data_84G
#
_chem_comp.id 84G
_chem_comp.name Arbekacin
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C22 H44 N6 O10"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms
(2S)-4-amino-N-{(1R,2S,3S,4R,5S)-5-amino-2-[(3-amino-3-deoxy-alpha-D-glucopyranosyl)oxy]-4-[(2,6-diamino-2,3,4,6-tetradeoxy-alpha-D-erythro-hexopyranosyl)oxy]-3-hydroxycyclohexyl}-2-hydroxybutanamide
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2016-12-23
_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 552.619
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 84G
_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 5U8B
_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.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
84G C1 C1 C 0 1 N N N N N N 36.402 -3.228 18.417 -4.536 3.418 -0.705 C1 84G 1
84G C2 C2 C 0 1 N N S N N N 37.617 -3.352 17.508 -4.646 2.494 0.510 C2 84G 2
84G C3 C3 C 0 1 N N N N N N 37.410 -4.535 16.494 -3.267 2.192 1.037 C3 84G 3
84G C4 C4 C 0 1 N N R N N N 37.485 -5.349 14.195 -1.055 1.199 0.795 C4 84G 4
84G C5 C5 C 0 1 N N N N N N 36.008 -5.718 14.072 -0.128 2.383 0.510 C5 84G 5
84G O1 O1 O 0 1 N N N N N N 37.075 -5.638 16.916 -2.942 2.576 2.141 O1 84G 6
84G O2 O2 O 0 1 N N N N N N 36.313 -9.325 13.159 3.125 0.536 0.856 O2 84G 7
84G O3 O3 O 0 1 N N N N N N 36.373 -10.902 14.903 4.451 0.889 -1.031 O3 84G 8
84G O4 O4 O 0 1 N N N N N N 38.885 -8.894 14.282 1.400 -1.531 -0.001 O4 84G 9
84G O5 O5 O 0 1 N N N N N N 39.725 -6.183 14.085 -1.375 -1.159 0.374 O5 84G 10
84G O O6 O 0 1 N N N N N N 37.833 -2.103 16.874 -5.415 3.137 1.529 O 84G 11
84G C C6 C 0 1 N N N N N N 36.617 -3.825 19.796 -5.924 3.625 -1.315 C 84G 12
84G N N1 N 0 1 N N N N N N 36.211 -2.876 20.875 -5.818 4.511 -2.482 N 84G 13
84G N1 N2 N 0 1 N N N N N N 37.614 -4.290 15.192 -2.395 1.493 0.283 N1 84G 14
84G C15 C7 C 0 1 N N S N N N 38.412 -6.528 14.565 -0.509 -0.053 0.107 C15 84G 15
84G C16 C8 C 0 1 N N S N N N 40.411 -5.161 14.762 -1.980 -1.718 -0.794 C16 84G 16
84G C21 C9 C 0 1 N N R N N N 41.857 -5.083 14.278 -3.173 -2.586 -0.384 C21 84G 17
84G O9 O7 O 0 1 N N N N N N 41.917 -4.739 12.900 -4.103 -1.799 0.362 O9 84G 18
84G C20 C10 C 0 1 N N S N N N 42.568 -6.408 14.550 -2.675 -3.747 0.483 C20 84G 19
84G N5 N3 N 0 1 N N N N N N 43.973 -6.361 14.131 -3.802 -4.628 0.818 N5 84G 20
84G C19 C11 C 0 1 N N S N N N 42.477 -6.688 16.046 -1.621 -4.538 -0.299 C19 84G 21
84G O8 O8 O 0 1 N N N N N N 43.026 -7.965 16.323 -1.097 -5.580 0.527 O8 84G 22
84G C17 C12 C 0 1 N N R N N N 41.012 -6.712 16.469 -0.489 -3.594 -0.712 C17 84G 23
84G C18 C13 C 0 1 N N N N N N 40.841 -6.899 17.963 0.539 -4.364 -1.544 C18 84G 24
84G O7 O9 O 0 1 N N N N N N 40.621 -5.649 18.616 1.701 -3.554 -1.734 O7 84G 25
84G O6 O10 O 0 1 N N N N N N 40.382 -5.460 16.137 -1.024 -2.521 -1.489 O6 84G 26
84G C14 C14 C 0 1 N N S N N N 38.094 -7.812 13.802 0.891 -0.361 0.642 C14 84G 27
84G C7 C15 C 0 1 N N R N N N 36.608 -8.123 13.897 1.817 0.823 0.356 C7 84G 28
