data_U54 # _chem_comp.id U54 _chem_comp.name "(1S,2R,3R,4R,5R)-5-[8-[4-(4-azanylbutyl)-1,2,3-triazol-1-yl]octylamino]-4-(hydroxymethyl)cyclohexane-1,2,3-triol" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C21 H41 N5 O4" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2023-01-25 _chem_comp.pdbx_modified_date 2024-09-27 _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 427.581 _chem_comp.one_letter_code ? _chem_comp.three_letter_code U54 _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 8CB6 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBE _chem_comp.pdbx_pcm Y # 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.pdbx_backbone_atom_flag _chem_comp_atom.pdbx_n_terminal_atom_flag _chem_comp_atom.pdbx_c_terminal_atom_flag _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 U54 C1 C1 C 0 1 N N R N N N -15.119 -32.112 95.859 -6.226 -0.094 0.110 C1 U54 1 U54 C2 C2 C 0 1 N N N N N N -13.949 -31.491 95.097 -6.534 -1.476 -0.469 C2 U54 2 U54 C3 C3 C 0 1 N N S N N N -12.581 -31.466 95.742 -7.757 -2.064 0.239 C3 U54 3 U54 C4 C4 C 0 1 N N R N N N -12.632 -31.544 97.269 -8.960 -1.143 0.028 C4 U54 4 U54 C5 C5 C 0 1 N N R N N N -13.886 -30.944 97.769 -8.651 0.240 0.607 C5 U54 5 U54 C6 C6 C 0 1 N N R N N N -15.079 -31.819 97.366 -7.429 0.828 -0.100 C6 U54 6 U54 C7 C7 C 0 1 N N N N N N -16.400 -31.233 97.860 -7.120 2.210 0.479 C7 U54 7 U54 O3 O1 O 0 1 N N N N N N -11.814 -32.539 95.269 -8.045 -3.355 -0.302 O3 U54 8 U54 O5 O2 O 0 1 N N N N N N -13.763 -30.802 99.191 -9.775 1.100 0.411 O5 U54 9 U54 O7 O3 O 0 1 N N N N N N -16.678 -29.962 97.275 -8.196 3.102 0.180 O7 U54 10 U54 O4 O4 O 0 1 N N N N N N -11.481 -30.794 97.705 -10.102 -1.692 0.689 O4 U54 11 U54 N1 N1 N 0 1 N N N N N N -15.321 -33.565 95.531 -5.052 0.471 -0.569 N1 U54 12 U54 C13 C8 C 0 1 N N N N N N -16.631 -34.073 96.026 -3.807 0.002 0.054 C13 U54 13 U54 C14 C9 C 0 1 N N N N N N -16.814 -35.528 95.515 -2.609 0.609 -0.679 C14 U54 14 U54 C15 C10 C 0 1 N N N N N N -18.156 -36.200 95.898 -1.313 0.121 -0.031 C15 U54 15 U54 C16 C11 C 0 1 N N N N N N -18.204 -37.701 95.536 -0.115 0.728 -0.764 C16 U54 16 U54 C17 C12 C 0 1 N N N N N N -19.628 -38.262 95.350 1.181 0.240 -0.115 C17 U54 17 U54 C18 C13 C 0 1 N N N N N N -19.683 -39.698 94.793 2.379 0.847 -0.848 C18 U54 18 U54 C19 C14 C 0 1 N N N N N N -20.895 -39.927 93.863 3.676 0.359 -0.200 C19 U54 19 U54 C20 C15 C 0 1 N N N N N N -21.450 -41.364 93.849 4.873 0.966 -0.933 C20 U54 20 U54 N49 N2 N 0 1 Y N N N N N -22.811 -41.468 93.284 