data_YS7 # _chem_comp.id YS7 _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]-alpha-D-erythro-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 ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2021-03-30 _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 YS7 _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 7LLD _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 YS7 C17 C1 C 0 1 N N R 20.014 49.639 -33.731 -0.011 -3.985 3.074 C17 YS7 1 YS7 C20 C2 C 0 1 N N N 17.824 48.913 -34.809 -2.374 -4.438 2.415 C20 YS7 2 YS7 C21 C3 C 0 1 N N S 17.443 48.999 -33.287 -2.263 -3.289 1.410 C21 YS7 3 YS7 C22 C4 C 0 1 N N N 17.752 47.777 -32.357 -3.628 -2.616 1.252 C22 YS7 4 YS7 C24 C5 C 0 1 N N N 18.530 47.335 -30.188 -4.846 -0.923 0.022 C24 YS7 5 YS7 C26 C6 C 0 1 Y N N 19.268 49.063 -28.495 -4.979 -0.206 -2.391 C26 YS7 6 YS7 C28 C7 C 0 1 Y N N 19.141 49.709 -27.262 -4.860 0.781 -3.359 C28 YS7 7 YS7 C01 C8 C 0 1 N N N 25.982 55.355 -32.142 6.032 1.842 2.341 C01 YS7 8 YS7 C02 C9 C 0 1 N N R 24.737 55.881 -31.368 5.410 2.099 0.967 C02 YS7 9 YS7 C04 C10 C 0 1 N N N 23.779 54.711 -31.213 3.918 1.756 1.008 C04 YS7 10 YS7 C06 C11 C 0 1 N N R 21.916 56.259 -31.122 3.925 1.109 -1.301 C06 YS7 11 YS7 C08 C12 C 0 1 N N S 20.226 54.945 -32.112 2.422 -0.746 -1.081 C08 YS7 12 YS7 C09 C13 C 0 1 N N R 18.960 55.666 -32.575 2.239 -1.333 -2.482 C09 YS7 13 YS7 C11 C14 C 0 1 N N N 17.682 54.770 -32.486 0.806 -1.849 -2.634 C11 YS7 14 YS7 C12 C15 C 0 1 N N S 17.871 53.468 -33.288 0.541 -2.933 -1.588 C12 YS7 15 YS7 C14 C16 C 0 1 N N R 19.157 52.768 -32.876 0.725 -2.345 -0.187 C14 YS7 16 YS7 C16 C17 C 0 1 N N R 19.411 50.512 -32.987 0.009 -2.853 2.043 C16 YS7 17 YS7 C19 C18 C 0 1 N N N 19.095 49.295 -35.088 -0.992 -5.068 2.613 C19 YS7 18 YS7 C25 C19 C 0 1 Y N N 18.366 48.059 -28.837 -4.728 0.118 -1.062 C25 YS7 19 YS7 C29 C20 C 0 1 N N N 20.127 50.816 -26.888 -5.130 0.446 -4.803 C29 YS7 20 YS7 C31 C21 C 0 1 Y N N 17.298 48.392 -26.714 -4.268 2.349 -1.778 C31 YS7 21 YS7 C32 C22 C 0 1 Y N N 17.364 47.704 -27.926 -4.366 1.421 -0.758 C32 YS7 22 YS7 C33 C23 C 0 1 N N N 16.291 46.576 -28.250 -4.083 1.821 0.667 C33 YS7 23 YS7 C40 C24 C 0 1 N N S 20.419 53.659 -32.927 2.157 -1.829 -0.034 C40 YS7 24 YS7 C42 C25 C 0 1 N N R 22.848 57.454 -31.414 5.417 1.426 -1.436 C42 YS7 25 YS7 C44 C26 C 0 1 N N R 24.123 57.040 -32.081 6.099 1.218 -0.080 C44 YS7 26 YS7 C46 C27 C 0 1 N N N 24.802 59.395 -32.916 8.322 0.473 -0.686 C46 YS7 27 YS7 N10 N1 N 0 1 N N N 18.737 56.854 -31.751 2.494 -0.293 -3.487 N10 YS7 28 YS7 N13 N2 N 0 1 N N N 16.756 52.548 -33.046 -0.835 -3.429 -1.734 N13 YS7 29 YS7 N18 N3 N 0 1 N N N 21.303 50.263 -34.202 1.335 -4.561 3.197 N18 YS7 30 YS7 N23 N4 N 0 1 N N N 18.173 48.221 -31.226 -3.550 -1.592 0.201 N23 YS7 31 YS7 N30 N5 N 0 1 Y N N 18.189 49.353 -26.436 -4.513 2.009 -3.028 N30 YS7 32 YS7 N45 N6 N 0 1 N N N 25.166 58.203 -32.060 7.516 1.592 -0.181 N45 YS7 33 YS7 O03 O1 O 0 1 N N N 25.139 56.267 -30.043 5.574 3.475 0.618 O03 YS7 34 YS7 O05 O2 O 0 1 N N N 22.583 55.160 -30.441 3.352 1.941 -0.290 O05 YS7 35 YS7 O07 O3 O 0 1 N N N 21.379 55.799 -32.341 3.760 -0.263 -0.939 O07 YS7 36 YS7 O15 O4 O 0 1 N N N 19.394 51.728 -33.784 0.476 -3.358 0.791 O15 YS7 37 YS7 O27 O5 O 0 1 N N N 20.314 49.443 -29.410 -5.342 -1.469 -2.736 O27 YS7 38 YS7 O34 O6 O 0 1 N N N 16.852 45.384 -28.781 -3.735 3.206 0.712 O34 YS7 39 YS7 O36 O7 O 0 1 N N N 16.646 43.081 -29.797 -2.902 5.477 1.742 O36 YS7 40 YS7 O37 O8 O 0 1 N N N 14.531 44.285 -29.292 -4.664 4.015 3.035 O37 YS7 41 YS7 O38 O9 O 0 1 N N N 15.971 44.971 -31.165 -2.270 3.259 2.768 O38 YS7 42 YS7 O39 O10 O 0 1 N N N 17.864 50.203 -32.679 -1.312 -2.333 1.885 O39 YS7 43 YS7 O41 O11 O 0 1 N N N 21.451 52.907 -32.388 2.328 -1.280 1.274 O41 YS7 44 YS7 O43 O12 O 0 1 N N N 22.078 58.367 -32.250 6.004 0.557 -2.406 O43 YS7 45 YS7 P35 P1 P 0 1 N N N 15.968 44.426 -29.784 -3.369 3.973 2.080 P35 YS7 46 YS7 H1 H1 H 0 1 N N N 20.222 48.691 -33.213 -0.329 -3.593 4.040 H1 YS7 47 YS7 H2 H2 H 0 1 N N N 17.138 49.561 -35.373 -2.739 -4.055 3.368 H2 YS7 48 YS7 H3 H3 H 0 1 N N N 17.697 47.871 -35.138 -3.066 -5.189 2.035 H3 YS7 49 YS7 H4 H4 H 0 1 N N N 16.344 49.048 -33.296 -1.936 -3.679 0.446 H4 YS7 50 YS7 H5 H5 H 0 1 N N N 16.837 47.185 -32.206 -4.372 -3.363 0.977 H5 YS7 51 YS7 H6 H6 H 0 1 N N N 18.525 47.146 -32.819 -3.914 -2.148 2.195 H6 YS7 52 YS7 H7 H7 H 0 1 N N N 17.876 46.451 -30.215 -5.140 -0.444 0.955 H7 YS7 53 YS7 H8 H8 H 0 1 N N N 19.577 47.021 -30.314 -5.598 -1.659 -0.262 H8 YS7 54 YS7 H9 H9 H 0 1 N N N 26.418 54.503 -31.600 5.908 0.792 2.605 H9 YS7 55 YS7 H10 H10 H 0 1 N N N 25.678 55.033 -33.149 7.094 2.087 2.310 H10 YS7 56 YS7 H11 H11 H 0 1 N N N 26.729 56.158 -32.224 5.537 2.465 3.086 H11 YS7 57 YS7 H12 H12 H 0 1 N N N 23.465 54.357 -32.206 3.793 0.717 1.315 H12 YS7 58 YS7 H13 H13 H 0 1 N N N 24.280 53.893 -30.674 3.415 2.409 1.721 H13 YS7 59 YS7 H14 H14 H 0 1 N N N 21.100 56.625 -30.482 3.427 1.296 -2.252 H14 YS7 60 YS7 H15 H15 H 0 1 N N N 20.137 54.693 -31.045 1.722 0.078 -0.938 H15 YS7 61 YS7 H16 H16 H 0 1 N N N 19.093 55.968 -33.624 2.939 -2.156 -2.625 H16 YS7 62 YS7 H17 H17 H 0 1 N N N 16.824 55.324 -32.894 0.106 -1.026 -2.491 H17 YS7 63 YS7 H18 H18 H 0 1 N N N 17.489 54.520 -31.432 0.675 -2.268 -3.632 H18 YS7 64 YS7 H19 H19 H 0 1 N N N 17.924 53.716 -34.358 1.241 -3.756 -1.731 H19 YS7 65 YS7 H20 H20 H 0 1 N N N 19.042 52.376 -31.855 0.024 -1.522 -0.044 H20 YS7 66 YS7 H21 H21 H 0 1 N N N 19.925 50.689 -32.031 0.673 -2.060 2.387 H21 YS7 67 YS7 H22 H22 H 0 1 N N N 19.587 48.482 -35.642 -0.647 -5.495 1.672 H22 YS7 68 YS7 H23 H23 H 0 1 N N N 19.055 50.197 -35.717 -1.053 -5.851 3.370 H23 YS7 69 YS7 H24 H24 H 0 1 N N N 19.885 51.201 -25.886 -6.185 0.610 -5.023 H24 YS7 70 YS7 H25 H25 H 0 1 N N N 21.150 50.411 -26.888 -4.521 1.084 -5.444 H25 YS7 71 YS7 H26 H26 H 0 1 N N N 20.056 51.633 -27.621 -4.879 -0.599 -4.987 H26 YS7 72 YS7 H27 H27 H 0 1 N N N 16.527 48.149 -25.998 -3.987 3.365 -1.547 H27 YS7 73 YS7 H28 H28 H 0 1 N N N 15.576 46.978 -28.982 -4.972 1.650 1.275 H28 YS7 74 YS7 H29 H29 H 0 1 N N N 15.761 46.325 -27.320 -3.257 1.225 1.055 H29 YS7 75 YS7 H30 H30 H 0 1 N N N 20.626 53.925 -33.974 2.857 -2.652 -0.178 H30 YS7 76 YS7 H31 H31 H 0 1 N N N 23.088 57.946 -30.460 5.542 2.462 -1.751 H31 YS7 77 YS7 H32 H32 H 0 1 N N N 23.920 56.766 -33.127 6.018 0.172 0.214 H32 YS7 78 YS7 H33 H33 H 0 1 N N N 25.591 60.158 -32.838 7.965 0.186 -1.675 H33 YS7 79 YS7 H34 H34 H 0 1 N N N 24.702 59.077 -33.964 9.366 0.777 -0.751 H34 YS7 80 YS7 H35 H35 H 0 1 N N N 23.848 59.818 -32.569 8.231 -0.375 -0.007 H35 YS7 81 YS7 H36 H36 H 0 1 N N N 19.543 57.445 -31.792 2.379 -0.656 -4.421 H36 YS7 82 YS7 H37 H37 H 0 1 N N N 17.941 57.353 -32.094 1.901 0.509 -3.335 H37 YS7 83 YS7 H39 H39 H 0 1 N N N 15.897 52.987 -33.310 -1.014 -3.723 -2.682 H39 YS7 84 YS7 H40 H40 H 0 1 N N N 16.886 51.717 -33.588 -1.021 -4.176 -1.082 H40 YS7 85 YS7 H42 H42 H 0 1 N N N 21.876 50.481 -33.412 1.348 -5.311 3.872 H42 YS7 86 YS7 H43 H43 H 0 1 N N N 21.786 49.621 -34.797 1.677 -4.875 2.301 H43 YS7 87 YS7 H45 H45 H 0 1 N N N 18.984 48.773 -31.421 -2.823 -0.923 0.402 H45 YS7 88 YS7 H47 H47 H 0 1 N N N 26.041 57.843 -32.384 7.868 1.919 0.707 H47 YS7 89 YS7 H49 H49 H 0 1 N N N 24.385 56.589 -29.564 5.159 4.090 1.238 H49 YS7 90 YS7 H50 H50 H 0 1 N N N 20.836 50.137 -29.024 -4.598 -2.048 -2.949 H50 YS7 91 YS7 H51 H51 H 0 1 N N N 16.926 42.876 -30.681 -2.666 5.999 2.521 H51 YS7 92 YS7 H52 H52 H 0 1 N N N 13.933 44.575 -29.971 -5.424 4.469 2.648 H52 YS7 93 YS7 H53 H53 H 0 1 N N N 22.253 53.416 -32.398 3.239 -1.028 1.478 H53 YS7 94 YS7 H54 H54 H 0 1 N N N 21.277 58.610 -31.800 5.616 0.633 -3.288 H54 YS7 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 YS7 C19 C20 SING N N 1 YS7 C19 C17 SING N N 2 YS7 C20 C21 SING N N 3 YS7 N18 C17 SING N N 4 YS7 O15 C16 SING N N 5 YS7 O15 C14 SING N N 6 YS7 C17 C16 SING N N 7 YS7 C12 N13 SING N N 8 YS7 C12 C14 SING N N 9 YS7 C12 C11 SING N N 10 YS7 C21 O39 SING N N 11 YS7 C21 C22 SING N N 12 YS7 C16 O39 SING N N 13 YS7 C40 C14 SING N N 14 YS7 C40 O41 SING N N 15 YS7 C40 C08 SING N N 16 YS7 C46 N45 SING N N 17 YS7 C09 C11 SING N N 18 YS7 C09 C08 SING N N 19 YS7 C09 N10 SING N N 20 YS7 