data_TOY
#
_chem_comp.id TOY
_chem_comp.name TOBRAMYCIN
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAD
_chem_comp.formula "C18 H37 N5 O9"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms
4-AMINO-2-[4,6-DIAMINO-3-(3-AMINO-6-AMINOMETHYL-5-HYDROXY-TETRAHYDRO-PYRAN-2-YLOXY)-2-HYDROXY-CYCLOHEXYLOXY]-6-HYDROXYMETHYL-TETRAHYDRO-PYRAN-3,5-DIOL
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2002-04-09
_chem_comp.pdbx_modified_date 2021-03-13
_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 467.514
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code TOY
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details ?
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 1LC4
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site EBI
#
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
TOY C11 C11 C 0 1 N N R N N N 11.840 -7.108 5.575 -1.142 -0.196 -2.574 C11 TOY 1
TOY O11 O11 O 0 1 N N N N N N 13.055 -7.680 5.183 0.028 -0.989 -2.371 O11 TOY 2
TOY C21 C21 C 0 1 N N R N N N 10.692 -7.628 4.673 -2.181 -1.012 -3.346 C21 TOY 3
TOY N21 N21 N 0 1 N N N N N N 10.573 -9.108 4.690 -2.551 -2.200 -2.565 N21 TOY 4
TOY C31 C31 C 0 1 N N N N N N 10.848 -7.107 3.231 -1.580 -1.445 -4.688 C31 TOY 5
TOY C41 C41 C 0 1 N N S N N N 10.940 -5.573 3.252 -1.058 -0.200 -5.414 C41 TOY 6
TOY O41 O41 O 0 1 N N N N N N 11.078 -5.083 1.923 -0.362 -0.593 -6.598 O41 TOY 7
TOY C51 C51 C 0 1 N N R N N N 12.136 -5.142 4.130 -0.102 0.554 -4.486 C51 TOY 8
TOY O51 O51 O 0 1 N N N N N N 11.964 -5.655 5.484 -0.799 0.973 -3.315 O51 TOY 9
TOY C61 C61 C 0 1 N N N N N N 12.296 -3.629 4.239 0.451 1.780 -5.215 C61 TOY 10
TOY N61 N61 N 0 1 N N N N N N 12.888 -3.046 3.011 1.371 2.503 -4.326 N61 TOY 11
TOY C12 C12 C 0 1 N N R N N N 16.671 -8.899 7.111 2.642 -0.465 0.915 C12 TOY 12
TOY N12 N12 N 0 1 N N N N N N 17.844 -8.943 8.018 3.431 0.201 1.959 N12 TOY 13
TOY C22 C22 C 0 1 N N N N N N 16.702 -7.619 6.265 3.100 0.022 -0.460 C22 TOY 14
TOY C32 C32 C 0 1 N N S N N N 15.481 -7.595 5.314 2.277 -0.671 -1.547 C32 TOY 15
TOY N32 N32 N 0 1 N N N N N N 15.602 -6.428 4.401 2.717 -0.203 -2.868 N32 TOY 16
TOY C42 C42 C 0 1 N N R N N N 14.164 -7.620 6.118 0.796 -0.341 -1.356 C42 TOY 17
TOY C52 C52 C 0 1 N N S N N N 14.122 -8.865 7.052 0.338 -0.829 0.019 C52 TOY 18
TOY O52 O52 O 0 1 N N N N N N 12.973 -8.788 7.881 -1.045 -0.520 0.198 O52 TOY 19
TOY C62 C62 C 0 1 N N S N N N 15.384 -8.933 7.949 1.160 -0.134 1.107 C62 TOY 20
TOY O62 O62 O 0 1 N N N N N N 15.356 -10.153 8.726 0.732 -0.590 2.392 O62 TOY 21
TOY C13 C13 C 0 1 N N S N N N 15.424 -10.045 10.116 0.951 0.485 3.306 C13 TOY 22
TOY C23 C23 C 0 1 N N R N N N 15.972 -11.354 10.714 0.886 -0.043 4.740 C23 TOY 23
TOY O23 O23 O 0 1 N N N N N N 17.273 -11.609 10.210 1.910 -1.021 4.936 O23 TOY 24
TOY C33 C33 C 0 1 N N S N N N 15.035 -12.506 10.356 -0.484 -0.683 4.976 C33 TOY 25
TOY N33 N33 N 0 1 N N N N N N 15.568 -13.807 10.829 -0.621 -1.059 6.389 N33 TOY 26
TOY C43 C43 C 0 1 N N S N N N 13.653 -12.229 10.970 -1.569 0.334 4.607 C43 TOY 27
TOY O43 O43 O 0 1 N N N N N N 12.748 -13.280 10.641 -2.854 -0.286 4.677 O43 TOY 28
TOY C53 C53 C 0 1 N N R N N N 13.107 -10.869 10.470 -1.320 0.835 3.183 C53 TOY 29
TOY O53 O53 O 0 1 N N N N N N 14.090 -9.783 10.648 -0.050 1.482 3.114 O53 TOY 30
TOY C63 C63 C 0 1 N N N N N N 11.851 -10.453 11.213 -2.418 1.828 2.795 C63 TOY 31
TOY O63 O63 O 0 1 N N N N N N 12.112 -10.225 12.594 -2.245 2.221 1.432 O63 TOY 32
TOY H11 H11 H 0 1 N N N N N N 11.598 -7.392 6.626 -1.554 0.094 -1.608 H11 TOY 33
