data_R7Y # _chem_comp.id R7Y _chem_comp.name ;(1S,2S,3R,4S,6R)-3-{[2-(acetylamino)-6-amino-2,3,6-trideoxy-alpha-D-ribo-hexopyranosyl]oxy}-4,6-diamino-2-hydroxycycloh exyl 3-amino-3-deoxy-alpha-D-glucopyranoside ; _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C20 H39 N5 O10" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms acetylated-tobramycin _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2020-02-07 _chem_comp.pdbx_modified_date 2021-05-28 _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 509.551 _chem_comp.one_letter_code ? _chem_comp.three_letter_code R7Y _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 6VR2 _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 R7Y C01 C1 C 0 1 N N N -14.157 14.298 21.609 -2.503 4.610 2.177 C01 R7Y 1 R7Y C02 C2 C 0 1 N N N -12.666 13.994 21.530 -3.174 3.740 1.145 C02 R7Y 2 R7Y C05 C3 C 0 1 N N R -10.668 13.225 20.274 -3.436 1.615 -0.018 C05 R7Y 3 R7Y C06 C4 C 0 1 N N N -9.862 14.434 20.018 -4.702 0.996 0.581 C06 R7Y 4 R7Y C07 C5 C 0 1 N N S -8.422 14.091 20.033 -5.333 0.054 -0.450 C07 R7Y 5 R7Y C09 C6 C 0 1 N N R -8.099 12.928 19.099 -4.305 -1.005 -0.858 C09 R7Y 6 R7Y C10 C7 C 0 1 N N N -6.715 12.355 19.373 -4.907 -1.914 -1.932 C10 R7Y 7 R7Y C13 C8 C 0 1 N N R -10.412 12.170 19.214 -2.481 0.497 -0.444 C13 R7Y 8 R7Y C15 C9 C 0 1 N N R -10.410 11.991 16.788 -0.980 -1.128 0.480 C15 R7Y 9 R7Y C16 C10 C 0 1 N N S -10.738 12.932 15.616 -1.091 -2.346 1.399 C16 R7Y 10 R7Y C18 C11 C 0 1 N N N -10.396 12.313 14.251 0.099 -3.277 1.158 C18 R7Y 11 R7Y C19 C12 C 0 1 N N R -11.037 10.933 14.077 1.400 -2.529 1.456 C19 R7Y 12 R7Y C21 C13 C 0 1 N N S -10.660 9.988 15.224 1.511 -1.311 0.537 C21 R7Y 13 R7Y C23 C14 C 0 1 N N S -10.456 7.737 14.583 3.845 -1.067 0.052 C23 R7Y 14 R7Y C25 C15 C 0 1 N N R -10.777 6.402 16.578 3.571 0.747 -1.493 C25 R7Y 15 R7Y C26 C16 C 0 1 N N N -10.025 5.708 17.717 3.378 1.056 -2.979 C26 R7Y 16 R7Y C28 C17 C 0 1 N N S -11.602 5.389 15.783 4.845 1.431 -0.991 C28 R7Y 17 R7Y C30 C18 C 0 1 N N S -12.266 6.062 14.657 5.063 1.069 0.482 C30 R7Y 18 R7Y C32 C19 C 0 1 N N R -11.307 6.745 13.782 5.130 -0.455 0.616 C32 R7Y 19 R7Y C34 C20 C 0 1 N N S -11.059 10.604 16.575 0.321 -0.380 0.778 C34 R7Y 20 R7Y N04 N1 N 0 1 N N N -12.098 13.511 20.290 -2.783 2.461 0.985 N04 R7Y 21 R7Y N11 N2 N 0 1 N N N -6.386 11.520 18.232 -3.966 -3.000 -2.237 N11 R7Y 22 R7Y N17 N3 N 0 1 N N N -10.043 14.213 15.794 -2.340 -3.064 1.113 N17 R7Y 23 R7Y N20 N4 N 0 1 N N N -10.700 10.374 12.770 2.543 -3.423 1.225 N20 R7Y 24 