6.115 0.498 -0.312 N49 U54 21 U54 C53 C16 C 0 1 Y N N N N N -23.889 -40.660 93.179 7.135 -0.122 -0.949 C53 U54 22 U54 C52 C17 C 0 1 Y N N N N N -24.901 -41.360 92.499 8.070 -0.377 -0.004 C52 U54 23 U54 N51 N3 N 0 1 Y N N N N N -24.416 -42.586 92.220 7.583 0.094 1.150 N51 U54 24 U54 N50 N4 N 0 1 Y N N N N N -23.102 -42.695 92.703 6.425 0.611 0.932 N50 U54 25 U54 C54 C18 C 0 1 N N N N N N -26.320 -40.914 92.129 9.399 -1.057 -0.210 C54 U54 26 U54 C55 C19 C 0 1 N N N N N N -26.434 -39.429 91.768 10.520 -0.155 0.310 C55 U54 27 U54 C56 C20 C 0 1 N N N N N N -26.720 -38.534 92.972 11.869 -0.846 0.100 C56 U54 28 U54 C57 C21 C 0 1 N N N N N N -26.659 -37.028 92.631 12.990 0.056 0.620 C57 U54 29 U54 N58 N5 N 0 1 N N N N N N -26.736 -36.216 93.867 14.285 -0.607 0.419 N58 U54 30 U54 H1 H1 H 0 1 N N N N N N -16.016 -31.596 95.487 -6.020 -0.184 1.177 H1 U54 31 U54 H2 H2 H 0 1 N N N N N N -14.223 -30.447 94.882 -6.740 -1.385 -1.535 H2 U54 32 U54 H3 H3 H 0 1 N N N N N N -13.849 -32.046 94.152 -5.677 -2.132 -0.319 H3 U54 33 U54 H4 H4 H 0 1 N N N N N N -12.094 -30.518 95.470 -7.551 -2.154 1.305 H4 U54 34 U54 H5 H5 H 0 1 N N N N N N -12.558 -32.594 97.587 -9.166 -1.052 -1.038 H5 U54 35 U54 H6 H6 H 0 1 N N N N N N -14.016 -29.953 97.310 -8.445 0.149 1.674 H6 U54 36 U54 H7 H7 H 0 1 N N N N N N -14.949 -32.786 97.874 -7.635 0.918 -1.167 H7 U54 37 U54 H8 H8 H 0 1 N N N N N N -16.349 -31.117 98.953 -7.002 2.133 1.560 H8 U54 38 U54 H9 H9 H 0 1 N N N N N N -17.214 -31.927 97.603 -6.199 2.591 0.038 H9 U54 39 U54 H10 H10 H 0 1 N N N N N N -10.956 -32.519 95.676 -8.810 -3.788 0.101 H10 U54 40 U54 H11 H11 H 0 1 N N N N N N -14.558 -30.417 99.541 -10.588 0.789 0.833 H11 U54 41 U54 H12 H12 H 0 1 N N N N N N -17.505 -29.634 97.608 -8.068 3.999 0.518 H12 U54 42 U54 H13 H13 H 0 1 N N N N N N -11.442 -30.796 98.654 -10.356 -2.569 0.372 H13 U54 43 U54 H16 H16 H 0 1 N N N N N N -17.444 -33.439 95.643 -3.786 0.308 1.100 H16 U54 44 U54 H17 H17 H 0 1 N N N N N N -16.643 -34.061 97.126 -3.757 -1.086 -0.008 H17 U54 45 U54 H18 H18 H 0 1 N N N N N N -15.998 -36.139 95.929 -2.630 0.303 -1.725 H18 U54 46 U54 H19 H19 H 0 1 N N N N N N -16.742 -35.514 94.417 -2.659 1.696 -0.618 H19 U54 47 U54 H20 H20 H 0 1 N N N N N N -18.303 -36.096 96.983 -1.292 0.426 1.015 H20 U54 48 U54 H21 H21 H 0 1 N N N N N N -18.970 -35.685 95.367 -1.263 -0.967 -0.093 H21 U54 49 U54 H22 H22 H 0 1 N N N N N N -17.713 -38.266 96.342 -0.136 0.422 -1.810 H22 U54 50 U54 H23 H23 H 0 1 N N N N N N -17.650 -37.847 94.597 -0.165 