84G C6 C16 C 0 1 N N S N N N 35.802 -6.990 13.260 1.272 2.075 1.045 C6 84G 29
84G N2 N4 N 0 1 N N N N N N 34.368 -7.286 13.149 2.161 3.212 0.770 N2 84G 30
84G C8 C17 C 0 1 N N R N N N 36.832 -10.558 13.614 3.987 -0.088 -0.097 C8 84G 31
84G C13 C18 C 0 1 N N R N N N 36.386 -11.596 12.585 5.185 -0.708 0.627 C13 84G 32
84G N4 N5 N 0 1 N N N N N N 36.521 -11.019 11.243 4.708 -1.670 1.630 N4 84G 33
84G C12 C19 C 0 1 N N N N N N 34.978 -12.154 12.751 5.983 0.400 1.320 C12 84G 34
84G C11 C20 C 0 1 N N N N N N 34.570 -12.341 14.200 6.408 1.437 0.276 C11 84G 35
84G C9 C21 C 0 1 N N S N N N 34.958 -11.126 15.000 5.163 1.975 -0.434 C9 84G 36
84G C10 C22 C 0 1 N N N N N N 34.729 -11.296 16.486 5.584 2.967 -1.520 C10 84G 37
84G N3 N6 N 0 1 N N N N N N 34.972 -10.064 17.213 4.388 3.571 -2.122 N3 84G 38
84G H1 H1 H 0 1 N N N N N N 36.161 -2.161 18.533 -4.128 4.380 -0.394 H1 84G 39
84G H2 H2 H 0 1 N N N N N N 35.556 -3.746 17.941 -3.877 2.966 -1.446 H2 84G 40
84G H3 H3 H 0 1 N N N N N N 38.487 -3.601 18.133 -5.135 1.565 0.218 H3 84G 41
84G H4 H4 H 0 1 N N N N N N 37.816 -4.958 13.222 -1.106 1.030 1.871 H4 84G 42
84G H5 H5 H 0 1 N N N N N N 35.476 -4.892 13.578 -0.077 2.553 -0.566 H5 84G 43
84G H6 H6 H 0 1 N N N N N N 35.595 -5.870 15.080 -0.517 3.275 1.000 H6 84G 44
84G H7 H7 H 0 1 N N N N N N 39.805 -8.670 14.210 2.247 -1.837 0.353 H7 84G 45
84G H8 H8 H 0 1 N N N N N N 37.951 -1.429 17.533 -5.038 3.972 1.838 H8 84G 46
84G H9 H9 H 0 1 N N N N N N 36.018 -4.744 19.885 -6.331 2.663 -1.625 H9 84G 47
84G H10 H10 H 0 1 N N N N N N 37.683 -4.069 19.917 -6.583 4.077 -0.574 H10 84G 48
84G H11 H11 H 0 1 N N N N N N 36.365 -3.300 21.768 -5.162 4.146 -3.155 H11 84G 49
84G H12 H12 H 0 1 N N N N N N 36.754 -2.039 20.805 -6.722 4.664 -2.903 H12 84G 50
84G H14 H14 H 0 1 N N N N N N 37.859 -3.366 14.898 -2.656 1.186 -0.600 H14 84G 51
84G H15 H15 H 0 1 N N N N N N 38.400 -6.704 15.651 -0.458 0.116 -0.969 H15 84G 52
84G H16 H16 H 0 1 N N N N N N 39.927 -4.191 14.575 -2.323 -0.914 -1.446 H16 84G 53
84G H17 H17 H 0 1 N N N N N N 42.365 -4.304 14.865 -3.660 -2.980 -1.276 H17 84G 54
84G H18 H18 H 0 1 N N N N N N 41.469 -3.913 12.759 -4.460 -1.044 -0.127 H18 84G 55
84G H19 H19 H 0 1 N N N N N N 42.046 -7.209 14.006 -2.232 -3.355 1.398 H19 84G 56
84G H20 H20 H 0 1 N N N N N N 44.408 -7.241 14.322 -4.514 -4.127 1.328 H20 84G 57
84G H21 H21 H 0 1 N N N N N N 44.022 -6.171 13.150 -4.185 -5.057 -0.011 H21 84G 58
84G H23 H23 H 0 1 N N N N N N 43.007 -5.900 16.601 -2.077 -4.972 -1.188 H23 84G 59
84G H24 H24 H 0 1 N N N N N N 42.969 -8.139 17.255 -0.423 -6.122 0.095 H24 84G 60
84G H25 H25 H 0 1 N N N N N N 40.506 -7.537 15.946 -0.007 -3.192 0.180 H25 84G 61
84G H26 H26 H 0 1 N N N N N N 39.978 -7.557 18.146 0.816 -5.280 -1.023 H26 84G 62
84G H27 H27 H 0 1 N N N N N N 41.750 -7.363 18.373 0.107 -4.613 -2.514 H27 84G 63
84G H28 H28 H 0 1 N N N N N N 40.517 -5.793 19.549 2.396 -3.979 -2.255 H28 84G 64