R7Y N31 N5 N 0 1 N N N -13.035 5.101 13.887 6.322 1.662 0.952 N31 R7Y 25 R7Y O03 O1 O 0 1 N N N -11.966 14.137 22.481 -4.067 4.192 0.459 O03 R7Y 26 R7Y O08 O2 O 0 1 N N N -7.650 15.175 19.597 -6.476 -0.584 0.123 O08 R7Y 27 R7Y O12 O3 O 0 1 N N N -9.007 11.791 19.223 -3.140 -0.361 -1.378 O12 R7Y 28 R7Y O14 O4 O 0 1 N N N -10.824 12.671 17.963 -2.092 -0.259 0.705 O14 R7Y 29 R7Y O22 O5 O 0 1 N N N -11.314 8.740 15.074 2.726 -0.613 0.815 O22 R7Y 30 R7Y O24 O6 O 0 1 N N N -9.812 7.072 15.710 3.687 -0.665 -1.311 O24 R7Y 31 R7Y O27 O7 O 0 1 N N N -8.958 4.980 17.168 2.141 0.497 -3.425 O27 R7Y 32 R7Y O29 O8 O 0 1 N N N -12.565 4.800 16.618 4.708 2.848 -1.118 O29 R7Y 33 R7Y O33 O9 O 0 1 N N N -12.003 7.435 12.783 5.261 -0.808 1.995 O33 R7Y 34 R7Y O35 O10 O 0 1 N N N -10.703 9.698 17.591 0.424 0.757 -0.081 O35 R7Y 35 R7Y H1 H1 H 0 1 N N N -14.409 14.639 22.624 -3.032 4.521 3.126 H1 R7Y 36 R7Y H2 H2 H 0 1 N N N -14.409 15.086 20.884 -1.469 4.289 2.305 H2 R7Y 37 R7Y H3 H3 H 0 1 N N N -14.729 13.388 21.375 -2.523 5.648 1.846 H3 R7Y 38 R7Y H4 H4 H 0 1 N N N -10.377 12.808 21.249 -3.701 2.219 -0.886 H4 R7Y 39 R7Y H5 H5 H 0 1 N N N -10.067 15.181 20.799 -4.444 0.433 1.478 H5 R7Y 40 R7Y H6 H6 H 0 1 N N N -10.128 14.848 19.034 -5.410 1.785 0.834 H6 R7Y 41 R7Y H7 H7 H 0 1 N N N -8.132 13.807 21.055 -5.636 0.625 -1.327 H7 R7Y 42 R7Y H8 H8 H 0 1 N N N -8.122 13.299 18.064 -4.033 -1.602 0.012 H8 R7Y 43 R7Y H9 H9 H 0 1 N N N -6.727 11.754 20.294 -5.843 -2.336 -1.567 H9 R7Y 44 R7Y H10 H10 H 0 1 N N N -5.980 13.167 19.475 -5.097 -1.333 -2.834 H10 R7Y 45 R7Y H11 H11 H 0 1 N N N -11.016 11.286 19.467 -1.596 0.931 -0.910 H11 R7Y 46 R7Y H12 H12 H 0 1 N N N -9.319 11.851 16.812 -0.981 -1.457 -0.560 H12 R7Y 47 R7Y H13 H13 H 0 1 N N N -11.822 13.119 15.634 -1.091 -2.017 2.439 H13 R7Y 48 R7Y H14 H14 H 0 1 N N N -9.304 12.211 14.170 0.020 -4.144 1.813 H14 R7Y 49 R7Y H15 H15 H 0 1 N N N -10.763 12.979 13.456 0.099 -3.605 0.119 H15 R7Y 50 R7Y H16 H16 H 0 1 N N N -12.127 11.073 14.117 1.400 -2.201 2.496 H16 R7Y 51 R7Y H17 H17 H 0 1 N N N -9.569 9.846 15.215 1.510 -1.640 -0.503 H17 R7Y 52 R7Y H18 H18 H 0 1 N N N -9.694 8.170 13.919 3.905 -2.154 0.106 H18 R7Y 53 R7Y H19 H19 H 0 1 N N N -11.460 7.147 17.012 2.713 1.117 -0.931 H19 R7Y 54 R7Y H20 H20 H 0 1 N N N -9.638 6.461 18.419 3.364 2.135 -3.127 H20 R7Y 55 R7Y H21 H21 H 0 1 N N N -10.705 5.026 18.249 4.199 0.622 -3.550 H21 R7Y 56 R7Y H22 H22 H 0 1 N N N -10.921 4.619 15.391 5.697 1.093 -1.580 H22 R7Y 57 R7Y H23 H23 H 0 1 N N N -12.957 6.814 15.065 