1.815 -0.702 H23 U54 51 U54 H24 H24 H 0 1 N N N N N N -20.168 -37.603 94.654 1.202 0.545 0.931 H24 U54 52 U54 H25 H25 H 0 1 N N N N N N -20.131 -38.254 96.328 1.231 -0.848 -0.177 H25 U54 53 U54 H26 H26 H 0 1 N N N N N N -19.748 -40.401 95.636 2.358 0.541 -1.894 H26 U54 54 U54 H27 H27 H 0 1 N N N N N N -18.761 -39.891 94.225 2.329 1.934 -0.787 H27 U54 55 U54 H28 H28 H 0 1 N N N N N N -20.590 -39.670 92.838 3.697 0.664 0.846 H28 U54 56 U54 H29 H29 H 0 1 N N N N N N -21.703 -39.254 94.185 3.726 -0.729 -0.261 H29 U54 57 U54 H30 H30 H 0 1 N N N N N N -21.474 -41.738 94.883 4.852 0.660 -1.979 H30 U54 58 U54 H31 H31 H 0 1 N N N N N N -20.775 -41.991 93.248 4.824 2.053 -0.871 H31 U54 59 U54 H32 H32 H 0 1 N N N N N N -23.961 -39.650 93.553 7.192 -0.365 -1.999 H32 U54 60 U54 H33 H33 H 0 1 N N N N N N -26.979 -41.113 92.987 9.411 -2.002 0.333 H33 U54 61 U54 H34 H34 H 0 1 N N N N N N -26.654 -41.506 91.265 9.549 -1.246 -1.273 H34 U54 62 U54 H35 H35 H 0 1 N N N N N N -25.487 -39.107 91.311 10.507 0.790 -0.233 H35 U54 63 U54 H36 H36 H 0 1 N N N N N N -27.251 -39.308 91.041 10.370 0.035 1.373 H36 U54 64 U54 H37 H37 H 0 1 N N N N N N -27.726 -38.767 93.352 11.882 -1.791 0.643 H37 U54 65 U54 H38 H38 H 0 1 N N N N N N -25.975 -38.747 93.753 12.019 -1.035 -0.963 H38 U54 66 U54 H39 H39 H 0 1 N N N N N N -25.713 -36.812 92.113 12.977 1.001 0.077 H39 U54 67 U54 H40 H40 H 0 1 N N N N N N -27.503 -36.770 91.975 12.840 0.246 1.683 H40 U54 68 U54 H41 H41 H 0 1 N N N N N N -26.695 -35.245 93.632 14.420 -0.851 -0.551 H41 U54 69 U54 H42 H42 H 0 1 N N N N N N -27.596 -36.409 94.339 15.043 -0.031 0.755 H42 U54 70 U54 H14 H14 H 0 1 N N N N N N -15.285 -33.680 94.538 -5.067 0.256 -1.555 H14 U54 71 # 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 U54 C55 C54 SING N N 1 U54 C55 C56 SING N N 2 U54 C54 C52 SING N N 3 U54 N51 C52 SING Y N 4 U54 N51 N50 DOUB Y N 5 U54 C52 C53 DOUB Y N 6 U54 C57 C56 SING N N 7 U54 C57 N58 SING N N 8 U54 N50 N49 SING Y N 9 U54 C53 N49 SING Y N 10 U54 N49 C20 SING N N 11 U54 C20 C19 SING N N 12 U54 C19 C18 SING N N 13 U54 C18 C17 SING N N 14 U54 C2 C3 SING N N 15 U54 C2 C1 SING N N 16 U54 O3 C3 SING N N 17 U54 C17 C16 SING N N 18 U54 C14 C15 SING N N 19 U54 C14 C13 SING N N 20 U54 N1 C1 SING N N 21 U54 N1 C13 SING N N 22 U54 C16 C15 SING N N 23 U54 C3 C4 SING N N 24 U54 C1 C6 SING N N 25 U54 C4 O4 SING N N 26 U54 C4 C5 SING N N 27 U54 O7 C7 SING N N 28 U54 C6 C5 SING N N 29 U54 C6 C7 SING N N 30 U54 C5 O5 SING N N 31 U54 C1 H1 SING N N 32 U54 C2 H2 