data_SBV # _chem_comp.id SBV _chem_comp.name "(1R,2S,3S,4R,6S)-4,6-diamino-3-{[3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranosyl]oxy}-2-hydroxycyclohexyl 2-amino-2,3,4,6-tetradeoxy-6-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]-beta-L-threo-hexopyranoside" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C27 H49 N6 O12 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms PLP-sisomicin _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2020-03-06 _chem_comp.pdbx_modified_date 2021-09-17 _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 680.685 _chem_comp.one_letter_code ? _chem_comp.three_letter_code SBV _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 6UY6 _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 SBV C4 C1 C 0 1 Y N N 2.088 32.159 -23.897 -3.993 1.103 2.216 C4 SBV 1 SBV C5 C2 C 0 1 Y N N 2.352 33.546 -24.164 -4.231 1.677 0.978 C5 SBV 2 SBV C6 C3 C 0 1 Y N N 1.271 34.367 -24.514 -4.095 3.045 0.831 C6 SBV 3 SBV C11 C4 C 0 1 N N R 1.341 27.892 -19.802 0.073 -3.387 0.324 C11 SBV 4 SBV C12 C5 C 0 1 N N R -2.781 29.800 -17.476 2.018 0.525 -2.636 C12 SBV 5 SBV C13 C6 C 0 1 N N R -5.068 28.190 -19.196 4.165 1.620 -0.543 C13 SBV 6 SBV N1 N1 N 0 1 Y N N -0.009 33.863 -24.574 -3.742 3.804 1.850 N1 SBV 7 SBV C3 C7 C 0 1 Y N N 0.779 31.661 -23.970 -3.627 1.933 3.271 C3 SBV 8 SBV C2 C8 C 0 1 Y N N -0.293 32.520 -24.307 -3.505 3.296 3.044 C2 SBV 9 SBV C21 C9 C 0 1 N N R 2.333 27.207 -19.644 0.039 -4.912 0.449 C21 SBV 10 SBV C22 C10 C 0 1 N N N -1.658 30.812 -17.671 0.518 0.277 -2.811 C22 SBV 11 SBV C23 C11 C 0 1 N N R -6.205 27.345 -18.766 5.663 1.883 -0.711 C23 SBV 12 SBV C2A C12 C 0 1 N N N -1.687 31.983 -24.389 -3.105 4.208 4.175 C2A SBV 13 SBV C31 C13 C 0 1 N N N 3.238 27.849 -18.416 -0.337 -5.291 1.884 C31 SBV 14 SBV C32 C14 C 0 1 N N S -0.297 30.149 -17.753 0.220 -1.211 -2.615 C32 SBV 15 SBV C33 C15 C 0 1 N N R -6.087 25.969 -19.176 6.450 0.846 0.097 C33 SBV 16 SBV C41 C16 C 0 1 N N N 3.788 29.039 -18.888 -1.683 -4.649 2.234 C41 SBV 17 SBV C42 C17 C 0 1 N N R -0.297 29.189 -18.740 0.647 -1.636 -1.209 C42 SBV 18 SBV C43 C18 C 0 1 N N R -5.701 25.851 -20.472 6.008 0.914 1.562 C43 SBV 19 SBV C4A C19 C 0 1 N N N 3.150 31.091 -23.583 -4.131 -0.384 2.416 C4A SBV 20 SBV C51 C20 C 0 1 N N R 3.204 29.522 -20.267 -1.582 -3.134 2.041 C51 SBV 21 SBV C52 C21 C 0 1 N N S -1.601 28.365 -18.934 2.147 -1.389 -1.035 C52 SBV 22 SBV C53 C22 C 0 1 N N N -4.550 26.689 -20.847 4.496 0.689 1.642 C53 SBV 23 SBV C5A