17.262 1.850 0.631 -1.434 H9 X8Y 40 X8Y H10 H10 H 0 1 N N N -9.265 38.091 15.054 0.516 -1.452 -1.609 H10 X8Y 41 X8Y H11 H11 H 0 1 N N N -9.878 37.572 16.661 0.645 -1.683 0.151 H11 X8Y 42 X8Y H12 H12 H 0 1 N N N -10.113 41.345 15.828 -1.844 -1.604 0.344 H12 X8Y 43 X8Y H13 H13 H 0 1 N N N -10.470 39.830 14.933 -1.974 -1.373 -1.416 H13 X8Y 44 X8Y H14 H14 H 0 1 N N N -12.955 39.988 18.573 -4.684 1.839 -0.119 H14 X8Y 45 X8Y H15 H15 H 0 1 N N N -5.661 32.691 12.988 8.309 -0.299 0.544 H15 X8Y 46 X8Y H16 H16 H 0 1 N N N -11.437 39.133 17.365 -3.001 0.558 0.712 H16 X8Y 47 X8Y H17 H17 H 0 1 N N N -11.665 40.912 17.469 -3.130 0.789 -1.048 H17 X8Y 48 X8Y H18 H18 H 0 1 N N N -17.481 40.185 16.553 -8.785 -0.996 0.257 H18 X8Y 49 X8Y H19 H19 H 0 1 N N N -14.958 40.116 20.023 -6.814 2.973 0.180 H19 X8Y 50 X8Y H20 H20 H 0 1 N N N -6.172 32.119 16.932 6.830 -2.278 0.172 H20 X8Y 51 X8Y H21 H21 H 0 1 N N N -4.030 32.851 15.231 5.417 0.119 1.427 H21 X8Y 52 X8Y H22 H22 H 0 1 N N N -7.646 33.983 11.805 8.972 1.106 -1.472 H22 X8Y 53 X8Y H23 H23 H 0 1 N N N -8.987 34.254 12.970 7.780 2.238 -2.156 H23 X8Y 54 X8Y H24 H24 H 0 1 N N N -8.174 40.093 16.303 -0.511 0.479 0.519 H24 X8Y 55 X8Y H25 H25 H 0 1 N N N -9.210 39.632 17.696 -0.640 0.710 -1.241 H25 X8Y 56 X8Y H26 H26 H 0 1 N N N -12.803 39.068 15.483 -4.269 -1.710 -0.393 H26 X8Y 57 X8Y H31 H31 H 0 1 N N N -4.070 33.780 13.752 8.040 1.098 2.463 H31 X8Y 58 X8Y H32 H32 H 0 1 N N N -8.902 32.049 12.195 9.242 3.315 -0.603 H32 X8Y 59 X8Y H33 H33 H 0 1 N N N -6.167 35.493 14.071 5.983 2.481 0.139 H33 X8Y 60 X8Y H34 H34 H 0 1 N N N -5.029 33.745 18.242 5.102 -2.835 1.724 H34 X8Y 61 X8Y H35 H35 H 0 1 N N N -5.465 31.172 15.587 6.036 -1.598 2.968 H35 X8Y 62 # # 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 X8Y C3 O2 SING N N 1 X8Y C3 C2 SING N N 2 X8Y O3 C2 SING N N 3 X8Y O1 C1 SING N N 4 X8Y C2 C1 SING N N 5 X8Y C2 C4 SING N N 6 X8Y C1 C19 SING N N 7 X8Y O5 N3 SING N N 8 X8Y O4 N3 DOUB N N 9 X8Y N3 C13 SING N N 10 X8Y O7 C19 SING N N 11 X8Y C19 C18 SING N N 12 X8Y C4 C5 SING N N 13 X8Y C10 C9 SING N N 14 X8Y C10 C11 SING N N 15 X8Y N2 C12 SING N N 16 X8Y N2 C11 SING N N 17 X8Y C8 C7 SING N N 18 X8Y C8 C9 SING N N 19 X8Y C13 C12 DOUB Y N 20 X8Y C13 C14 SING Y N 21 X8Y C7 C6 SING N N 22 X8Y C5 C18 SING N N 23 X8Y C5 N1 SING N N 24 X8Y C18 