data_XOD # _chem_comp.id XOD _chem_comp.name "(1S,2S,3R,4S,5S)-1-(hydroxymethyl)-5-[(6-{[2-nitro-4-(pyrimidin-2-yl)phenyl]amino}hexyl)amino]cyclohexane-1,2,3,4-tetrol" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C23 H33 N5 O7" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2020-12-22 _chem_comp.pdbx_modified_date 2021-10-01 _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 491.537 _chem_comp.one_letter_code ? _chem_comp.three_letter_code XOD _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 7KB6 _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 XOD N1 N1 N 0 1 N N N 11.298 22.874 13.147 5.264 -0.202 -0.806 N1 XOD 1 XOD N3 N2 N 0 1 Y N N 22.019 29.987 14.952 -8.585 2.615 0.219 N3 XOD 2 XOD C4 C1 C 0 1 N N S 8.967 23.156 12.866 6.926 -1.520 0.418 C4 XOD 3 XOD C5 C2 C 0 1 N N S 10.315 23.848 12.680 6.482 -1.011 -0.954 C5 XOD 4 XOD C6 C3 C 0 1 N N N 10.555 24.154 11.191 7.593 -0.153 -1.564 C6 XOD 5 XOD C7 C4 C 0 1 N N N 10.396 23.242 8.839 8.990 1.896 -1.256 C7 XOD 6 XOD C8 C5 C 0 1 N N N 12.614 23.479 13.087 4.066 -1.052 -0.803 C8 XOD 7 XOD C10 C6 C 0 1 N N N 14.747 22.093 13.101 1.572 -1.061 -0.644 C10 XOD 8 XOD C13 C7 C 0 1 N N N 17.552 24.413 13.044 -2.166 -0.195 -0.329 C13 XOD 9 XOD C15 C8 C 0 1 Y N N 20.485 25.935 14.538 -5.747 -1.276 -0.069 C15 XOD 10 XOD C17 C9 C 0 1 Y N N 20.943 28.128 13.696 -7.132 0.680 0.071 C17 XOD 11 XOD C20 C10 C 0 1 Y N N 21.628 29.502 13.787 -8.474 1.293 0.211 C20 XOD 12 XOD C21 C11 C 0 1 Y N N 22.599 31.181 15.041 -9.767 3.193 0.342 C21 XOD 13 XOD C22 C12 C 0 1 Y N N 22.787 31.927 13.885 -10.899 2.400 0.464 C22 XOD 14 XOD C1 C13 C 0 1 N N S 10.390 22.894 10.327 7.879 1.038 -0.646 C1 XOD 15 XOD C11 C14 C 0 1 N N N 16.103 22.446 13.716 0.327 -0.185 -0.488 C11 XOD 16 XOD C12 C15 C 0 1 N N N 17.047 23.021 12.659 -0.921 -1.070 -0.485 C12 XOD 17 XOD C14 C16 C 0 1 Y N N 19.653 25.669 13.471 -4.624 -0.465 -0.196 C14 XOD 18 XOD C16 C17 C 0 1 Y N N 21.136 27.162 14.663 -6.996 -0.708 0.061 C16 XOD 19 XOD C18 C18 C 0 1 Y N N 20.101 27.861 12.625 -6.004 1.491 -0.061 C18 XOD 20 XOD C19 C19 C 0 1 Y N N 19.458 26.634 12.513 -4.758 0.919 -0.191 C19 XOD 21 XOD C2 C20 C 0 1 N N S 9.093 22.130 10.598 8.323 0.528 0.726 C2 XOD 22 XOD C23 C21 C 0 1 Y N N 22.353 31.372 12.689 -10.747 1.021 0.452 C23 XOD 23 XOD C3 C22 C 0 1 N N R 8.972 21.831 12.093 7.213 -0.330 1.336 C3 XOD 24 XOD C9 C23 C 0 1 N N N 13.595 22.667 13.923 2.821 -0.176 -0.647 C9 XOD 25 XOD N2 N3 N 0 1 N N N 18.971 24.382 13.356 -3.361 -1.042 -0.326 N2 XOD 26 XOD N4 N4 N 0 1 Y N N 21.783 30.176 12.666 -9.536 0.507 0.326 N4 XOD 27 XOD N5 N5 N 1 1 N N N 20.672 24.914 15.531 -5.602 -2.749 -0.081 N5 XOD 28 XOD O1 O1 O 0 1 N N N 11.442 22.015 10.622 6.695 1.824 -0.502 O1 XOD 29 XOD O2 O2 O 0 1 N N N 9.487 24.286 8.609 9.338 2.941 -0.346 O2 XOD 30 XOD O3 O3 O 0 1 N N N 7.723 21.227 12.300 7.628 -0.805 2.618 O3 XOD 31 XOD O4 O4 O 0 1 N N N 