C23 C 0 1 N N N 3.720 34.193 -24.091 -4.635 0.821 -0.195 C5A SBV 24 SBV C61 C24 C 0 1 N N N 3.687 30.960 -20.754 -2.940 -2.491 2.331 C61 SBV 25 SBV C62 C25 C 0 1 N N S -2.875 29.004 -18.533 2.444 0.099 -1.230 C62 SBV 26 SBV C83 C26 C 0 1 N N N -5.312 24.503 -20.814 6.730 -0.170 2.364 C83 SBV 27 SBV C93 C27 C 0 1 N N N -7.861 24.993 -17.546 8.466 0.538 -1.209 C93 SBV 28 SBV N12 N2 N 0 1 N N N -3.939 30.485 -17.263 2.304 1.953 -2.824 N12 SBV 29 SBV N21 N3 N 0 1 N N N 2.096 25.863 -19.630 -0.959 -5.458 -0.481 N21 SBV 30 SBV N32 N4 N 0 1 N N N 0.623 31.082 -17.960 -1.220 -1.448 -2.783 N32 SBV 31 SBV N33 N5 N 0 1 N N N -7.335 25.165 -18.978 7.887 1.135 0.002 N33 SBV 32 SBV N61 N6 N 0 1 N N N 3.558 30.726 -22.303 -2.843 -1.037 2.145 N61 SBV 33 SBV O11 O1 O 0 1 N N N 0.774 28.293 -18.560 0.368 -3.026 -1.027 O11 SBV 34 SBV O1P O2 O 0 1 N N N 6.326 32.791 -23.142 -5.242 2.252 -3.870 O1P SBV 35 SBV O23 O3 O 0 1 N N N -6.284 27.593 -17.417 6.015 1.779 -2.092 O23 SBV 36 SBV O2P O4 O 0 1 N N N 6.621 35.015 -24.182 -6.738 0.445 -2.683 O2P SBV 37 SBV O3 O5 O 0 1 N N N 0.516 30.364 -23.703 -3.388 1.416 4.504 O3 SBV 38 SBV O3P O6 O 0 1 N N N 7.097 32.919 -25.451 -4.306 0.007 -3.194 O3P SBV 39 SBV O43 O7 O 0 1 N N N -6.756 26.198 -21.372 6.329 2.199 2.098 O43 SBV 40 SBV O4P O8 O 0 1 N N N 4.673 33.538 -24.883 -4.820 1.647 -1.346 O4P SBV 41 SBV O51 O9 O 0 1 N N N 1.836 29.169 -20.593 -1.199 -2.851 0.693 O51 SBV 42 SBV O52 O10 O 0 1 N N N -1.707 28.182 -19.910 2.545 -1.786 0.279 O52 SBV 43 SBV O53 O11 O 0 1 N N N -4.751 28.053 -20.494 3.827 1.668 0.845 O53 SBV 44 SBV O62 O12 O 0 1 N N N -3.966 27.916 -18.368 3.845 0.330 -1.067 O62 SBV 45 SBV P P1 P 0 1 N N N 6.213 33.569 -24.423 -5.256 1.064 -2.783 P SBV 46 SBV H1 H1 H 0 1 N N N 1.444 35.409 -24.740 -4.279 3.499 -0.132 H1 SBV 47 SBV H2 H2 H 0 1 N N N 0.572 27.400 -20.416 0.842 -2.985 0.984 H2 SBV 48 SBV H3 H3 H 0 1 N N N -2.536 29.209 -16.581 2.570 -0.057 -3.375 H3 SBV 49 SBV H4 H4 H 0 1 N N N -5.366 29.234 -19.019 3.600 2.381 -1.081 H4 SBV 50 SBV H5 H5 H 0 1 N N N 2.977 27.372 -20.520 1.021 -5.319 0.209 H5 SBV 51 SBV H6 H6 H 0 1 N N N -1.661 31.512 -16.822 -0.034 0.859 -2.072 H6 SBV 52 SBV H7 H7 H 0 1 N N N -1.839 31.366 -18.604 0.214 0.580 -3.813 H7 SBV 53 SBV H8 H8 H 0 1 N N N -7.107 27.754 -19.245 5.901 2.884 -0.349 H8 SBV 54 SBV H9 H9 H 0 1 N N N -2.376 32.791 -24.676 -3.997 4.553 4.697 H9 SBV 55 SBV H10 H10 H 0 1 N N N -1.728 31.182 -25.142 -2.465 3.664 4.870 H10 SBV 56 SBV H11 H11 H 0 1 N N N -1.983 