84G H29 H29 H 0 1 N N N N N N 38.332 -7.638 12.742 0.839 -0.530 1.717 H29 84G 65
84G H30 H30 H 0 1 N N N N N N 36.319 -8.232 14.953 1.869 0.993 -0.719 H30 84G 66
84G H31 H31 H 0 1 N N N N N N 36.204 -6.816 12.251 1.220 1.906 2.120 H31 84G 67
84G H32 H32 H 0 1 N N N N N N 33.899 -6.510 12.727 1.735 4.081 1.055 H32 84G 68
84G H33 H33 H 0 1 N N N N N N 34.239 -8.101 12.584 3.057 3.085 1.216 H33 84G 69
84G H35 H35 H 0 1 N N N N N N 37.931 -10.521 13.609 3.440 -0.867 -0.628 H35 84G 70
84G H36 H36 H 0 1 N N N N N N 37.082 -12.445 12.659 5.823 -1.219 -0.094 H36 84G 71
84G H37 H37 H 0 1 N N N N N N 37.444 -10.651 11.129 5.481 -2.089 2.125 H37 84G 72
84G H38 H38 H 0 1 N N N N N N 36.358 -11.728 10.557 4.062 -1.234 2.270 H38 84G 73
84G H40 H40 H 0 1 N N N N N N 34.270 -11.459 12.276 5.361 0.879 2.077 H40 84G 74
84G H41 H41 H 0 1 N N N N N N 34.928 -13.130 12.246 6.868 -0.027 1.791 H41 84G 75
84G H42 H42 H 0 1 N N N N N N 33.481 -12.483 14.257 6.929 2.258 0.770 H42 84G 76
84G H43 H43 H 0 1 N N N N N N 35.078 -13.226 14.611 7.071 0.970 -0.452 H43 84G 77
84G H44 H44 H 0 1 N N N N N N 34.400 -10.250 14.638 4.521 2.477 0.288 H44 84G 78
84G H45 H45 H 0 1 N N N N N N 33.687 -11.608 16.652 6.203 3.748 -1.079 H45 84G 79
84G H46 H46 H 0 1 N N N N N N 35.409 -12.073 16.865 6.154 2.444 -2.289 H46 84G 80
84G H47 H47 H 0 1 N N N N N N 34.811 -10.215 18.188 3.810 4.007 -1.419 H47 84G 81
84G H48 H48 H 0 1 N N N N N N 35.919 -9.775 17.072 4.640 4.231 -2.843 H48 84G 82
#
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
84G N4 C13 SING N N 1
84G C13 C12 SING N N 2
84G C13 C8 SING N N 3
84G C12 C11 SING N N 4
84G O9 C21 SING N N 5
84G N2 C6 SING N N 6
84G O2 C8 SING N N 7
84G O2 C7 SING N N 8
84G C6 C7 SING N N 9
84G C6 C5 SING N N 10
84G C8 O3 SING N N 11
84G C14 C7 SING N N 12
84G C14 O4 SING N N 13
84G C14 C15 SING N N 14
84G C5 C4 SING N N 15
84G O5 C15 SING N N 16
84G O5 C16 SING N N 17
84G N5 C20 SING N N 18
84G C4 C15 SING N N 19
84G C4 N1 SING N N 20
84G C11 C9 SING N N 21
84G C21 C20 SING N N 22
84G C21 C16 SING N N 23
84G C20 C19 SING N N 24
84G C16 O6 SING N N 25
84G O3 C9 SING N N 26
84G C9 C10 SING N N 27
84G N1 C3 SING N N 28
84G C19 O8 SING N N 29
84G C19 C17 SING N N 30
84G O6 C17 SING N N 31
84G C17 C18 SING N N 32
84G C10 N3 SING N N 33
84G C3 O1 DOUB N N 34
84G C3 C2 SING N N 35
84G O C2 SING N N 36
84G C2 C1 SING N N 37
84G C18 O7 SING N N 38
84G C1 C SING N N 39
84G C N SING N N 40
84G C1 H1 SING N N 41
84G C1 H2 SING N N 42
84G C2 H3 SING N N 43
84G C4 H4 SING N N 44
84G C5 H5 SING N N 45
84G C5 H6 SING N N 46
84G O4 H7 SING N N 47
84G O H8 SING N N 48
84G C H9 SING N N 49
84G C H10 SING N N 50
84G N H11 SING N N 51
84G N H12 SING N N 52
84G N1 H14 SING N N 53
84G C15 H15 SING N N 54
84G C16 H16 SING N N 55
84G C21 H17 SING N N 56
84G O9 H18 SING N N 57
84G C20 H19 SING N N 58
84G N5 H20 SING N N 59
84G N5 H21 SING N N 60
84G C19 H23 SING N N 61
84G O8 H24 SING N N 62
84G C17 H25 SING N N 63