4.235 1.452 1.078 H23 R7Y 58 R7Y H24 H24 H 0 1 N N N -10.636 6.000 13.330 5.988 -0.833 0.060 H24 R7Y 59 R7Y H25 H25 H 0 1 N N N -12.150 10.742 16.572 0.321 -0.052 1.817 H25 R7Y 60 R7Y H26 H26 H 0 1 N N N -12.664 13.379 19.476 -2.070 2.099 1.534 H26 R7Y 61 R7Y H27 H27 H 0 1 N N N -5.480 11.117 18.363 -3.723 -3.513 -1.404 H27 R7Y 62 R7Y H28 H28 H 0 1 N N N -7.065 10.791 18.145 -4.341 -3.615 -2.944 H28 R7Y 63 R7Y H30 H30 H 0 1 N N N -10.278 14.599 16.686 -2.381 -3.936 1.619 H30 R7Y 64 R7Y H31 H31 H 0 1 N N N -9.055 14.066 15.744 -3.143 -2.489 1.319 H31 R7Y 65 R7Y H33 H33 H 0 1 N N N -11.125 9.474 12.672 2.493 -4.235 1.821 H33 R7Y 66 R7Y H34 H34 H 0 1 N N N -11.037 10.982 12.051 2.602 -3.690 0.254 H34 R7Y 67 R7Y H36 H36 H 0 1 N N N -13.687 4.638 14.487 6.488 1.436 1.922 H36 R7Y 68 R7Y H37 H37 H 0 1 N N N -13.530 5.577 13.160 7.097 1.370 0.375 H37 R7Y 69 R7Y H39 H39 H 0 1 N N N -7.818 15.928 20.152 -7.167 0.029 0.408 H39 R7Y 70 R7Y H40 H40 H 0 1 N N N -8.481 4.543 17.864 1.953 0.654 -4.361 H40 R7Y 71 R7Y H41 H41 H 0 1 N N N -12.132 4.366 17.344 4.562 3.149 -2.026 H41 R7Y 72 R7Y H42 H42 H 0 1 N N N -12.532 6.823 12.284 5.305 -1.760 2.155 H42 R7Y 73 R7Y H43 H43 H 0 1 N N N -10.941 10.060 18.436 1.194 1.315 0.096 H43 R7Y 74 # # 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 R7Y N20 C19 SING N N 1 R7Y O33 C32 SING N N 2 R7Y C32 C23 SING N N 3 R7Y C32 C30 SING N N 4 R7Y N31 C30 SING N N 5 R7Y C19 C18 SING N N 6 R7Y C19 C21 SING N N 7 R7Y C18 C16 SING N N 8 R7Y C23 O22 SING N N 9 R7Y C23 O24 SING N N 10 R7Y C30 C28 SING N N 11 R7Y O22 C21 SING N N 12 R7Y C21 C34 SING N N 13 R7Y C16 N17 SING N N 14 R7Y C16 C15 SING N N 15 R7Y O24 C25 SING N N 16 R7Y C28 C25 SING N N 17 R7Y C28 O29 SING N N 18 R7Y C34 C15 SING N N 19 R7Y C34 O35 SING N N 20 R7Y C25 C26 SING N N 21 R7Y C15 O14 SING N N 22 R7Y O27 C26 SING N N 23 R7Y O14 C13 SING N N 24 R7Y N11 C10 SING N N 25 R7Y C09 O12 SING N N 26 R7Y C09 C10 SING N N 27 R7Y C09 C07 SING N N 28 R7Y C13 O12 SING N N 29 R7Y C13 C05 SING N N 30 R7Y O08 C07 SING N N 31 R7Y C06 C07 SING N N 32 R7Y C06 C05 SING N N 33 R7Y C05 N04 SING N N 34 R7Y N04 C02 SING N N 35 R7Y C02 C01 SING N N 36 R7Y C02 O03 DOUB N N 37 R7Y C01 H1 SING N N 38 R7Y C01 H2 SING N N 39 R7Y C01 H3 SING N N 40 R7Y C05 H4 SING N N 41 R7Y C06 H5 SING N N 42 R7Y C06 H6 SING N N 43 R7Y C07 H7 SING N N 44 R7Y C09 H8 SING N N 45 R7Y C10 H9 SING N N 46 R7Y C10 H10 SING N N 47 R7Y C13 H11 SING N N 48 R7Y C15 H12 SING N N 49 R7Y C16 H13 SING N N 50 R7Y C18 H14 SING N N 51 R7Y