31.580 -23.409 -2.562 5.065 3.776 H11 SBV 57 SBV H12 H12 H 0 1 N N N 2.600 28.049 -17.543 -0.418 -6.375 1.966 H12 SBV 58 SBV H13 H13 H 0 1 N N N 4.039 27.150 -18.133 0.430 -4.930 2.569 H13 SBV 59 SBV H14 H14 H 0 1 N N N -0.116 29.662 -16.783 0.772 -1.792 -3.354 H14 SBV 60 SBV H15 H15 H 0 1 N N N -5.315 25.507 -18.543 6.252 -0.151 -0.299 H15 SBV 61 SBV H16 H16 H 0 1 N N N 4.872 28.895 -19.005 -2.458 -5.049 1.581 H16 SBV 62 SBV H17 H17 H 0 1 N N N 3.601 29.825 -18.141 -1.932 -4.869 3.273 H17 SBV 63 SBV H18 H18 H 0 1 N N N -0.130 29.702 -19.699 0.094 -1.055 -0.470 H18 SBV 64 SBV H19 H19 H 0 1 N N N 2.782 30.165 -24.049 -4.431 -0.586 3.444 H19 SBV 65 SBV H20 H20 H 0 1 N N N 4.063 31.424 -24.099 -4.886 -0.774 1.734 H20 SBV 66 SBV H21 H21 H 0 1 N N N 3.766 28.879 -20.960 -0.835 -2.729 2.724 H21 SBV 67 SBV H22 H22 H 0 1 N N N -1.486 27.471 -18.303 2.699 -1.970 -1.773 H22 SBV 68 SBV H23 H23 H 0 1 N N N -4.400 26.621 -21.935 4.257 -0.308 1.271 H23 SBV 69 SBV H24 H24 H 0 1 N N N -3.654 26.316 -20.329 4.170 0.779 2.678 H24 SBV 70 SBV H25 H25 H 0 1 N N N 4.061 34.177 -23.045 -3.854 0.088 -0.396 H25 SBV 71 SBV H26 H26 H 0 1 N N N 3.635 35.235 -24.433 -5.567 0.305 0.036 H26 SBV 72 SBV H27 H27 H 0 1 N N N 4.722 31.176 -20.451 -3.687 -2.895 1.648 H27 SBV 73 SBV H28 H28 H 0 1 N N N 3.025 31.764 -20.398 -3.232 -2.707 3.359 H28 SBV 74 SBV H29 H29 H 0 1 N N N -3.196 29.612 -19.391 1.892 0.680 -0.491 H29 SBV 75 SBV H30 H30 H 0 1 N N N -4.497 24.177 -20.151 7.807 -0.012 2.302 H30 SBV 76 SBV H31 H31 H 0 1 N N N -6.174 23.831 -20.693 6.415 -0.121 3.407 H31 SBV 77 SBV H32 H32 H 0 1 N N N -4.968 24.475 -21.859 6.482 -1.150 1.956 H32 SBV 78 SBV H33 H33 H 0 1 N N N -8.776 24.383 -17.562 9.530 0.768 -1.254 H33 SBV 79 SBV H34 H34 H 0 1 N N N -7.097 24.492 -16.933 8.328 -0.543 -1.182 H34 SBV 80 SBV H35 H35 H 0 1 N N N -8.086 25.981 -17.117 7.968 0.946 -2.089 H35 SBV 81 SBV H36 H36 H 0 1 N N N -3.836 31.074 -16.462 2.030 2.259 -3.746 H36 SBV 82 SBV H37 H37 H 0 1 N N N -4.147 31.046 -18.064 1.855 2.508 -2.111 H37 SBV 83 SBV H39 H39 H 0 1 N N N 2.958 25.373 -19.496 -1.000 -6.464 -0.417 H39 SBV 84 SBV H40 H40 H 0 1 N N N 1.469 25.643 -18.883 -1.867 -5.048 -0.318 H40 SBV 85 SBV H42 H42 H 0 1 N N N 0.587 31.756 -17.222 -1.527 -1.175 -3.704 H42 SBV 86 SBV H43 H43 H 0 1 N N N 1.529 30.658 -17.981 -1.452 -2.412 -2.595 H43 SBV 87 SBV H45 H45 H 0 1 N N N -8.059 25.604 -19.510 8.058 2.129 0.032 H45 SBV 88 SBV H47 H47 H 0 1 N N N 3.108 29.834 -22.267 -2.511 -0.812 1.219 H47 SBV 89 SBV