data_AKN
# 
_chem_comp.id                                    AKN 
_chem_comp.name                                  
;(2S)-N-[(1R,2S,3S,4R,5S)-4-[(2R,3R,4S,5S,6R)-6-(aminomethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-5-azanyl-2-[(2S,3R,4S,5S
,6R)-4-azanyl-6-(hydroxymethyl)-3,5-bis(oxidanyl)oxan-2-yl]oxy-3-oxidanyl-cyclohexyl]-4-azanyl-2-oxidanyl-butanamide
;
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C22 H43 N5 O13" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         AMIKACIN 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2006-02-28 
_chem_comp.pdbx_modified_date                    2020-06-17 
_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                        585.603 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     AKN 
_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        4P20 
_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 
AKN C1  C1  C 0 1 N N R 25.987 6.448  5.168  3.606  0.410  0.388  C1  AKN 1  
AKN C3  C2  C 0 1 N N R 26.160 4.927  4.776  4.838  1.068  -0.240 C3  AKN 2  
AKN C4  C3  C 0 1 N N S 26.265 4.770  3.233  5.690  -0.007 -0.921 C4  AKN 3  
AKN C5  C4  C 0 1 N N S 24.921 5.332  2.611  6.064  -1.076 0.110  C5  AKN 4  
AKN C7  C5  C 0 1 N N R 24.776 6.873  3.008  4.786  -1.652 0.724  C7  AKN 5  
AKN C9  C6  C 0 1 N N N 23.487 7.493  2.473  5.152  -2.678 1.798  C9  AKN 6  
AKN O6  O1  O 0 1 N N N 24.950 5.191  1.170  6.799  -2.121 -0.531 O6  AKN 7  
AKN O2  O2  O 0 1 N N N 27.149 7.172  4.719  2.811  -0.188 -0.638 O2  AKN 8  
AKN O8  O3  O 0 1 N N N 24.754 6.999  4.523  4.025  -0.595 1.314  O8  AKN 9  
AKN N10 N1  N 0 1 N N N 23.020 8.627  3.330  3.929  -3.316 2.303  N10 AKN 10 
AKN C11 C7  C 0 1 N N R 29.721 10.353 6.178  -1.298 -1.195 -0.758 C11 AKN 11 
AKN N12 N2  N 0 1 N N N 30.099 11.587 6.780  -2.624 -1.626 -0.309 N12 AKN 12 
AKN C13 C8  C 0 1 N N N 28.799 10.656 4.955  -0.285 -2.312 -0.503 C13 AKN 13 
AKN C14 C9  C 0 1 N N S 28.344 9.312  4.271  1.100  -1.862 -0.972 C14 AKN 14 
AKN N15 N3  N 0 1 N N N 27.464 9.623  3.100  2.073  -2.935 -0.727 N15 AKN 15 
AKN C16 C10 C 0 1 N N R 27.583 8.419  5.361  1.518  -0.609 -0.200 C16 AKN 16 
AKN C17 C11 C 0 1 N N S 28.569 8.145  6.568  0.504  0.509  -0.456 C17 AKN 17 
AKN O18 O4  O 0 1 N N N 27.906 7.365  7.549  0.894  1.679  0.266  O18 AKN 18 
AKN C19 C12 C 0 1 N N S 28.999 9.488  7.213  -0.881 0.059  0.014  C19 AKN 19 