84G C18 H26 SING N N 64
84G C18 H27 SING N N 65
84G O7 H28 SING N N 66
84G C14 H29 SING N N 67
84G C7 H30 SING N N 68
84G C6 H31 SING N N 69
84G N2 H32 SING N N 70
84G N2 H33 SING N N 71
84G C8 H35 SING N N 72
84G C13 H36 SING N N 73
84G N4 H37 SING N N 74
84G N4 H38 SING N N 75
84G C12 H40 SING N N 76
84G C12 H41 SING N N 77
84G C11 H42 SING N N 78
84G C11 H43 SING N N 79
84G C9 H44 SING N N 80
84G C10 H45 SING N N 81
84G C10 H46 SING N N 82
84G N3 H47 SING N N 83
84G N3 H48 SING N N 84
#
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
84G SMILES ACDLabs 12.01 C(CN)C(C(=O)NC3C(OC1OC(C(C(C1O)N)O)CO)C(O)C(OC2OC(CCC2N)CN)C(C3)N)O
84G InChI InChI 1.03 InChI=1S/C22H44N6O10/c23-4-3-12(30)20(34)28-11-5-10(26)18(37-21-9(25)2-1-8(6-24)35-21)17(33)19(11)38-22-16(32)14(27)15(31)13(7-29)36-22/h8-19,21-22,29-33H,1-7,23-27H2,(H,28,34)/t8-,9+,10-,11+,12-,13+,14-,15+,16+,17-,18+,19-,21+,22+/m0/s1
84G InChIKey InChI 1.03 MKKYBZZTJQGVCD-XTCKQBCOSA-N
84G 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)CC[C@H]2N)[C@H](O)[C@H]1O[C@H]3O[C@H](CO)[C@@H](O)[C@H](N)[C@H]3O
84G SMILES CACTVS 3.385 NCC[CH](O)C(=O)N[CH]1C[CH](N)[CH](O[CH]2O[CH](CN)CC[CH]2N)[CH](O)[CH]1O[CH]3O[CH](CO)[CH](O)[CH](N)[CH]3O
84G SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 C1C[C@H]([C@H](O[C@@H]1CN)O[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)NC(=O)[C@H](CCN)O)N)N
84G SMILES "OpenEye OEToolkits" 2.0.6 C1CC(C(OC1CN)OC2C(CC(C(C2O)OC3C(C(C(C(O3)CO)O)N)O)NC(=O)C(CCN)O)N)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
84G "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-[(2,6-diamino-2,3,4,6-tetradeoxy-alpha-D-erythro-hexopyranosyl)oxy]-3-hydroxycyclohexyl}-2-hydroxybutanamide
84G "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 (2~{S})-~{N}-[(1~{R},2~{S},3~{S},4~{R},5~{S})-4-[(2~{R},3~{R},6~{S})-6-(aminomethyl)-3-azanyl-oxan-2-yl]oxy-5-azanyl-2-[(2~{S},3~{R},4~{S},5~{S},6~{R})-4-azanyl-6-(hydroxymethyl)-3,5-bis(oxidanyl)oxan-2-yl]oxy-3-oxidanyl-cyclohexyl]-4-azanyl-2-oxidanyl-butanamide
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
84G 'Create component' 2016-12-23 RCSB
84G 'Initial release' 2018-04-11 RCSB
84G 'Modify synonyms' 2021-03-13 RCSB
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id 84G
_pdbx_chem_comp_synonyms.name
(2S)-4-amino-N-{(1R,2S,3S,4R,5S)-5-amino-2-[(3-amino-3-deoxy-alpha-D-glucopyranosyl)oxy]-4-[(2,6-diamino-2,3,4,6-tetradeoxy-alpha-D-erythro-hexopyranosyl)oxy]-3-hydroxycyclohexyl}-2-hydroxybutanamide
_pdbx_chem_comp_synonyms.provenance PDB
_pdbx_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_drugbank_details.comp_id 84G
_pdbe_chem_comp_drugbank_details.drugbank_id DB06696
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name Arbekacin
_pdbe_chem_comp_drugbank_details.description
'An semisynthetic aminoglycoside antibiotic. Often used for treatment of multi-resistant bacterial infection such as methicillin-resistant _Staphylococcus aureus_ (MRSA).'