C18 H15 SING N N 52 R7Y C19 H16 SING N N 53 R7Y C21 H17 SING N N 54 R7Y C23 H18 SING N N 55 R7Y C25 H19 SING N N 56 R7Y C26 H20 SING N N 57 R7Y C26 H21 SING N N 58 R7Y C28 H22 SING N N 59 R7Y C30 H23 SING N N 60 R7Y C32 H24 SING N N 61 R7Y C34 H25 SING N N 62 R7Y N04 H26 SING N N 63 R7Y N11 H27 SING N N 64 R7Y N11 H28 SING N N 65 R7Y N17 H30 SING N N 66 R7Y N17 H31 SING N N 67 R7Y N20 H33 SING N N 68 R7Y N20 H34 SING N N 69 R7Y N31 H36 SING N N 70 R7Y N31 H37 SING N N 71 R7Y O08 H39 SING N N 72 R7Y O27 H40 SING N N 73 R7Y O29 H41 SING N N 74 R7Y O33 H42 SING N N 75 R7Y O35 H43 SING N N 76 # # 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 R7Y SMILES ACDLabs 12.01 "CC(=O)NC1CC(C(OC1OC2C(N)CC(C(C2O)OC3OC(CO)C(O)C(C3O)N)N)CN)O" R7Y InChI InChI 1.03 "InChI=1S/C20H39N5O10/c1-6(27)25-9-3-10(28)11(4-21)32-19(9)34-17-7(22)2-8(23)18(16(17)31)35-20-15(30)13(24)14(29)12(5-26)33-20/h7-20,26,28-31H,2-5,21-24H2,1H3,(H,25,27)/t7-,8+,9+,10-,11+,12+,13-,14+,15+,16-,17+,18-,19+,20+/m0/s1" R7Y InChIKey InChI 1.03 DMDYSSAQCCMAGB-VMNCQBCKSA-N R7Y SMILES_CANONICAL CACTVS 3.385 "CC(=O)N[C@@H]1C[C@H](O)[C@@H](CN)O[C@@H]1O[C@@H]2[C@@H](N)C[C@@H](N)[C@H](O[C@H]3O[C@H](CO)[C@@H](O)[C@H](N)[C@H]3O)[C@H]2O" R7Y SMILES CACTVS 3.385 "CC(=O)N[CH]1C[CH](O)[CH](CN)O[CH]1O[CH]2[CH](N)C[CH](N)[CH](O[CH]3O[CH](CO)[CH](O)[CH](N)[CH]3O)[CH]2O" R7Y SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC(=O)N[C@@H]1C[C@@H]([C@H](O[C@@H]1O[C@@H]2[C@H](C[C@H]([C@@H]([C@H]2O)O[C@@H]3[C@@H]([C@H]([C@@H]([C@H](O3)CO)O)N)O)N)N)CN)O" R7Y SMILES "OpenEye OEToolkits" 2.0.7 "CC(=O)NC1CC(C(OC1OC2C(CC(C(C2O)OC3C(C(C(C(O3)CO)O)N)O)N)N)CN)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 R7Y "SYSTEMATIC NAME" ACDLabs 12.01 "(1S,2S,3R,4S,6R)-3-{[2-(acetylamino)-6-amino-2,3,6-trideoxy-alpha-D-ribo-hexopyranosyl]oxy}-4,6-diamino-2-hydroxycyclohexyl 3-amino-3-deoxy-alpha-D-glucopyranoside" R7Y "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "~{N}-[(2~{R},3~{R},5~{S},6~{R})-6-(aminomethyl)-2-[(1~{R},2~{S},3~{S},4~{R},6~{S})-4,6-bis(azanyl)-3-[(2~{S},3~{R},4~{S},5~{S},6~{R})-4-azanyl-6-(hydroxymethyl)-3,5-bis(oxidanyl)oxan-2-yl]oxy-2-oxidanyl-cyclohexyl]oxy-5-oxidanyl-oxan-3-yl]ethanamide" # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id R7Y _pdbx_chem_comp_synonyms.name acetylated-tobramycin _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 R7Y "Create component" 2020-02-07 RCSB R7Y "Modify synonyms" 2020-02-07 RCSB R7Y "Modify synonyms" 2020-06-05 PDBE R7Y "Initial release" 2021-06-02 RCSB ##