AKN O20 O5  O 0 1 N N N 29.889 9.224  8.302  -1.827 1.102  -0.225 O20 AKN 20 
AKN C21 C13 C 0 1 N N S 29.709 9.688  9.581  -2.348 1.698  0.965  C21 AKN 21 
AKN C22 C14 C 0 1 N N R 31.124 9.766  10.218 -3.717 2.317  0.669  C22 AKN 22 
AKN O23 O6  O 0 1 N N N 31.925 10.627 9.472  -4.595 1.311  0.159  O23 AKN 23 
AKN C24 C15 C 0 1 N N S 31.787 8.330  10.339 -3.551 3.428  -0.373 C24 AKN 24 
AKN N25 N4  N 0 1 N N N 33.139 8.429  10.967 -4.847 4.078  -0.607 N25 AKN 25 
AKN C26 C16 C 0 1 N N S 30.823 7.400  11.198 -2.548 4.459  0.152  C26 AKN 26 
AKN O27 O7  O 0 1 N N N 31.375 6.089  11.341 -2.331 5.463  -0.842 O27 AKN 27 
AKN C28 C17 C 0 1 N N R 29.418 7.349  10.491 -1.225 3.757  0.468  C28 AKN 28 
AKN O29 O8  O 0 1 N N N 28.854 8.757  10.339 -1.454 2.716  1.419  O29 AKN 29 
AKN C30 C18 C 0 1 N N N 28.436 6.491  11.284 -0.236 4.770  1.049  C30 AKN 30 
AKN O31 O9  O 0 1 N N N 27.506 7.243  12.099 1.031  4.140  1.246  O31 AKN 31 
AKN O32 O10 O 0 1 N N N 27.361 4.419  5.406  4.423  2.033  -1.208 O32 AKN 32 
AKN O33 O11 O 0 1 N N N 26.418 3.427  2.939  6.878  0.588  -1.448 O33 AKN 33 
AKN N37 N5  N 0 1 N N N 34.428 14.890 9.205  -5.865 -5.062 2.172  N37 AKN 34 
AKN C35 C19 C 0 1 N N N 31.356 12.187 6.427  -3.411 -2.350 -1.129 C35 AKN 35 
AKN O36 O12 O 0 1 N N N 32.236 11.509 5.782  -3.021 -2.645 -2.239 O36 AKN 36 
AKN C37 C20 C 0 1 N N S 31.579 13.663 6.874  -4.775 -2.794 -0.667 C37 AKN 37 
AKN C38 C21 C 0 1 N N N 32.746 13.665 7.907  -4.626 -3.770 0.501  C38 AKN 38 
AKN C39 C22 C 0 1 N N N 33.341 15.037 8.216  -6.009 -4.124 1.050  C39 AKN 39 
AKN O40 O13 O 0 1 N N N 30.562 14.150 7.502  -5.456 -3.440 -1.745 O40 AKN 40 
AKN H1  H1  H 0 1 N N N 25.892 6.517  6.262  3.018  1.163  0.911  H1  AKN 41 
AKN H2  H2  H 0 1 N N N 25.279 4.372  5.131  5.423  1.560  0.537  H2  AKN 42 
AKN H3  H3  H 0 1 N N N 27.109 5.370  2.862  5.122  -0.464 -1.731 H3  AKN 43 
AKN H4  H4  H 0 1 N N N 24.073 4.777  3.038  6.675  -0.628 0.894  H4  AKN 44 
AKN H5  H5  H 0 1 N N N 25.641 7.421  2.606  4.194  -2.135 -0.054 H5  AKN 45 
AKN H6  H6  H 0 1 N N N 23.668 7.867  1.454  5.807  -3.436 1.368  H6  AKN 46 
AKN H7  H7  H 0 1 N N N 22.704 6.721  2.447  5.665  -2.177 2.619  H7  AKN 47 
AKN H8  H8  H 0 1 N N N 25.036 4.273  0.943  7.623  -1.827 -0.942 H8  AKN 48 
AKN H9  H9  H 0 1 N N N 22.177 9.007  2.950  3.401  -3.733 1.550  H9  AKN 49 