TOY H21 H21 H 0 1 N N N N N N 9.743 -7.226 5.099 -3.067 -0.402 -3.523 H21 TOY 34
TOY HN21 1HN2 H 0 0 N N N N N N 10.475 -9.456 5.644 -3.234 -2.704 -3.111 HN21 TOY 35
TOY HN22 2HN2 H 0 0 N N N N N N 9.817 -9.450 4.096 -1.729 -2.784 -2.518 HN22 TOY 36
TOY H311 1H31 H 0 0 N N N N N N 10.036 -7.472 2.560 -0.758 -2.139 -4.514 H311 TOY 37
TOY H312 2H31 H 0 0 N N N N N N 11.712 -7.575 2.704 -2.347 -1.926 -5.294 H312 TOY 38
TOY H41 H41 H 0 1 N N N N N N 10.008 -5.142 3.688 -1.895 0.444 -5.680 H41 TOY 39
TOY H41O OH41 H 0 0 N N N N N N 11.135 -4.135 1.936 -0.997 -1.071 -7.150 H41O TOY 40
TOY H51 H51 H 0 1 N N N N N N 13.043 -5.558 3.633 0.720 -0.101 -4.203 H51 TOY 41
TOY H611 1H61 H 0 0 N N N N N N 12.882 -3.348 5.145 -0.370 2.436 -5.499 H611 TOY 42
TOY H612 2H61 H 0 0 N N N N N N 11.329 -3.137 4.496 0.986 1.460 -6.109 H612 TOY 43
TOY HN61 1HN6 H 0 0 N N N N N N 12.352 -3.303 2.183 1.710 3.299 -4.846 HN61 TOY 44
TOY HN62 2HN6 H 0 0 N N N N N N 12.995 -2.034 3.084 0.814 2.867 -3.568 HN62 TOY 45
TOY H12 H12 H 0 1 N N N N N N 16.701 -9.780 6.429 2.785 -1.543 0.984 H12 TOY 46
TOY HN11 1HN1 H 0 0 N N N N N N 17.910 -8.105 8.597 4.396 -0.043 1.794 HN11 TOY 47
TOY HN12 2HN1 H 0 0 N N N N N N 17.823 -9.794 8.580 3.352 1.193 1.794 HN12 TOY 48
TOY H221 1H22 H 0 0 N N N N N N 17.665 -7.501 5.716 4.155 -0.212 -0.596 H221 TOY 49
TOY H222 2H22 H 0 0 N N N N N N 16.763 -6.700 6.894 2.956 1.101 -0.529 H222 TOY 50
TOY H32 H32 H 0 1 N N N N N N 15.461 -8.512 4.680 2.421 -1.750 -1.478 H32 TOY 51
TOY HN1 1HN H 0 1 N N N N N N 16.488 -6.420 3.896 3.723 -0.277 -2.882 HN1 TOY 52
TOY HN2 2HN H 0 1 N N N N N N 14.797 -6.412 3.774 2.368 -0.867 -3.542 HN2 TOY 53
TOY H42 H42 H 0 1 N N N N N N 14.094 -6.702 6.747 0.653 0.737 -1.425 H42 TOY 54
TOY H52 H52 H 0 1 N N N N N N 14.086 -9.780 6.416 0.481 -1.907 0.088 H52 TOY 55
TOY H52O OH52 H 0 0 N N N N N N 12.947 -9.548 8.451 -1.325 -0.955 1.015 H52O TOY 56
TOY H62 H62 H 0 1 N N N N N N 15.379 -8.043 8.621 1.017 0.943 1.037 H62 TOY 57
TOY H13 H13 H 0 1 N N N N N N 16.105 -9.205 10.389 1.934 0.921 3.124 H13 TOY 58
TOY H23 H23 H 0 1 N N N N N N 16.031 -11.259 11.823 1.029 0.779 5.440 H23 TOY 59
TOY H23O OH23 H 0 0 N N N N N N 17.611 -12.416 10.579 2.754 -0.577 4.778 H23O TOY 60
TOY H33 H33 H 0 1 N N N N N N 14.949 -12.573 9.246 -0.587 -1.570 4.350 H33 TOY 61
TOY HN31 1HN3 H 0 0 N N N N N N 15.769 -13.787 11.829 0.110 -1.726 6.584 HN31 TOY 62
TOY HN32 2HN3 H 0 0 N N N N N N 14.942 -14.576 10.590 -0.411 -0.233 6.930 HN32 TOY 63
TOY H43 H43 H 0 1 N N N N N N 13.756 -12.183 12.079 -1.532 1.174 5.301 H43 TOY 64
TOY H43O OH43 H 0 0 N N N N N N 11.894 -13.109 11.020 -3.504 0.386 4.432 H43O TOY 65
TOY H53 H53 H 0 1 N N N N N N 12.885 -11.022 9.388 -1.335 -0.008 2.494 H53 TOY 66
TOY H631 1H63 H 0 0 N N N N N N 11.029 -11.193 11.070 -3.393 1.356 2.916 H631 TOY 67
TOY H632 2H63 H 0 0 N N N N N N 11.371 -9.566 10.737 -2.357 2.707 3.437 H632 TOY 68
TOY H63O OH63 H 0 0 N N N N N N 11.326 -9.965 13.059 -2.905 2.903 1.252 H63O TOY 69
#
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
TOY C11 O11 SING N N 1
TOY C11 C21 SING N N 2
TOY C11 O51 SING N N 3
TOY C11 H11 SING N N 4
TOY O11 C42 SING N N 5
TOY C21 N21 SING N N 6
TOY C21 C31 SING N N 7
TOY C21 H21 SING N N 8
TOY N21 HN21 SING N N 9
TOY N21 HN22 SING N N 10
TOY C31 C41 SING N N 11
TOY C31 H311 SING N N 12
TOY C31 H312 SING N N 13
TOY C41 O41 SING N N 14
TOY C41 C51 SING N N 15
TOY C41 H41 SING N N 16
TOY O41 H41O SING N N 17
TOY C51 O51 SING N N 18
TOY C51 C61 SING N N 19
TOY C51 H51 SING N N 20
TOY C61 N61 SING N N 21