_pdbe_chem_comp_drugbank_details.cas_number 51025-85-5
_pdbe_chem_comp_drugbank_details.mechanism_of_action
'Arbekacin irreversibly binds bacterial 30S and 16S ribosomal subunits inhibiting protein synthesis. Arbekacin binds to 4 nucleotides of the 16S subunit and 1 amino acid of protein S12 to interfere with the decoding site around nucleotide 1400 in the 16S subunit. Interference with the decoding site interferes with its interaction with the wobble base of tRNA. This hindered interaction causes mRNA to be misread and the incorrect amino acids are inserted into protein. These error filled proteins are not able to function or may even be toxic.'
#
loop_
_pdbe_chem_comp_synonyms.comp_id
_pdbe_chem_comp_synonyms.name
_pdbe_chem_comp_synonyms.provenance
_pdbe_chem_comp_synonyms.type
84G '(2S)-4-amino-N-{(1R,2S,3S,4R,5S)-5-amino-2-[(3-amino-3-deoxy-alpha-D-glucopyranosyl)oxy]-4-[(2,6-diamino-2,3,4,6-tetradeoxy-alpha-D-erythro-hexopyranosyl)oxy]-3-hydroxycyclohexyl}-2-hydroxybutanamide' wwPDB ?
84G ABK DrugBank ?
84G Arbekacin DrugBank ?
84G Arbekacinum DrugBank ?
84G Haberacin DrugBank ?
#
_pdbe_chem_comp_drugbank_classification.comp_id 84G
_pdbe_chem_comp_drugbank_classification.drugbank_id DB06696
_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.'
#
_pdbe_chem_comp_drugbank_targets.comp_id 84G
_pdbe_chem_comp_drugbank_targets.drugbank_id DB06696
_pdbe_chem_comp_drugbank_targets.name '30S ribosomal protein S12'
_pdbe_chem_comp_drugbank_targets.organism 'Escherichia coli (strain K12)'
_pdbe_chem_comp_drugbank_targets.uniprot_id P0A7S3
_pdbe_chem_comp_drugbank_targets.pharmacologically_active yes
_pdbe_chem_comp_drugbank_targets.ordinal 1
#
loop_
_software.name
_software.version
_software.description
rdkit 2023.09.6 'Core functionality.'
pdbeccdutils 0.8.6 '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
84G C1 C 16.796 -1.168 1
84G C2 C 15.497 -1.918 2
84G C3 C 14.198 -1.168 3
84G C4 C 11.600 -1.168 4
84G C5 C 11.600 0.332 5
84G O1 O 14.198 0.332 6
84G O2 O 7.702 1.082 7
84G O3 O 7.702 3.680 8
84G O4 O 7.702 -1.918 9
84G O5 O 10.301 -3.418 10
84G O O 15.497 -3.418 11
84G C C 18.095 -1.918 12
84G N N 19.394 -1.168 13
84G N1 N 12.899 -1.918 14
84G C15 C 10.301 -1.918 15
84G C16 C 9.002 -4.168 16
84G C21 C 9.002 -5.668 17
84G O9 O 10.301 -6.418 18
84G C20 C 7.702 -6.418 19
84G N5 N 7.702 -7.918 20
84G C19 C 6.404 -5.668 21
84G O8 O 5.104 -6.418 22
84G C17 C 6.404 -4.168 23
84G C18 C 5.104 -3.418 24
84G O7 O 3.805 -4.168 25
84G O6 O 7.702 -3.418 26
84G C14 C 9.002 -1.168 27
84G C7 C 9.002 0.332 28
84G C6 C 10.301 1.082 29
84G N2 N 11.051 2.381 30
84G C8 C 6.952 2.381 31
84G C13 C 5.452 2.381 32
84G N4 N 4.702 1.082 33
84G C12 C 4.702 3.680 34