AKN H10 H10 H 0 1 N N N 22.848 8.295  4.257  4.144  -3.999 3.014  H10 AKN 50 
AKN H12 H12 H 0 1 N N N 30.610 9.813  5.820  -1.331 -0.971 -1.825 H12 AKN 51 
AKN H13 H13 H 0 1 N N N 29.496 12.032 7.442  -2.936 -1.390 0.578  H13 AKN 52 
AKN H14 H14 H 0 1 N N N 29.352 11.266 4.225  -0.252 -2.536 0.563  H14 AKN 53 
AKN H15 H15 H 0 1 N N N 27.911 11.208 5.297  -0.582 -3.205 -1.053 H15 AKN 54 
AKN H16 H16 H 0 1 N N N 29.237 8.765  3.933  1.067  -1.638 -2.038 H16 AKN 55 
AKN H17 H17 H 0 1 N N N 27.174 8.771  2.665  1.727  -3.821 -1.064 H17 AKN 56 
AKN H18 H18 H 0 1 N N N 26.659 10.128 3.413  2.966  -2.715 -1.140 H18 AKN 57 
AKN H20 H20 H 0 1 N N N 26.714 8.982  5.732  1.550  -0.833 0.866  H20 AKN 58 
AKN H21 H21 H 0 1 N N N 29.460 7.626  6.186  0.472  0.733  -1.522 H21 AKN 59 
AKN H22 H22 H 0 1 N N N 28.496 7.199  8.275  1.688  2.109  -0.082 H22 AKN 60 
AKN H23 H23 H 0 1 N N N 28.102 10.018 7.566  -0.848 -0.166 1.080  H23 AKN 61 
AKN H24 H24 H 0 1 N N N 29.262 10.693 9.585  -2.453 0.935  1.737  H24 AKN 62 
AKN H25 H25 H 0 1 N N N 31.008 10.158 11.239 -4.133 2.735  1.585  H25 AKN 63 
AKN H26 H26 H 0 1 N N N 32.790 10.674 9.863  -4.742 0.573  0.766  H26 AKN 64 
AKN H27 H27 H 0 1 N N N 31.877 7.901  9.330  -3.183 3.001  -1.306 H27 AKN 65 
AKN H28 H28 H 0 1 N N N 33.543 7.517  11.036 -5.528 3.415  -0.947 H28 AKN 66 
AKN H29 H29 H 0 1 N N N 33.726 9.011  10.405 -5.177 4.539  0.227  H29 AKN 67 
AKN H31 H31 H 0 1 N N N 30.694 7.866  12.186 -2.941 4.922  1.057  H31 AKN 68 
AKN H32 H32 H 0 1 N N N 30.785 5.551  11.856 -1.705 6.150  -0.576 H32 AKN 69 
AKN H33 H33 H 0 1 N N N 29.550 6.908  9.492  -0.812 3.331  -0.446 H33 AKN 70 
AKN H34 H34 H 0 1 N N N 27.857 5.884  10.572 -0.123 5.606  0.358  H34 AKN 71 
AKN H35 H35 H 0 1 N N N 29.014 5.828  11.945 -0.611 5.137  2.005  H35 AKN 72 
AKN H36 H36 H 0 1 N N N 26.931 6.643  12.559 1.709  4.725  1.613  H36 AKN 73 
AKN H37 H37 H 0 1 N N N 27.291 4.518  6.348  3.874  2.742  -0.846 H37 AKN 74 
AKN H38 H38 H 0 1 N N N 27.228 3.109  3.320  6.714  1.279  -2.104 H38 AKN 75 
AKN H39 H39 H 0 1 N N N 34.818 15.788 9.408  -5.263 -4.681 2.886  H39 AKN 76 
AKN H40 H40 H 0 1 N N N 34.063 14.488 10.045 -6.766 -5.311 2.553  H40 AKN 77 
AKN H42 H42 H 0 1 N N N 31.874 14.261 5.999  -5.349 -1.925 -0.343 H42 AKN 78 
AKN H43 H43 H 0 1 N N N 32.368 13.239 8.848  -4.129 -4.677 0.155  H43 AKN 79 
AKN H44 H44 H 0 1 N N N 33.550 13.027 7.512  -4.029 -3.308 1.287  H44 AKN 80 