TOY C61 H611 SING N N 22
TOY C61 H612 SING N N 23
TOY N61 HN61 SING N N 24
TOY N61 HN62 SING N N 25
TOY C12 N12 SING N N 26
TOY C12 C22 SING N N 27
TOY C12 C62 SING N N 28
TOY C12 H12 SING N N 29
TOY N12 HN11 SING N N 30
TOY N12 HN12 SING N N 31
TOY C22 C32 SING N N 32
TOY C22 H221 SING N N 33
TOY C22 H222 SING N N 34
TOY C32 N32 SING N N 35
TOY C32 C42 SING N N 36
TOY C32 H32 SING N N 37
TOY N32 HN1 SING N N 38
TOY N32 HN2 SING N N 39
TOY C42 C52 SING N N 40
TOY C42 H42 SING N N 41
TOY C52 O52 SING N N 42
TOY C52 C62 SING N N 43
TOY C52 H52 SING N N 44
TOY O52 H52O SING N N 45
TOY C62 O62 SING N N 46
TOY C62 H62 SING N N 47
TOY O62 C13 SING N N 48
TOY C13 C23 SING N N 49
TOY C13 O53 SING N N 50
TOY C13 H13 SING N N 51
TOY C23 O23 SING N N 52
TOY C23 C33 SING N N 53
TOY C23 H23 SING N N 54
TOY O23 H23O SING N N 55
TOY C33 N33 SING N N 56
TOY C33 C43 SING N N 57
TOY C33 H33 SING N N 58
TOY N33 HN31 SING N N 59
TOY N33 HN32 SING N N 60
TOY C43 O43 SING N N 61
TOY C43 C53 SING N N 62
TOY C43 H43 SING N N 63
TOY O43 H43O SING N N 64
TOY C53 O53 SING N N 65
TOY C53 C63 SING N N 66
TOY C53 H53 SING N N 67
TOY C63 O63 SING N N 68
TOY C63 H631 SING N N 69
TOY C63 H632 SING N N 70
TOY O63 H63O SING N N 71
#
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
TOY SMILES ACDLabs 10.04 O(C2C(O)C(OC1OC(CN)C(O)CC1N)C(N)CC2N)C3OC(C(O)C(N)C3O)CO
TOY SMILES_CANONICAL CACTVS 3.341 NC[C@H]1O[C@H](O[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)[C@H](N)C[C@@H]1O
TOY SMILES CACTVS 3.341 NC[CH]1O[CH](O[CH]2[CH](N)C[CH](N)[CH](O[CH]3O[CH](CO)[CH](O)[CH](N)[CH]3O)[CH]2O)[CH](N)C[CH]1O
TOY SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C1[C@@H]([C@H]([C@@H]([C@H]([C@@H]1N)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[C@@H]([C@H](O3)CN)O)N)N
TOY SMILES "OpenEye OEToolkits" 1.5.0 C1C(C(C(C(C1N)OC2C(C(C(C(O2)CO)O)N)O)O)OC3C(CC(C(O3)CN)O)N)N
TOY InChI InChI 1.03 InChI=1S/C18H37N5O9/c19-3-9-8(25)2-7(22)17(29-9)31-15-5(20)1-6(21)16(14(15)28)32-18-13(27)11(23)12(26)10(4-24)30-18/h5-18,24-28H,1-4,19-23H2/t5-,6+,7+,8-,9+,10+,11-,12+,13+,14-,15+,16-,17+,18+/m0/s1
TOY InChIKey InChI 1.03 NLVFBUXFDBBNBW-PBSUHMDJSA-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
TOY "SYSTEMATIC NAME" ACDLabs 10.04 "(1S,2S,3R,4S,6R)-4,6-diamino-3-[(2,6-diamino-2,3,6-trideoxy-alpha-D-ribo-hexopyranosyl)oxy]-2-hydroxycyclohexyl 3-amino-3-deoxy-alpha-D-glucopyranoside"
TOY "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 (2S,3R,4S,5S,6R)-4-amino-2-[(1S,2S,3R,4S,6R)-4,6-diamino-3-[(2R,3R,5S,6R)-3-amino-6-(aminomethyl)-5-hydroxy-oxan-2-yl]oxy-2-hydroxy-cyclohexyl]oxy-6-(hydroxymethyl)oxane-3,5-diol
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
TOY 'Create component' 2002-04-09 EBI
TOY 'Modify descriptor' 2011-06-04 RCSB
TOY 'Modify synonyms' 2021-03-13 RCSB
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id TOY
_pdbx_chem_comp_synonyms.name
4-AMINO-2-[4,6-DIAMINO-3-(3-AMINO-6-AMINOMETHYL-5-HYDROXY-TETRAHYDRO-PYRAN-2-YLOXY)-2-HYDROXY-CYCLOHEXYLOXY]-6-HYDROXYMETHYL-TETRAHYDRO-PYRAN-3,5-DIOL
_pdbx_chem_comp_synonyms.provenance PDB
_pdbx_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_drugbank_details.comp_id TOY
_pdbe_chem_comp_drugbank_details.drugbank_id DB00684
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name Tobramycin
_pdbe_chem_comp_drugbank_details.description