8.796 22.872 14.235 5.889 -2.321 0.988 O4 XOD 32 XOD O5 O5 O 0 1 N N N 9.150 20.908 9.907 8.591 1.640 1.583 O5 XOD 33 XOD O6 O6 O 0 1 N N N 20.575 25.222 16.898 -6.438 -3.439 -0.637 O6 XOD 34 XOD O7 O7 O -1 1 N N N 20.956 23.610 15.102 -4.646 -3.271 0.465 O7 XOD 35 XOD H1 H1 H 0 1 N N N 11.091 22.612 14.089 5.307 0.366 0.027 H1 XOD 36 XOD H3 H3 H 0 1 N N N 8.162 23.802 12.486 7.830 -2.120 0.308 H3 XOD 37 XOD H4 H4 H 0 1 N N N 10.356 24.775 13.271 6.278 -1.859 -1.608 H4 XOD 38 XOD H5 H5 H 0 1 N N N 11.576 24.543 11.065 8.496 -0.752 -1.674 H5 XOD 39 XOD H6 H6 H 0 1 N N N 9.830 24.913 10.860 7.276 0.210 -2.542 H6 XOD 40 XOD H7 H7 H 0 1 N N N 10.100 22.360 8.253 9.864 1.275 -1.448 H7 XOD 41 XOD H8 H8 H 0 1 N N N 11.406 23.559 8.539 8.640 2.331 -2.192 H8 XOD 42 XOD H9 H9 H 0 1 N N N 12.957 23.503 12.042 4.008 -1.602 -1.742 H9 XOD 43 XOD H10 H10 H 0 1 N N N 12.562 24.505 13.480 4.121 -1.756 0.027 H10 XOD 44 XOD H11 H11 H 0 1 N N N 14.699 22.504 12.082 1.628 -1.765 0.186 H11 XOD 45 XOD H12 H12 H 0 1 N N N 14.647 20.998 13.060 1.515 -1.611 -1.584 H12 XOD 46 XOD H13 H13 H 0 1 N N N 17.383 25.103 12.204 -2.108 0.355 0.610 H13 XOD 47 XOD H14 H14 H 0 1 N N N 16.997 24.766 13.926 -2.222 0.509 -1.160 H14 XOD 48 XOD H15 H15 H 0 1 N N N 22.919 31.565 15.999 -9.851 4.270 0.348 H15 XOD 49 XOD H16 H16 H 0 1 N N N 23.253 32.901 13.915 -11.877 2.847 0.567 H16 XOD 50 XOD H17 H17 H 0 1 N N N 16.552 21.538 14.144 0.385 0.364 0.451 H17 XOD 51 XOD H18 H18 H 0 1 N N N 15.955 23.192 14.511 0.272 0.518 -1.319 H18 XOD 52 XOD H19 H19 H 0 1 N N N 16.510 23.090 11.702 -0.865 -1.774 0.345 H19 XOD 53 XOD H20 H20 H 0 1 N N N 17.910 22.348 12.548 -0.979 -1.620 -1.425 H20 XOD 54 XOD H21 H21 H 0 1 N N N 21.783 27.354 15.506 -7.869 -1.337 0.154 H21 XOD 55 XOD H22 H22 H 0 1 N N N 19.944 28.616 11.869 -6.109 2.566 -0.061 H22 XOD 56 XOD H23 H23 H 0 1 N N N 18.806 26.440 11.674 -3.885 1.546 -0.293 H23 XOD 57 XOD H24 H24 H 0 1 N N N 8.234 22.735 10.273 9.227 -0.071 0.616 H24 XOD 58 XOD H25 H25 H 0 1 N N N 22.481 31.921 11.768 -11.608 0.376 0.545 H25 XOD 59 XOD H26 H26 H 0 1 N N N 9.806 21.196 12.427 6.310 0.270 1.446 H26 XOD 60 XOD H27 H27 H 0 1 N N N 14.013 23.319 14.705 2.878 0.374 0.292 H27 XOD 61 XOD H28 H28 H 0 1 N N N 13.050 21.834 14.392 2.765 0.528 -1.477 H28 XOD 62 XOD H29 H29 H 0 1 N N N 19.078 23.905 14.228 -3.274 -2.004 -0.416 H29 XOD 63 XOD H30 H30 H 0 1 N N N 11.430 21.805 11.548 6.803 2.598 0.068 H30 XOD 64 XOD H31 H31 H 0 1 N N N 9.486 24.508 7.685 10.038 3.525 -0.668 H31 XOD 65 XOD H32 H32 H 0 1 N N N 7.616 21.028 13.223 6.971 -1.358 3.064 H32 XOD 66 XOD H33 H33 H 0 1 N N N 8.791 23.683 14.729 6.102 -2.679 1.861 H33 XOD 67 XOD H34 H34 H 0 1 N N N 8.351 20.418 10.063 8.878 1.391 2.472 H34 XOD 68 # # 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 XOD O2 C7 SING N N 1 XOD C7 C1 SING N N 2 XOD O5 C2 SING N N 3 XOD C1 C2 SING N N 4 XOD C1 O1 SING N N 5 XOD C1 C6 