H49 H49 H 0 1 N N N 6.927 32.065 -23.264 -5.494 1.972 -4.761 H49 SBV 90 SBV H50 H50 H 0 1 N N N -6.996 27.088 -17.043 5.550 2.405 -2.664 H50 SBV 91 SBV H51 H51 H 0 1 N N N 7.364 35.231 -24.733 -7.414 1.083 -2.418 H51 SBV 92 SBV H52 H52 H 0 1 N N N 1.326 29.913 -23.494 -2.468 1.158 4.651 H52 SBV 93 SBV H53 H53 H 0 1 N N N -7.527 25.681 -21.171 6.076 2.313 3.024 H53 SBV 94 SBV H54 H54 H 0 1 N N N -2.499 27.678 -20.054 3.500 -1.751 0.427 H54 SBV 95 # # 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 SBV O3P P DOUB N N 1 SBV O4P P SING N N 2 SBV O4P C5A SING N N 3 SBV N1 C6 DOUB Y N 4 SBV N1 C2 SING Y N 5 SBV C6 C5 SING Y N 6 SBV P O2P SING N N 7 SBV P O1P SING N N 8 SBV C2A C2 SING N N 9 SBV C2 C3 DOUB Y N 10 SBV C5 C5A SING N N 11 SBV C5 C4 DOUB Y N 12 SBV C3 C4 SING Y N 13 SBV C3 O3 SING N N 14 SBV C4 C4A SING N N 15 SBV C4A N61 SING N N 16 SBV N61 C61 SING N N 17 SBV O43 C43 SING N N 18 SBV C53 O53 SING N N 19 SBV C53 C43 SING N N 20 SBV C83 C43 SING N N 21 SBV C61 C51 SING N N 22 SBV O51 C51 SING N N 23 SBV O51 C11 SING N N 24 SBV O53 C13 SING N N 25 SBV C43 C33 SING N N 26 SBV C51 C41 SING N N 27 SBV O52 C52 SING N N 28 SBV C11 C21 SING N N 29 SBV C11 O11 SING N N 30 SBV C21 N21 SING N N 31 SBV C21 C31 SING N N 32 SBV C13 C23 SING N N 33 SBV C13 O62 SING N N 34 SBV C33 N33 SING N N 35 SBV C33 C23 SING N N 36 SBV N33 C93 SING N N 37 SBV C52 C42 SING N N 38 SBV C52 C62 SING N N 39 SBV C41 C31 SING N N 40 SBV C23 O23 SING N N 41 SBV C42 O11 SING N N 42 SBV C42 C32 SING N N 43 SBV C62 O62 SING N N 44 SBV C62 C12 SING N N 45 SBV N32 C32 SING N N 46 SBV C32 C22 SING N N 47 SBV C22 C12 SING N N 48 SBV C12 N12 SING N N 49 SBV C6 H1 SING N N 50 SBV C11 H2 SING N N 51 SBV C12 H3 SING N N 52 SBV C13 H4 SING N N 53 SBV C21 H5 SING N N 54 SBV C22 H6 SING N N 55 SBV C22 H7 SING N N 56 SBV C23 H8 SING N N 57 SBV C2A H9 SING N N 58 SBV C2A H10 SING N N 59 SBV C2A H11 SING N N 60 SBV C31 H12 SING N N 61 SBV C31 H13 SING N N 62 SBV C32 H14 SING N N 63 SBV C33 H15 SING N N 64 SBV C41 H16 SING N N 65 SBV C41 H17 SING N N 66 SBV C42 H18 SING N N 67 SBV C4A H19 SING N N 68 SBV C4A H20 SING N N 69 SBV C51 H21 SING N N 70 SBV C52 H22 SING N N 71 SBV C53 H23 SING N N 72 SBV C53 H24 SING N N 73 SBV C5A H25 SING N N 74 SBV C5A H26 SING N N 75 SBV C61 H27 SING N N 76 SBV C61 H28 SING N N 77 SBV C62 H29 SING N N 78 SBV C83 H30 SING N N 79 SBV C83 H31 SING N N 80 SBV C83 H32 SING N N 81 SBV C93 H33 SING N N 82 SBV C93 H34 SING N N 83 SBV C93 H35 SING N N 84 SBV