'Aminoglycosides, many of which are derived directly from _Streptomyces_ spp., are concentration-dependent bactericidal antibiotics with a broad spectrum of activity against Gram-positive and Gram-negative organisms.[A232294] Inhaled tobramycin is notable for its use in treating chronic _Pseudomonas aeruginosa_ infections in cystic fibrosis patients, as _P. aeruginosa_ is notoriously inherently resistant to many antibiotics.[A232294, A232299, L32739] However, tobramycin can also be administered intravenously and topically to treat a variety of infections caused by susceptible bacteria.[L32744, L32749] Its use is limited in some cases by characteristic toxicities such as nephrotoxicity and ototoxicity, yet it remains a valuable option in the face of growing resistance to front-line antibiotics such as β-lactams and cephalosporins.[A232294, A232349, L32739, L32749]  Tobramycin was approved by the FDA in 1975 and is currently available in a variety of forms for administration by inhalation, injection, and external application to the eye (ophthalmic).[L32739, L32744, L32749]'
_pdbe_chem_comp_drugbank_details.cas_number 32986-56-4
_pdbe_chem_comp_drugbank_details.mechanism_of_action
'Tobramycin is a 4,6-disubstituted 2-deoxystreptamine (DOS) ring-containing aminoglycoside antibiotic with activity against various Gram-negative and some Gram-positive bacteria.[L32739, L32744, L32749] The mechanism of action of tobramycin has not been unambiguously elucidated, and some insights into its mechanism rely on results using similar aminoglycosides. In general, like other aminoglycosides, tobramycin is bactericidal and exhibits both immediate and delayed killing, which are attributed to different mechanisms, as outlined below.[A232294, A232299]  Aminoglycosides are polycationic at physiological pH, such that they readily bind to bacterial membranes ("ionic binding"); this includes binding to lipopolysaccharide and phospholipids within the outer membrane of Gram-negative bacteria and to teichoic acid and phospholipids within the cell membrane of Gram-positive bacteria. This binding displaces divalent cations and increases membrane permeability, which allows aminoglycoside entry.[A232294, A232304, A232309, A232314] Additional aminoglycoside entry ("energy-dependent phase I") into the cytoplasm requires the proton-motive force, allowing access of the aminoglycoside to its primary intracellular target of the bacterial 30S ribosome.[A232294, A232314] Mistranslated proteins produced as a result of aminoglycoside binding to the ribosome (see below) integrate into and disrupt the cell membrane, which allows more of the aminoglycoside into the cell ("energy-dependent phase II").[A232294, A232314, A232319] Hence, tobramycin and other aminoglycosides have both immediate bactericidal effects through membrane disruption and delayed bactericidal effects through impaired protein synthesis; observed experimental data and mathematical modelling support this two-mechanism model.[A232294, A232299]  Inhibition of protein synthesis was the first recognized effect of aminoglycoside antibiotics. Structural and cell biological studies suggest that aminoglycosides bind to the 16S rRNA in helix 44 (h44), near the A site of the 30S ribosomal subunit, altering interactions between h44 and h45. This binding also displaces two important residues, A1492 and A1493, from h44, mimicking normal conformational changes that occur with successful codon-anticodon pairing in the A site.[A232324, A232329] Overall, aminoglycoside binding has several negative effects, including inhibiting translation initiation and elongation and ribosome recycling.