84G C11 C 5.452 4.979 35
84G C9 C 6.952 4.979 36
84G C10 C 7.702 6.278 37
84G N3 N 6.952 7.577 38
#
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
84G C13 N4 SINGLE BEGINDASH 1
84G C13 C12 SINGLE NONE 2
84G C13 C8 SINGLE NONE 3
84G C12 C11 SINGLE NONE 4
84G C21 O9 SINGLE BEGINDASH 5
84G C6 N2 SINGLE BEGINWEDGE 6
84G C8 O2 SINGLE BEGINDASH 7
84G C7 O2 SINGLE BEGINDASH 8
84G C6 C7 SINGLE NONE 9
84G C6 C5 SINGLE NONE 10
84G C8 O3 SINGLE NONE 11
84G C14 C7 SINGLE NONE 12
84G C14 O4 SINGLE BEGINWEDGE 13
84G C14 C15 SINGLE NONE 14
84G C5 C4 SINGLE NONE 15
84G C15 O5 SINGLE BEGINDASH 16
84G C16 O5 SINGLE BEGINDASH 17
84G C20 N5 SINGLE BEGINWEDGE 18
84G C4 C15 SINGLE NONE 19
84G C4 N1 SINGLE BEGINWEDGE 20
84G C11 C9 SINGLE NONE 21
84G C21 C20 SINGLE NONE 22
84G C21 C16 SINGLE NONE 23
84G C20 C19 SINGLE NONE 24
84G C16 O6 SINGLE NONE 25
84G O3 C9 SINGLE NONE 26
84G C9 C10 SINGLE BEGINWEDGE 27
84G N1 C3 SINGLE NONE 28
84G C19 O8 SINGLE BEGINDASH 29
84G C19 C17 SINGLE NONE 30
84G O6 C17 SINGLE NONE 31
84G C17 C18 SINGLE BEGINWEDGE 32
84G C10 N3 SINGLE NONE 33
84G C3 O1 DOUBLE NONE 34
84G C3 C2 SINGLE NONE 35
84G C2 O SINGLE BEGINDASH 36
84G C2 C1 SINGLE NONE 37
84G C18 O7 SINGLE NONE 38
84G C1 C SINGLE NONE 39
84G C N SINGLE NONE 40
#
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
84G 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
84G amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
84G cyclohexane F2 fragment C1CCCCC1 InChI=1S/C6H12/c1-2-4-6-5-3-1/h1-6H2 XDTMQSROBMDMFD-UHFFFAOYSA-N
84G pyranose F3 fragment OC1CCCCO1 InChI=1S/C5H10O2/c6-5-3-1-2-4-7-5/h5-6H,1-4H2 CELWCAITJAEQNL-UHFFFAOYSA-N
84G Z2856434893 F4 fragment CC(O)CNC1CCCCC1 InChI=1S/C9H19NO/c1-8(11)7-10-9-5-3-2-4-6-9/h8-11H,2-7H2,1H3 HFHPBMVMXFZJNO-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
84G C4 S1 1
84G C5 S1 1
84G O2 S1 1
84G O3 S1 1
84G O5 S1 1
84G C15 S1 1
84G C16 S1 1
84G C21 S1 1
84G C20 S1 1
84G C19 S1 1
84G C17 S1 1
84G O6 S1 1
84G C14 S1 1
84G C7 S1 1
84G C6 S1 1
84G C8 S1 1
84G C13 S1 1
84G C12 S1 1
84G C11 S1 1
84G C9 S1 1
84G N1 F1 1
84G C3 F1 1
84G O1 F1 1
84G C2 F1 1
84G C4 F2 1
84G C5 F2 1
84G C6 F2 1
84G C7 F2 1
84G C14 F2 1
84G C15 F2 1
84G C19 F3 1
84G C17 F3 1
84G O6 F3 1
84G C16 F3 1
84G C21 F3 1
84G C20 F3 1
84G O5 F3 1
84G C11 F3 2
84G C9 F3 2
84G O3 F3 2
84G C8 F3 2
84G C13 F3 2
84G C12 F3 2
84G O2 F3 2
84G C1 F4 1
84G C2 F4 1
84G O F4 1
84G C3 F4 1
84G N1 F4 1
84G C4 F4 1
84G C5 F4 1
84G C6 F4 1
84G C7 F4 1
84G C14 F4 1
84G C15 F4 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 84G
_pdbe_chem_comp_rdkit_properties.exactmw 552.312
_pdbe_chem_comp_rdkit_properties.amw 552.626
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 16