O6 SING N N 25 X8Y C6 N1 SING N N 26 X8Y C12 C17 SING Y N 27 X8Y C14 C15 DOUB Y N 28 X8Y C17 C16 DOUB Y N 29 X8Y C15 C16 SING Y N 30 X8Y C15 N4 SING N N 31 X8Y N5 N4 DOUB N N 32 X8Y N5 N6 DOUB N N 33 X8Y N1 H1 SING N N 34 X8Y C4 H3 SING N N 35 X8Y C4 H4 SING N N 36 X8Y C5 H5 SING N N 37 X8Y C6 H6 SING N N 38 X8Y C6 H7 SING N N 39 X8Y C7 H8 SING N N 40 X8Y C7 H9 SING N N 41 X8Y C8 H10 SING N N 42 X8Y C8 H11 SING N N 43 X8Y C10 H12 SING N N 44 X8Y C10 H13 SING N N 45 X8Y C17 H14 SING N N 46 X8Y C1 H15 SING N N 47 X8Y C11 H16 SING N N 48 X8Y C11 H17 SING N N 49 X8Y C14 H18 SING N N 50 X8Y C16 H19 SING N N 51 X8Y C18 H20 SING N N 52 X8Y C19 H21 SING N N 53 X8Y C3 H22 SING N N 54 X8Y C3 H23 SING N N 55 X8Y C9 H24 SING N N 56 X8Y C9 H25 SING N N 57 X8Y N2 H26 SING N N 58 X8Y O1 H31 SING N N 59 X8Y O2 H32 SING N N 60 X8Y O3 H33 SING N N 61 X8Y O6 H34 SING N N 62 X8Y O7 H35 SING N N 63 # # 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 X8Y SMILES ACDLabs 12.01 "N(C1CC(C(C(C1O)O)O)(CO)O)CCCCCCNc2c([N+](=O)[O-])cc(cc2)N=[N+]=[N-]" X8Y InChI InChI 1.03 "InChI=1S/C19H30N6O7/c20-24-23-12-5-6-13(15(9-12)25(31)32)21-7-3-1-2-4-8-22-14-10-19(30,11-26)18(29)17(28)16(14)27/h5-6,9,14,16-18,21-22,26-30H,1-4,7-8,10-11H2/t14-,16-,17+,18-,19-/m0/s1" X8Y InChIKey InChI 1.03 LQGVNQLERZVIBK-UJCHZGTJSA-N X8Y SMILES_CANONICAL CACTVS 3.385 "OC[C@@]1(O)C[C@H](NCCCCCCNc2ccc(cc2[N+]([O-])=O)N=[N+]=[N-])[C@H](O)[C@@H](O)[C@@H]1O" X8Y SMILES CACTVS 3.385 "OC[C]1(O)C[CH](NCCCCCCNc2ccc(cc2[N+]([O-])=O)N=[N+]=[N-])[CH](O)[CH](O)[CH]1O" X8Y SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1cc(c(cc1N=[N+]=[N-])[N+](=O)[O-])NCCCCCCN[C@H]2C[C@@]([C@H]([C@@H]([C@H]2O)O)O)(CO)O" X8Y SMILES "OpenEye OEToolkits" 2.0.7 "c1cc(c(cc1N=[N+]=[N-])[N+](=O)[O-])NCCCCCCNC2CC(C(C(C2O)O)O)(CO)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 X8Y "SYSTEMATIC NAME" ACDLabs 12.01 "(1S,2S,3R,4S,5S)-5-({6-[(4-azido-2-nitrophenyl)amino]hexyl}amino)-1-(hydroxymethyl)cyclohexane-1,2,3,4-tetrol" X8Y "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(1~{S},2~{S},3~{R},4~{S},5~{S})-5-[6-[(4-azido-2-nitro-phenyl)amino]hexylamino]-1-(hydroxymethyl)cyclohexane-1,2,3,4-tetrol" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site X8Y "Create component" 2020-12-06 RCSB X8Y "Initial release" 2021-12-01 RCSB ##