[A232294, A232334, A232339] Recent evidence suggests that the latter effect is due to a cryptic second binding site situated in h69 of the 23S rRNA of the 50S ribosomal subunit.[A232329, A232339] Also, by stabilizing a conformation that mimics correct codon-anticodon pairing, aminoglycosides promote error-prone translation;[A232344] mistranslated proteins can incorporate into the cell membrane, inducing the damage discussed above.[A232294, A232319]  Although direct mutation of the 16S rRNA is a rare resistance mechanism, due to the gene being present in numerous copies, posttranscriptional 16S rRNA modification by 16S rRNA methyltransferases (16S-RMTases) at the N7 position of G1405 or the N1 position of A1408 are common resistance mechanisms in aminoglycoside-resistant bacteria.[A232294, A232349] These mutants also further support the proposed mechanism of action of aminoglycosides. Direct modification of the aminoglycoside itself through acetylation, adenylation, and phosphorylation by aminoglycoside-modifying enzymes (AMEs) are also commonly encountered resistance mutations.[A232294, A232349] Finally, due to the requirement for active transport of aminoglycosides across bacterial membranes, they are not active against obligately anaerobic bacteria.[A232294]'
#
loop_
_pdbe_chem_comp_synonyms.comp_id
_pdbe_chem_comp_synonyms.name
_pdbe_chem_comp_synonyms.provenance
_pdbe_chem_comp_synonyms.type
TOY Aktob ChEMBL Tradename
TOY Bethkis ChEMBL Tradename
TOY Nebicin ChEMBL Tradename
TOY Nebramycin ChEMBL Tradename
TOY Obramycin ChEMBL Tradename
TOY Tobi ChEMBL Tradename
TOY Tobramycin ChEMBL Tradename
TOY Tobrex ChEMBL Tradename
TOY 'Tobradex St' ChEMBL Tradename
TOY Tobradex ChEMBL Tradename
TOY '4-AMINO-2-[4,6-DIAMINO-3-(3-AMINO-6-AMINOMETHYL-5-HYDROXY-TETRAHYDRO-PYRAN-2-YLOXY)-2-HYDROXY-CYCLOHEXYLOXY]-6-HYDROXYMETHYL-TETRAHYDRO-PYRAN-3,5-DIOL' wwPDB ?
TOY "3'-Deoxykanamycin B" DrugBank ?
TOY 'Nebramycin 6' DrugBank ?
TOY O-3-Amino-3-deoxy-alpha-D-glucopyranosyl-(1-4)-O-(2,6-diamino-2,3,6-trideoxy-alpha-D-ribohexopyranosyl-(1-4))-2-deoxy-D-streptamine DrugBank ?
TOY Tobramycin DrugBank ?
TOY Tobramycinum DrugBank ?
TOY Aktob DrugBank 'International brand'
TOY Alveoterol DrugBank 'International brand'
TOY Amgy DrugBank 'International brand'
TOY Bactob DrugBank 'International brand'
TOY Belbarmicina DrugBank 'International brand'
TOY 'Bideon Biotic' DrugBank 'International brand'
TOY Bioptic DrugBank 'International brand'
TOY Bramitob DrugBank 'International brand'
TOY Gernebcin DrugBank 'International brand'
TOY Nebcin DrugBank 'International brand'
TOY Obracin DrugBank 'International brand'
TOY Tobracin DrugBank 'International brand'
TOY Tobramaxin DrugBank 'International brand'
#
_pdbe_chem_comp_drugbank_classification.comp_id TOY
_pdbe_chem_comp_drugbank_classification.drugbank_id DB00684
_pdbe_chem_comp_drugbank_classification.parent '4,6-disubstituted 2-deoxystreptamines'
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class 'Organooxygen compounds'
_pdbe_chem_comp_drugbank_classification.superclass 'Organic oxygen compounds'
_pdbe_chem_comp_drugbank_classification.description
'This compound belongs to the class of organic compounds known as 4,6-disubstituted 2-deoxystreptamines. These are 2-deoxystreptamine aminoglycosides that a glycosidically linked to a pyranose of furanose unit at the C4- and C6-positions.'
#
loop_
_software.name
_software.version
_software.description
rdkit 2023.03.3 'Core functionality.'
pdbeccdutils 0.8.4 'Wrapper to provide 2D templates and molecular fragments.'