C22 N23 SING N N 21 YS7 O07 C08 SING N N 22 YS7 O07 C06 SING N N 23 YS7 O43 C42 SING N N 24 YS7 C01 C02 SING N N 25 YS7 C44 N45 SING N N 26 YS7 C44 C42 SING N N 27 YS7 C44 C02 SING N N 28 YS7 C42 C06 SING N N 29 YS7 C02 C04 SING N N 30 YS7 C02 O03 SING N N 31 YS7 N23 C24 SING N N 32 YS7 C04 O05 SING N N 33 YS7 O38 P35 DOUB N N 34 YS7 C06 O05 SING N N 35 YS7 C24 C25 SING N N 36 YS7 O36 P35 SING N N 37 YS7 P35 O37 SING N N 38 YS7 P35 O34 SING N N 39 YS7 O27 C26 SING N N 40 YS7 C25 C26 DOUB Y N 41 YS7 C25 C32 SING Y N 42 YS7 O34 C33 SING N N 43 YS7 C26 C28 SING Y N 44 YS7 C33 C32 SING N N 45 YS7 C32 C31 DOUB Y N 46 YS7 C28 C29 SING N N 47 YS7 C28 N30 DOUB Y N 48 YS7 C31 N30 SING Y N 49 YS7 C17 H1 SING N N 50 YS7 C20 H2 SING N N 51 YS7 C20 H3 SING N N 52 YS7 C21 H4 SING N N 53 YS7 C22 H5 SING N N 54 YS7 C22 H6 SING N N 55 YS7 C24 H7 SING N N 56 YS7 C24 H8 SING N N 57 YS7 C01 H9 SING N N 58 YS7 C01 H10 SING N N 59 YS7 C01 H11 SING N N 60 YS7 C04 H12 SING N N 61 YS7 C04 H13 SING N N 62 YS7 C06 H14 SING N N 63 YS7 C08 H15 SING N N 64 YS7 C09 H16 SING N N 65 YS7 C11 H17 SING N N 66 YS7 C11 H18 SING N N 67 YS7 C12 H19 SING N N 68 YS7 C14 H20 SING N N 69 YS7 C16 H21 SING N N 70 YS7 C19 H22 SING N N 71 YS7 C19 H23 SING N N 72 YS7 C29 H24 SING N N 73 YS7 C29 H25 SING N N 74 YS7 C29 H26 SING N N 75 YS7 C31 H27 SING N N 76 YS7 C33 H28 SING N N 77 YS7 C33 H29 SING N N 78 YS7 C40 H30 SING N N 79 YS7 C42 H31 SING N N 80 YS7 C44 H32 SING N N 81 YS7 C46 H33 SING N N 82 YS7 C46 H34 SING N N 83 YS7 C46 H35 SING N N 84 YS7 N10 H36 SING N N 85 YS7 N10 H37 SING N N 86 YS7 N13 H39 SING N N 87 YS7 N13 H40 SING N N 88 YS7 N18 H42 SING N N 89 YS7 N18 H43 SING N N 90 YS7 N23 H45 SING N N 91 YS7 N45 H47 SING N N 92 YS7 O03 H49 SING N N 93 YS7 O27 H50 SING N N 94 YS7 O36 H51 SING N N 95 YS7 O37 H52 SING N N 96 YS7 O41 H53 SING N N 97 YS7 O43 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 YS7 SMILES ACDLabs 12.01 "O=P(O)(O)OCc1cnc(C)c(O)c1CNCC1CCC(N)C(O1)OC1C(O)C(OC2OCC(C)(O)C(NC)C2O)C(N)CC1N" YS7 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-/m0/s1" YS7 InChIKey InChI 1.03 RIDGEVUBNCTQEZ-IXQBVWJDSA-N YS7 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" YS7 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" YS7 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" YS7 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 YS7 "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]-alpha-D-erythro-hexopyranoside" YS7 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[4-[[[(2~{S},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" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site YS7 "Create component" 2021-03-30 RCSB YS7 "Initial release" 2021-09-22 RCSB ##