AKN H45 H45 H 0 1 N N N 33.743 15.479 7.292  -6.605 -4.587 0.264  H45 AKN 81 
AKN H46 H46 H 0 1 N N N 32.558 15.692 8.626  -6.505 -3.217 1.396  H46 AKN 82 
AKN H47 H47 H 0 1 N N N 30.745 15.048 7.753  -5.001 -4.223 -2.084 H47 AKN 83 
# 
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 
AKN O6  C5  SING N N 1  
AKN C9  C7  SING N N 2  
AKN C9  N10 SING N N 3  
AKN C5  C7  SING N N 4  
AKN C5  C4  SING N N 5  
AKN O33 C4  SING N N 6  
AKN C7  O8  SING N N 7  
AKN N15 C14 SING N N 8  
AKN C4  C3  SING N N 9  
AKN C14 C13 SING N N 10 
AKN C14 C16 SING N N 11 
AKN O8  C1  SING N N 12 
AKN O2  C1  SING N N 13 
AKN O2  C16 SING N N 14 
AKN C3  C1  SING N N 15 
AKN C3  O32 SING N N 16 
AKN C13 C11 SING N N 17 
AKN C16 C17 SING N N 18 
AKN O36 C35 DOUB N N 19 
AKN C11 N12 SING N N 20 
AKN C11 C19 SING N N 21 
AKN C35 N12 SING N N 22 
AKN C35 C37 SING N N 23 
AKN C17 C19 SING N N 24 
AKN C17 O18 SING N N 25 
AKN C37 O40 SING N N 26 
AKN C37 C38 SING N N 27 
AKN C19 O20 SING N N 28 
AKN C38 C39 SING N N 29 
AKN C39 N37 SING N N 30 
AKN O20 C21 SING N N 31 
AKN O23 C22 SING N N 32 
AKN C21 C22 SING N N 33 
AKN C21 O29 SING N N 34 
AKN C22 C24 SING N N 35 
AKN O29 C28 SING N N 36 
AKN C24 N25 SING N N 37 
AKN C24 C26 SING N N 38 
AKN C28 C26 SING N N 39 
AKN C28 C30 SING N N 40 
AKN C26 O27 SING N N 41 
AKN C30 O31 SING N N 42 
AKN C1  H1  SING N N 43 
AKN C3  H2  SING N N 44 
AKN C4  H3  SING N N 45 
AKN C5  H4  SING N N 46 
AKN C7  H5  SING N N 47 
AKN C9  H6  SING N N 48 
AKN C9  H7  SING N N 49 
AKN O6  H8  SING N N 50 
AKN N10 H9  SING N N 51 
AKN N10 H10 SING N N 52 
AKN C11 H12 SING N N 53 
AKN N12 H13 SING N N 54 
AKN C13 H14 SING N N 55 
AKN C13 H15 SING N N 56 
AKN C14 H16 SING N N 57 
AKN N15 H17 SING N N 58 
AKN N15 H18 SING N N 59 
AKN C16 H20 SING N N 60 
AKN C17 H21 SING N N 61 
AKN O18 H22 SING N N 62 
AKN C19 H23 SING N N 63 
AKN C21 H24 SING N N 64 
AKN C22 H25 SING N N 65 
AKN O23 H26 SING N N 66 
AKN C24 H27 SING N N 67 
AKN N25 H28 SING N N 68 
AKN N25 H29 SING N N 69 
AKN C26 H31 SING N N 70 
AKN O27 H32 SING N N 71 
AKN C28 H33 SING N N 72 
AKN C30 H34 SING N N 73 
AKN C30 H35 SING N N 74 
AKN O31 H36 SING N N 75 
AKN O32 H37 SING N N 76 
AKN O33 H38 SING N N 77 
AKN N37 H39 SING N N 78 
AKN N37 H40 SING N N 79 
AKN C37 H42 SING N N 80 
AKN C38 H43 SING N N 81 
AKN C38 H44 SING N N 82 
AKN C39 H45 SING N N 83 
AKN C39 H46 SING N N 84 