#
loop_
_pdbe_chem_comp_atom_depiction.comp_id
_pdbe_chem_comp_atom_depiction.atom_id
_pdbe_chem_comp_atom_depiction.element
_pdbe_chem_comp_atom_depiction.model_Cartn_x
_pdbe_chem_comp_atom_depiction.model_Cartn_y
_pdbe_chem_comp_atom_depiction.pdbx_ordinal
TOY C11 C 6.952 2.381 1
TOY O11 O 7.702 1.082 2
TOY C21 C 5.452 2.381 3
TOY N21 N 4.702 1.082 4
TOY C31 C 4.702 3.680 5
TOY C41 C 5.452 4.979 6
TOY O41 O 4.702 6.278 7
TOY C51 C 6.952 4.979 8
TOY O51 O 7.702 3.680 9
TOY C61 C 7.702 6.278 10
TOY N61 N 6.952 7.577 11
TOY C12 C 11.600 -1.168 12
TOY N12 N 12.899 -1.918 13
TOY C22 C 11.600 0.332 14
TOY C32 C 10.301 1.082 15
TOY N32 N 11.051 2.381 16
TOY C42 C 9.002 0.332 17
TOY C52 C 9.002 -1.168 18
TOY O52 O 7.702 -1.918 19
TOY C62 C 10.301 -1.918 20
TOY O62 O 10.301 -3.418 21
TOY C13 C 9.002 -4.168 22
TOY C23 C 9.002 -5.668 23
TOY O23 O 10.301 -6.418 24
TOY C33 C 7.702 -6.418 25
TOY N33 N 7.702 -7.918 26
TOY C43 C 6.404 -5.668 27
TOY O43 O 5.104 -6.418 28
TOY C53 C 6.404 -4.168 29
TOY O53 O 7.702 -3.418 30
TOY C63 C 5.104 -3.418 31
TOY O63 O 3.805 -4.168 32
#
loop_
_pdbe_chem_comp_bond_depiction.comp_id
_pdbe_chem_comp_bond_depiction.atom_id_1
_pdbe_chem_comp_bond_depiction.atom_id_2
_pdbe_chem_comp_bond_depiction.value_order
_pdbe_chem_comp_bond_depiction.bond_dir
_pdbe_chem_comp_bond_depiction.pdbx_ordinal
TOY C11 O11 SINGLE BEGINDASH 1
TOY C11 C21 SINGLE NONE 2
TOY C11 O51 SINGLE NONE 3
TOY C42 O11 SINGLE BEGINDASH 4
TOY C21 N21 SINGLE BEGINDASH 5
TOY C21 C31 SINGLE NONE 6
TOY C31 C41 SINGLE NONE 7
TOY C41 O41 SINGLE BEGINDASH 8
TOY C41 C51 SINGLE NONE 9
TOY C51 O51 SINGLE NONE 10
TOY C51 C61 SINGLE BEGINWEDGE 11
TOY C61 N61 SINGLE NONE 12
TOY C12 N12 SINGLE BEGINWEDGE 13
TOY C12 C22 SINGLE NONE 14
TOY C12 C62 SINGLE NONE 15
TOY C22 C32 SINGLE NONE 16
TOY C32 N32 SINGLE BEGINWEDGE 17
TOY C32 C42 SINGLE NONE 18
TOY C42 C52 SINGLE NONE 19
TOY C52 O52 SINGLE BEGINWEDGE 20
TOY C52 C62 SINGLE NONE 21
TOY C62 O62 SINGLE BEGINDASH 22
TOY C13 O62 SINGLE BEGINDASH 23
TOY C13 C23 SINGLE NONE 24
TOY C13 O53 SINGLE NONE 25
TOY C23 O23 SINGLE BEGINDASH 26
TOY C23 C33 SINGLE NONE 27
TOY C33 N33 SINGLE BEGINWEDGE 28
TOY C33 C43 SINGLE NONE 29
TOY C43 O43 SINGLE BEGINDASH 30
TOY C43 C53 SINGLE NONE 31
TOY C53 O53 SINGLE NONE 32
TOY C53 C63 SINGLE BEGINWEDGE 33
TOY C63 O63 SINGLE NONE 34
#
loop_
_pdbe_chem_comp_substructure.comp_id
_pdbe_chem_comp_substructure.substructure_name
_pdbe_chem_comp_substructure.id
_pdbe_chem_comp_substructure.substructure_type
_pdbe_chem_comp_substructure.substructure_smiles
_pdbe_chem_comp_substructure.substructure_inchis
_pdbe_chem_comp_substructure.substructure_inchikeys
TOY MurckoScaffold S1 scaffold 'C1CC[C@@H](O[C@@H]2CCC[C@H](O[C@@H]3CCCCO3)C2)OC1' InChI=1S/C16H28O4/c1-3-10-17-15(8-1)19-13-6-5-7-14(12-13)20-16-9-2-4-11-18-16/h13-16H,1-12H2/t13-,14+,15-,16-/m1/s1 UOYDWHSPHHJHEM-QKPAOTATSA-N
TOY cyclohexane F1 fragment C1CCCCC1 InChI=1S/C6H12/c1-2-4-6-5-3-1/h1-6H2 XDTMQSROBMDMFD-UHFFFAOYSA-N
TOY pyranose F2 fragment OC1CCCCO1 InChI=1S/C5H10O2/c6-5-3-1-2-4-7-5/h5-6H,1-4H2 CELWCAITJAEQNL-UHFFFAOYSA-N
#
loop_
_pdbe_chem_comp_substructure_mapping.comp_id
_pdbe_chem_comp_substructure_mapping.atom_id
_pdbe_chem_comp_substructure_mapping.substructure_id
_pdbe_chem_comp_substructure_mapping.substructure_ordinal
TOY C11 S1 1
TOY O11 S1 1
TOY C21 S1 1
TOY C31 S1 1
TOY C41 S1 1
TOY C51 S1 1
TOY O51 S1 1
TOY C12 S1 1
TOY C22 S1 1
TOY C32 S1 1
TOY C42 S1 1