N12 H36 SING N N 85 SBV N12 H37 SING N N 86 SBV N21 H39 SING N N 87 SBV N21 H40 SING N N 88 SBV N32 H42 SING N N 89 SBV N32 H43 SING N N 90 SBV N33 H45 SING N N 91 SBV N61 H47 SING N N 92 SBV O1P H49 SING N N 93 SBV O23 H50 SING N N 94 SBV O2P H51 SING N N 95 SBV O3 H52 SING N N 96 SBV O43 H53 SING N N 97 SBV O52 H54 SING N N 98 # # 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 SBV SMILES ACDLabs 12.01 "c4(CNCC3CCC(C(OC1C(CC(N)C(C1O)OC2C(O)C(NC)C(CO2)(C)O)N)O3)N)c(COP(O)(O)=O)cnc(c4O)C" SBV InChI InChI 1.03 "InChI=1S/C27H49N6O12P/c1-12-19(34)15(13(7-33-12)10-42-46(38,39)40)9-32-8-14-4-5-16(28)25(43-14)44-22-17(29)6-18(30)23(20(22)35)45-26-21(36)24(31-3)27(2,37)11-41-26/h7,14,16-18,20-26,31-32,34-37H,4-6,8-11,28-30H2,1-3H3,(H2,38,39,40)/t14-,16-,17+,18-,20+,21-,22-,23+,24-,25-,26-,27+/m1/s1" SBV InChIKey InChI 1.03 RIDGEVUBNCTQEZ-LVJYRULHSA-N SBV SMILES_CANONICAL CACTVS 3.385 "CN[C@@H]1[C@@H](O)[C@H](OC[C@]1(C)O)O[C@H]2[C@H](N)C[C@H](N)[C@@H](O[C@H]3O[C@H](CC[C@H]3N)CNCc4c(O)c(C)ncc4CO[P](O)(O)=O)[C@@H]2O" SBV SMILES CACTVS 3.385 "CN[CH]1[CH](O)[CH](OC[C]1(C)O)O[CH]2[CH](N)C[CH](N)[CH](O[CH]3O[CH](CC[CH]3N)CNCc4c(O)c(C)ncc4CO[P](O)(O)=O)[CH]2O" SBV SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "Cc1c(c(c(cn1)COP(=O)(O)O)CNC[C@H]2CC[C@H]([C@H](O2)O[C@@H]3[C@H](C[C@H]([C@@H]([C@H]3O)O[C@@H]4[C@@H]([C@H]([C@@](CO4)(C)O)NC)O)N)N)N)O" SBV SMILES "OpenEye OEToolkits" 2.0.7 "Cc1c(c(c(cn1)COP(=O)(O)O)CNCC2CCC(C(O2)OC3C(CC(C(C3O)OC4C(C(C(CO4)(C)O)NC)O)N)N)N)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 SBV "SYSTEMATIC NAME" ACDLabs 12.01 "(1R,2S,3S,4R,6S)-4,6-diamino-3-{[3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranosyl]oxy}-2-hydroxycyclohexyl 2-amino-2,3,4,6-tetradeoxy-6-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]-beta-L-threo-hexopyranoside" SBV "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[4-[[[(2~{R},5~{R},6~{R})-5-azanyl-6-[(1~{R},2~{S},3~{S},4~{R},6~{S})-4,6-bis(azanyl)-3-[(2~{R},3~{R},4~{R},5~{R})-5-methyl-4-(methylamino)-3,5-bis(oxidanyl)oxan-2-yl]oxy-2-oxidanyl-cyclohexyl]oxy-oxan-2-yl]methylamino]methyl]-6-methyl-5-oxidanyl-pyridin-3-yl]methyl dihydrogen phosphate" # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id SBV _pdbx_chem_comp_synonyms.name PLP-sisomicin _pdbx_chem_comp_synonyms.provenance AUTHOR _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 SBV "Create component" 2020-03-06 RCSB SBV "Modify coordinates" 2021-02-05 RCSB SBV "Initial release" 2021-09-22 RCSB ##