AKN O40 H47 SING N N 85 
# 
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 
AKN SMILES           ACDLabs              12.01 "O=C(NC3C(OC1OC(C(O)C(N)C1O)CO)C(O)C(OC2OC(CN)C(O)C(O)C2O)C(N)C3)C(O)CCN" 
AKN InChI            InChI                1.03  
"InChI=1S/C22H43N5O13/c23-2-1-8(29)20(36)27-7-3-6(25)18(39-22-16(34)15(33)13(31)9(4-24)37-22)17(35)19(7)40-21-14(32)11(26)12(30)10(5-28)38-21/h6-19,21-22,28-35H,1-5,23-26H2,(H,27,36)/t6-,7+,8-,9+,10+,11-,12+,13+,14+,15-,16+,17-,18+,19-,21+,22+/m0/s1" 
AKN InChIKey         InChI                1.03  LKCWBDHBTVXHDL-RMDFUYIESA-N 
AKN SMILES_CANONICAL CACTVS               3.385 "NCC[C@H](O)C(=O)N[C@@H]1C[C@H](N)[C@@H](O[C@H]2O[C@H](CN)[C@@H](O)[C@H](O)[C@H]2O)[C@H](O)[C@H]1O[C@H]3O[C@H](CO)[C@@H](O)[C@H](N)[C@H]3O" 
AKN SMILES           CACTVS               3.385 "NCC[CH](O)C(=O)N[CH]1C[CH](N)[CH](O[CH]2O[CH](CN)[CH](O)[CH](O)[CH]2O)[CH](O)[CH]1O[CH]3O[CH](CO)[CH](O)[CH](N)[CH]3O" 
AKN SMILES_CANONICAL "OpenEye OEToolkits" 1.9.2 "C1[C@@H]([C@H]([C@@H]([C@H]([C@@H]1NC(=O)[C@H](CCN)O)O[C@@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CO)O)N)O)O)O[C@@H]3[C@@H]([C@H]([C@@H]([C@H](O3)CN)O)O)O)N" 
AKN SMILES           "OpenEye OEToolkits" 1.9.2 "C1C(C(C(C(C1NC(=O)C(CCN)O)OC2C(C(C(C(O2)CO)O)N)O)O)OC3C(C(C(C(O3)CN)O)O)O)N" 
# 
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 
AKN "SYSTEMATIC NAME" ACDLabs              12.01 "(2S)-4-amino-N-{(1R,2S,3S,4R,5S)-5-amino-2-[(3-amino-3-deoxy-alpha-D-glucopyranosyl)oxy]-4-[(6-amino-6-deoxy-alpha-D-glucopyranosyl)oxy]-3-hydroxycyclohexyl}-2-hydroxybutanamide" 
AKN "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.9.2 
"(2S)-N-[(1R,2S,3S,4R,5S)-4-[(2R,3R,4S,5S,6R)-6-(aminomethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-5-azanyl-2-[(2S,3R,4S,5S,6R)-4-azanyl-6-(hydroxymethyl)-3,5-bis(oxidanyl)oxan-2-yl]oxy-3-oxidanyl-cyclohexyl]-4-azanyl-2-oxidanyl-butanamide" 
# 
_pdbx_chem_comp_synonyms.ordinal      1 
_pdbx_chem_comp_synonyms.comp_id      AKN 
_pdbx_chem_comp_synonyms.name         AMIKACIN 
_pdbx_chem_comp_synonyms.provenance   ? 
_pdbx_chem_comp_synonyms.type         ? 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
AKN "Create component"   2006-02-28 RCSB 
AKN "Modify descriptor"  2011-06-04 RCSB 
AKN "Other modification" 2014-03-13 RCSB 
AKN "Modify descriptor"  2014-09-05 RCSB 
AKN "Modify synonyms"    2020-06-05 PDBE 
# 