SING N N 33 U54 C2 H3 SING N N 34 U54 C3 H4 SING N N 35 U54 C4 H5 SING N N 36 U54 C5 H6 SING N N 37 U54 C6 H7 SING N N 38 U54 C7 H8 SING N N 39 U54 C7 H9 SING N N 40 U54 O3 H10 SING N N 41 U54 O5 H11 SING N N 42 U54 O7 H12 SING N N 43 U54 O4 H13 SING N N 44 U54 C13 H16 SING N N 45 U54 C13 H17 SING N N 46 U54 C14 H18 SING N N 47 U54 C14 H19 SING N N 48 U54 C15 H20 SING N N 49 U54 C15 H21 SING N N 50 U54 C16 H22 SING N N 51 U54 C16 H23 SING N N 52 U54 C17 H24 SING N N 53 U54 C17 H25 SING N N 54 U54 C18 H26 SING N N 55 U54 C18 H27 SING N N 56 U54 C19 H28 SING N N 57 U54 C19 H29 SING N N 58 U54 C20 H30 SING N N 59 U54 C20 H31 SING N N 60 U54 C53 H32 SING N N 61 U54 C54 H33 SING N N 62 U54 C54 H34 SING N N 63 U54 C55 H35 SING N N 64 U54 C55 H36 SING N N 65 U54 C56 H37 SING N N 66 U54 C56 H38 SING N N 67 U54 C57 H39 SING N N 68 U54 C57 H40 SING N N 69 U54 N58 H41 SING N N 70 U54 N58 H42 SING N N 71 U54 N1 H14 SING N N 72 # 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 U54 InChI InChI 1.06 "InChI=1S/C21H41N5O4/c22-10-6-5-9-16-14-26(25-24-16)12-8-4-2-1-3-7-11-23-18-13-19(28)21(30)20(29)17(18)15-27/h14,17-21,23,27-30H,1-13,15,22H2/t17-,18+,19-,20+,21+/m0/s1" U54 InChIKey InChI 1.06 IZNFXKUUDPEZNL-QGLKVJOYSA-N U54 SMILES_CANONICAL CACTVS 3.385 "NCCCCc1cn(CCCCCCCCN[C@@H]2C[C@H](O)[C@@H](O)[C@H](O)[C@H]2CO)nn1" U54 SMILES CACTVS 3.385 "NCCCCc1cn(CCCCCCCCN[CH]2C[CH](O)[CH](O)[CH](O)[CH]2CO)nn1" U54 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1c(nnn1CCCCCCCCN[C@@H]2C[C@@H]([C@H]([C@@H]([C@H]2CO)O)O)O)CCCCN" U54 SMILES "OpenEye OEToolkits" 2.0.7 "c1c(nnn1CCCCCCCCNC2CC(C(C(C2CO)O)O)O)CCCCN" # _pdbx_chem_comp_identifier.comp_id U54 _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 "(1~{S},2~{R},3~{R},4~{R},5~{R})-5-[8-[4-(4-azanylbutyl)-1,2,3-triazol-1-yl]octylamino]-4-(hydroxymethyl)cyclohexane-1,2,3-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 U54 "Create component" 2023-01-25 PDBE U54 "Initial release" 2023-09-13 RCSB U54 "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id U54 _pdbx_chem_comp_pcm.modified_residue_id ASP _pdbx_chem_comp_pcm.type None _pdbx_chem_comp_pcm.category "Covalent chemical modification" _pdbx_chem_comp_pcm.position "Amino-acid side chain" _pdbx_chem_comp_pcm.polypeptide_position "Any position" _pdbx_chem_comp_pcm.comp_id_linking_atom C2 _pdbx_chem_comp_pcm.modified_residue_id_linking_atom OD2 _pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ? _pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ? #