SING N N 6 XOD C2 C3 SING N N 7 XOD C6 C5 SING N N 8 XOD C3 O3 SING N N 9 XOD C3 C4 SING N N 10 XOD C19 C18 DOUB Y N 11 XOD C19 C14 SING Y N 12 XOD C18 C17 SING Y N 13 XOD C12 C13 SING N N 14 XOD C12 C11 SING N N 15 XOD N4 C23 DOUB Y N 16 XOD N4 C20 SING Y N 17 XOD C5 C4 SING N N 18 XOD C5 N1 SING N N 19 XOD C23 C22 SING Y N 20 XOD C4 O4 SING N N 21 XOD C13 N2 SING N N 22 XOD C8 N1 SING N N 23 XOD C8 C9 SING N N 24 XOD C10 C11 SING N N 25 XOD C10 C9 SING N N 26 XOD N2 C14 SING N N 27 XOD C14 C15 DOUB Y N 28 XOD C17 C20 SING N N 29 XOD C17 C16 DOUB Y N 30 XOD C20 N3 DOUB Y N 31 XOD C22 C21 DOUB Y N 32 XOD C15 C16 SING Y N 33 XOD C15 N5 SING N N 34 XOD N3 C21 SING Y N 35 XOD O7 N5 SING N N 36 XOD N5 O6 DOUB N N 37 XOD N1 H1 SING N N 38 XOD C4 H3 SING N N 39 XOD C5 H4 SING N N 40 XOD C6 H5 SING N N 41 XOD C6 H6 SING N N 42 XOD C7 H7 SING N N 43 XOD C7 H8 SING N N 44 XOD C8 H9 SING N N 45 XOD C8 H10 SING N N 46 XOD C10 H11 SING N N 47 XOD C10 H12 SING N N 48 XOD C13 H13 SING N N 49 XOD C13 H14 SING N N 50 XOD C21 H15 SING N N 51 XOD C22 H16 SING N N 52 XOD C11 H17 SING N N 53 XOD C11 H18 SING N N 54 XOD C12 H19 SING N N 55 XOD C12 H20 SING N N 56 XOD C16 H21 SING N N 57 XOD C18 H22 SING N N 58 XOD C19 H23 SING N N 59 XOD C2 H24 SING N N 60 XOD C23 H25 SING N N 61 XOD C3 H26 SING N N 62 XOD C9 H27 SING N N 63 XOD C9 H28 SING N N 64 XOD N2 H29 SING N N 65 XOD O1 H30 SING N N 66 XOD O2 H31 SING N N 67 XOD O3 H32 SING N N 68 XOD O4 H33 SING N N 69 XOD O5 H34 SING N N 70 # # 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 XOD SMILES ACDLabs 12.01 "N(C1C(O)C(C(C(C1)(CO)O)O)O)CCCCCCNc3c(cc(c2ncccn2)cc3)[N+](=O)[O-]" XOD InChI InChI 1.03 "InChI=1S/C23H33N5O7/c29-14-23(33)13-17(19(30)20(31)21(23)32)25-9-4-2-1-3-8-24-16-7-6-15(12-18(16)28(34)35)22-26-10-5-11-27-22/h5-7,10-12,17,19-21,24-25,29-33H,1-4,8-9,13-14H2/t17-,19-,20+,21-,23-/m0/s1" XOD InChIKey InChI 1.03 MZOLIRUJMQEVFZ-BYGOBXPBSA-N XOD SMILES_CANONICAL CACTVS 3.385 "OC[C@@]1(O)C[C@H](NCCCCCCNc2ccc(cc2[N+]([O-])=O)c3ncccn3)[C@H](O)[C@@H](O)[C@@H]1O" XOD SMILES CACTVS 3.385 "OC[C]1(O)C[CH](NCCCCCCNc2ccc(cc2[N+]([O-])=O)c3ncccn3)[CH](O)[CH](O)[CH]1O" XOD SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1cnc(nc1)c2ccc(c(c2)[N+](=O)[O-])NCCCCCCN[C@H]3C[C@@]([C@H]([C@@H]([C@H]3O)O)O)(CO)O" XOD SMILES "OpenEye OEToolkits" 2.0.7 "c1cnc(nc1)c2ccc(c(c2)[N+](=O)[O-])NCCCCCCNC3CC(C(C(C3O)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 XOD "SYSTEMATIC NAME" ACDLabs 12.01 "(1S,2S,3R,4S,5S)-1-(hydroxymethyl)-5-[(6-{[2-nitro-4-(pyrimidin-2-yl)phenyl]amino}hexyl)amino]cyclohexane-1,2,3,4-tetrol" XOD "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(1~{S},2~{S},3~{R},4~{S},5~{S})-1-(hydroxymethyl)-5-[6-[(2-nitro-4-pyrimidin-2-yl-phenyl)amino]hexylamino]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 XOD "Create component" 2020-12-22 RCSB XOD "Initial release" 2021-10-06 RCSB ##