TOY C52 S1 1
TOY C62 S1 1
TOY O62 S1 1
TOY C13 S1 1
TOY C23 S1 1
TOY C33 S1 1
TOY C43 S1 1
TOY C53 S1 1
TOY O53 S1 1
TOY C12 F1 1
TOY C22 F1 1
TOY C32 F1 1
TOY C42 F1 1
TOY C52 F1 1
TOY C62 F1 1
TOY C41 F2 1
TOY C51 F2 1
TOY O51 F2 1
TOY C11 F2 1
TOY C21 F2 1
TOY C31 F2 1
TOY O11 F2 1
TOY C43 F2 2
TOY C53 F2 2
TOY O53 F2 2
TOY C13 F2 2
TOY C23 F2 2
TOY C33 F2 2
TOY O62 F2 2
#
_pdbe_chem_comp_rdkit_properties.comp_id TOY
_pdbe_chem_comp_rdkit_properties.exactmw 467.259
_pdbe_chem_comp_rdkit_properties.amw 467.520
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 14
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 15
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 16
_pdbe_chem_comp_rdkit_properties.NumHBD 10
_pdbe_chem_comp_rdkit_properties.NumHBA 14
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 32
_pdbe_chem_comp_rdkit_properties.NumAtoms 69
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 14
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 1
_pdbe_chem_comp_rdkit_properties.NumRings 3
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 3
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 3
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 14
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 238.048
_pdbe_chem_comp_rdkit_properties.tpsa 268.170
_pdbe_chem_comp_rdkit_properties.CrippenClogP -6.296
_pdbe_chem_comp_rdkit_properties.CrippenMR 108.371
_pdbe_chem_comp_rdkit_properties.chi0v 14.910
_pdbe_chem_comp_rdkit_properties.chi1v 7.772
_pdbe_chem_comp_rdkit_properties.chi2v 3.506
_pdbe_chem_comp_rdkit_properties.chi3v 3.506
_pdbe_chem_comp_rdkit_properties.chi4v 2.091
_pdbe_chem_comp_rdkit_properties.chi0n 51.910
_pdbe_chem_comp_rdkit_properties.chi1n 25.285
_pdbe_chem_comp_rdkit_properties.chi2n 3.506
_pdbe_chem_comp_rdkit_properties.chi3n 3.506
_pdbe_chem_comp_rdkit_properties.chi4n 2.091
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.560
_pdbe_chem_comp_rdkit_properties.kappa1 5.871
_pdbe_chem_comp_rdkit_properties.kappa2 10.794
_pdbe_chem_comp_rdkit_properties.kappa3 5.236
_pdbe_chem_comp_rdkit_properties.Phi 1.980
#
loop_
_pdbe_chem_comp_external_mappings.comp_id
_pdbe_chem_comp_external_mappings.source
_pdbe_chem_comp_external_mappings.resource
_pdbe_chem_comp_external_mappings.resource_id
TOY UniChem ChEMBL CHEMBL1747
TOY UniChem DrugBank DB00684
TOY UniChem PDBe TOY
TOY UniChem 'Guide to Pharmacology' 10930
TOY UniChem 'KEGG LIGAND' C00397
TOY UniChem ChEBI 28864
TOY UniChem ZINC ZINC000008214692
TOY UniChem eMolecules 36516853
TOY UniChem fdasrs VZ8RRZ51VK
TOY UniChem PharmGKB PA451704
TOY UniChem HMDB HMDB0014822
TOY UniChem Selleck Tobramycin(free-base)
TOY UniChem NMRShiftDB 60027632
TOY UniChem LINCS LSM-6534
TOY UniChem ACTor 11098-01-4
TOY UniChem BindingDb 50366778
TOY UniChem DrugCentral 2684
TOY UniChem MetaboLights MTBLC28864
TOY UniChem BRENDA 107368
TOY UniChem BRENDA 107369
TOY UniChem BRENDA 51945
TOY UniChem BRENDA 939
TOY UniChem BRENDA 94477
TOY UniChem ChemicalBook CB7154445
TOY UniChem DailyMed TOBRAMYCIN
TOY UniChem ClinicalTrials AKTOB
TOY UniChem ClinicalTrials 'KITABIS PAK'
TOY UniChem ClinicalTrials NEBCIN
TOY UniChem ClinicalTrials 'TOBI PODHALER'
TOY UniChem ClinicalTrials TOBRAMYCIN
TOY UniChem ClinicalTrials 'TOBRAMYCIN SULFATE'
TOY UniChem ClinicalTrials TOBREX
TOY UniChem ClinicalTrials VANTOBRA
TOY UniChem rxnorm BETHKIS
TOY UniChem rxnorm TOBI
TOY UniChem rxnorm TOBRAMYCIN