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 16
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 20
_pdbe_chem_comp_rdkit_properties.NumHBD 11
_pdbe_chem_comp_rdkit_properties.NumHBA 15
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 38
_pdbe_chem_comp_rdkit_properties.NumAtoms 82
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 16
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 1
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.955
_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 283.112
_pdbe_chem_comp_rdkit_properties.tpsa 297.270
_pdbe_chem_comp_rdkit_properties.CrippenClogP -6.399
_pdbe_chem_comp_rdkit_properties.CrippenMR 130.615
_pdbe_chem_comp_rdkit_properties.chi0v 17.766
_pdbe_chem_comp_rdkit_properties.chi1v 9.173
_pdbe_chem_comp_rdkit_properties.chi2v 3.939
_pdbe_chem_comp_rdkit_properties.chi3v 3.939
_pdbe_chem_comp_rdkit_properties.chi4v 2.334
_pdbe_chem_comp_rdkit_properties.chi0n 61.766
_pdbe_chem_comp_rdkit_properties.chi1n 30.134
_pdbe_chem_comp_rdkit_properties.chi2n 3.939
_pdbe_chem_comp_rdkit_properties.chi3n 3.939
_pdbe_chem_comp_rdkit_properties.chi4n 2.334
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.090
_pdbe_chem_comp_rdkit_properties.kappa1 6.924
_pdbe_chem_comp_rdkit_properties.kappa2 14.000
_pdbe_chem_comp_rdkit_properties.kappa3 7.154
_pdbe_chem_comp_rdkit_properties.Phi 2.551
#
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
84G UniChem ChEMBL CHEMBL426926
84G UniChem DrugBank DB06696
84G UniChem 'Guide to Pharmacology' 7345
84G UniChem 'PubChem DOTF' 12012746
84G UniChem ChEBI 37922
84G UniChem ZINC ZINC000009575047
84G UniChem fdasrs G7V6SLI20L
84G UniChem SureChEMBL SCHEMBL18413
84G UniChem HMDB HMDB0015642
84G UniChem 'PubChem TPHARMA' 15012131
84G UniChem ACTor 51025-85-5
84G UniChem ACTor 52444-06-1
84G UniChem DrugCentral 235
84G UniChem ChemicalBook CB7347991
84G UniChem ClinicalTrials ARBEKACIN
84G UniChem ClinicalTrials 'ARBEKACIN SULFATE'
84G UniChem ClinicalTrials ME-1100
84G UniChem ClinicalTrials ME1100
84G UniChem rxnorm ARBEKACIN
84G UniChem rxnorm 'ARBEKACIN SULFATE'
84G UniChem 'Probes And Drugs' PD009288
84G UniChem 'EPA CompTox Dashboard' DTXSID8048319
84G UniChem PubChem 68682
84G UniChem Nikkaji J33.173B
#
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
84G C1 -4.761 3.957 -1.239 ETKDGv3 1
84G C2 -3.274 3.916 -1.640 ETKDGv3 2
84G C3 -2.394 3.535 -0.476 ETKDGv3 3
84G C4 -0.795 1.887 0.625 ETKDGv3 4
84G C5 0.520 2.660 0.328 ETKDGv3 5
84G O1 -2.176 4.388 0.427 ETKDGv3 6
84G O2 3.119 0.755 0.971 ETKDGv3 7
84G O3 4.493 0.614 -0.892 ETKDGv3 8
84G O4 0.980 -1.349 1.442 ETKDGv3 9
84G O5 -1.550 -0.205 1.583 ETKDGv3 10
84G O -3.074 3.037 -2.717 ETKDGv3 11