TOY UniChem rxnorm 'TOBRAMYCIN SULFATE'
TOY UniChem rxnorm TOBREX
TOY UniChem MedChemExpress HY-B0441
TOY UniChem 'Probes And Drugs' PD001728
TOY UniChem 'EPA CompTox Dashboard' DTXSID8023680
TOY UniChem eMolecules 3716283
TOY UniChem SureChEMBL SCHEMBL2838
TOY UniChem 'PubChem TPHARMA' 14760717
TOY UniChem 'PubChem TPHARMA' 14931869
TOY UniChem PubChem 36294
TOY UniChem ACTor 32986-56-4
TOY UniChem Nikkaji J4.533K
#
loop_
_pdbe_chem_comp_rdkit_conformer.comp_id
_pdbe_chem_comp_rdkit_conformer.atom_id
_pdbe_chem_comp_rdkit_conformer.Cartn_x_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_y_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_z_rdkit
_pdbe_chem_comp_rdkit_conformer.rdkit_method
_pdbe_chem_comp_rdkit_conformer.rdkit_ordinal
TOY C11 -3.356 -0.273 0.068 ETKDGv3 1
TOY O11 -2.382 -1.219 0.468 ETKDGv3 2
TOY C21 -4.649 -0.523 0.870 ETKDGv3 3
TOY N21 -5.114 -1.911 0.753 ETKDGv3 4
TOY C31 -5.742 0.454 0.416 ETKDGv3 5
TOY C41 -5.886 0.496 -1.112 ETKDGv3 6
TOY O41 -6.565 -0.656 -1.543 ETKDGv3 7
TOY C51 -4.503 0.588 -1.814 ETKDGv3 8
TOY O51 -3.598 -0.397 -1.329 ETKDGv3 9
TOY C61 -3.880 2.010 -1.792 ETKDGv3 10
TOY N61 -4.448 2.881 -2.822 ETKDGv3 11
TOY C12 1.393 -2.714 -0.197 ETKDGv3 12
TOY N12 2.376 -2.791 -1.282 ETKDGv3 13
TOY C22 0.007 -3.204 -0.694 ETKDGv3 14
TOY C32 -0.869 -2.059 -1.237 ETKDGv3 15
TOY N32 -0.244 -1.465 -2.423 ETKDGv3 16
TOY C42 -1.125 -0.972 -0.147 ETKDGv3 17
TOY C52 -0.043 -0.958 0.962 ETKDGv3 18
TOY O52 -0.044 0.304 1.580 ETKDGv3 19
TOY C62 1.350 -1.269 0.377 ETKDGv3 20
TOY O62 2.323 -1.155 1.408 ETKDGv3 21
TOY C13 3.310 -0.190 1.092 ETKDGv3 22
TOY C23 4.460 -0.268 2.125 ETKDGv3 23
TOY O23 3.985 -0.627 3.400 ETKDGv3 24
TOY C33 5.243 1.069 2.203 ETKDGv3 25
TOY N33 6.644 0.808 2.547 ETKDGv3 26
TOY C43 5.119 1.851 0.878 ETKDGv3 27
TOY O43 5.780 3.086 0.999 ETKDGv3 28
TOY C53 3.610 2.084 0.549 ETKDGv3 29
TOY O53 2.739 1.108 1.115 ETKDGv3 30
TOY C63 3.346 2.208 -0.960 ETKDGv3 31
TOY O63 3.965 3.358 -1.467 ETKDGv3 32
TOY H11 -2.990 0.747 0.331 ETKDGv3 33
TOY H21 -4.440 -0.315 1.944 ETKDGv3 34
TOY HN21 -5.032 -2.239 -0.236 ETKDGv3 35
TOY HN22 -4.489 -2.521 1.328 ETKDGv3 36
TOY H311 -5.486 1.472 0.783 ETKDGv3 37
TOY H312 -6.714 0.180 0.882 ETKDGv3 38
TOY H41 -6.502 1.389 -1.365 ETKDGv3 39
TOY H41O -6.918 -0.461 -2.451 ETKDGv3 40
TOY H51 -4.670 0.336 -2.884 ETKDGv3 41
TOY H611 -2.785 1.931 -1.970 ETKDGv3 42
TOY H612 -4.020 2.492 -0.802 ETKDGv3 43
TOY HN61 -5.481 2.954 -2.688 ETKDGv3 44
TOY HN62 -4.274 2.457 -3.763 ETKDGv3 45
TOY H12 1.711 -3.410 0.614 ETKDGv3 46
TOY HN11 2.447 -3.786 -1.597 ETKDGv3 47
TOY HN12 3.317 -2.557 -0.890 ETKDGv3 48
TOY H221 0.119 -3.994 -1.468 ETKDGv3 49
TOY H222 -0.533 -3.681 0.154 ETKDGv3 50
TOY H32 -1.845 -2.501 -1.545 ETKDGv3 51
TOY HN1 -0.116 -2.215 -3.142 ETKDGv3 52
TOY HN2 -0.918 -0.784 -2.843 ETKDGv3 53
TOY H42 -1.076 0.031 -0.643 ETKDGv3 54
TOY H52 -0.294 -1.743 1.717 ETKDGv3 55
TOY H52O 0.324 0.182 2.494 ETKDGv3 56
TOY H62 1.511 -0.550 -0.466 ETKDGv3 57
TOY H13 3.742 -0.420 0.088 ETKDGv3 58
TOY H23 5.145 -1.077 1.786 ETKDGv3 59
TOY H23O 3.293 0.035 3.661 ETKDGv3 60
TOY H33 4.800 1.701 3.006 ETKDGv3 61
TOY HN31 7.119 1.717 2.749 ETKDGv3 62
TOY HN32 7.131 0.375 1.728 ETKDGv3 63
TOY H43 5.594 1.239 0.073 ETKDGv3 64
TOY H43O 6.084 3.344 0.090 ETKDGv3 65
TOY H53 3.315 3.053 1.009 ETKDGv3 66
TOY H631 3.724 1.310 -1.496 ETKDGv3 67
TOY H632 2.248 2.279 -1.130 ETKDGv3 68
TOY H63O 3.760 3.377 -2.437 ETKDGv3 69
#