84G C -5.290 2.601 -0.744 ETKDGv3 12
84G N -6.732 2.646 -0.511 ETKDGv3 13
84G N1 -1.821 2.219 -0.374 ETKDGv3 14
84G C15 -0.578 0.345 0.703 ETKDGv3 15
84G C16 -2.061 -1.447 1.121 ETKDGv3 16
84G C21 -3.320 -1.216 0.243 ETKDGv3 17
84G O9 -4.053 -0.102 0.686 ETKDGv3 18
84G C20 -4.235 -2.471 0.196 ETKDGv3 19
84G N5 -4.862 -2.588 -1.123 ETKDGv3 20
84G C19 -3.415 -3.738 0.519 ETKDGv3 21
84G O8 -4.217 -4.894 0.497 ETKDGv3 22
84G C17 -2.712 -3.578 1.904 ETKDGv3 23
84G C18 -1.458 -4.458 2.006 ETKDGv3 24
84G O7 -0.902 -4.342 3.287 ETKDGv3 25
84G O6 -2.405 -2.229 2.250 ETKDGv3 26
84G C14 0.838 0.033 1.233 ETKDGv3 27
84G C7 1.923 0.524 0.238 ETKDGv3 28
84G C6 1.522 1.837 -0.501 ETKDGv3 29
84G N2 0.958 1.537 -1.822 ETKDGv3 30
84G C8 4.223 0.079 0.398 ETKDGv3 31
84G C13 5.438 0.253 1.326 ETKDGv3 32
84G N4 5.676 1.672 1.612 ETKDGv3 33
84G C12 6.671 -0.425 0.705 ETKDGv3 34
84G C11 6.867 -0.008 -0.756 ETKDGv3 35
84G C9 5.547 -0.070 -1.557 ETKDGv3 36
84G C10 5.138 -1.500 -1.984 ETKDGv3 37
84G N3 5.948 -1.957 -3.110 ETKDGv3 38
84G H1 -5.356 4.284 -2.120 ETKDGv3 39
84G H2 -4.905 4.719 -0.441 ETKDGv3 40
84G H3 -2.975 4.944 -1.954 ETKDGv3 41
84G H4 -1.160 2.229 1.620 ETKDGv3 42
84G H5 0.315 3.623 -0.187 ETKDGv3 43
84G H6 1.006 2.927 1.293 ETKDGv3 44
84G H7 1.779 -1.471 2.019 ETKDGv3 45
84G H8 -3.452 3.478 -3.523 ETKDGv3 46
84G H9 -5.071 1.806 -1.490 ETKDGv3 47
84G H10 -4.786 2.335 0.209 ETKDGv3 48
84G H11 -6.940 3.407 0.176 ETKDGv3 49
84G H12 -7.212 2.887 -1.408 ETKDGv3 50
84G H14 -2.164 1.478 -1.025 ETKDGv3 51
84G H15 -0.652 -0.068 -0.332 ETKDGv3 52
84G H16 -1.296 -2.000 0.521 ETKDGv3 53
84G H17 -2.960 -0.993 -0.785 ETKDGv3 54
84G H18 -4.289 -0.256 1.639 ETKDGv3 55
84G H19 -5.034 -2.373 0.968 ETKDGv3 56
84G H20 -5.410 -1.715 -1.302 ETKDGv3 57
84G H21 -5.564 -3.362 -1.091 ETKDGv3 58
84G H23 -2.644 -3.852 -0.276 ETKDGv3 59
84G H24 -4.956 -4.763 1.147 ETKDGv3 60
84G H25 -3.420 -3.939 2.682 ETKDGv3 61
84G H26 -1.736 -5.519 1.818 ETKDGv3 62
84G H27 -0.708 -4.150 1.245 ETKDGv3 63
84G H28 -0.097 -4.923 3.291 ETKDGv3 64
84G H29 0.957 0.562 2.209 ETKDGv3 65
84G H30 2.034 -0.282 -0.531 ETKDGv3 66
84G H31 2.433 2.462 -0.648 ETKDGv3 67
84G H32 0.719 2.440 -2.294 ETKDGv3 68
84G H33 1.707 1.100 -2.407 ETKDGv3 69
84G H35 3.988 -1.010 0.349 ETKDGv3 70
84G H36 5.213 -0.259 2.289 ETKDGv3 71
84G H37 5.920 2.182 0.733 ETKDGv3 72
84G H38 6.491 1.754 2.263 ETKDGv3 73
84G H40 6.542 -1.528 0.754 ETKDGv3 74
84G H41 7.583 -0.177 1.290 ETKDGv3 75
84G H42 7.643 -0.649 -1.223 ETKDGv3 76
84G H43 7.255 1.033 -0.785 ETKDGv3 77
84G H44 5.729 0.494 -2.498 ETKDGv3 78
84G H45 5.233 -2.219 -1.141 ETKDGv3 79
84G H46 4.071 -1.482 -2.297 ETKDGv3 80
84G H47 5.505 -2.825 -3.490 ETKDGv3 81
84G H48 6.886 -2.245 -2.749 ETKDGv3 82
#