data_EDS # _chem_comp.id EDS _chem_comp.name ;(2S)-4-amino-N-[(1R,2S,3S,4R,5S)-5-amino-4-{[(2S,3R)-3-amino-6-{[(2-hydroxyethyl)amino]methyl}-3,4-dihydro-2H-pyran-2-y l]oxy}-2-{[3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranosyl]oxy}-3-hydroxycyclohexyl]-2-hydroxybutanamide ; _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C25 H48 N6 O10" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms plazomicin _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2018-01-02 _chem_comp.pdbx_modified_date 2020-06-17 _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 592.683 _chem_comp.one_letter_code ? _chem_comp.three_letter_code EDS _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 6C0C _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 EDS CAQ C1 C 0 1 N N S 53.192 -1.449 -6.021 0.853 0.045 0.245 CAQ EDS 1 EDS CAR C2 C 0 1 N N R 54.283 -2.113 -5.197 1.267 -1.078 1.198 CAR EDS 2 EDS CAS C3 C 0 1 N N S 52.790 -2.314 -7.212 -0.247 0.887 0.896 CAS EDS 3 EDS CAT C4 C 0 1 N N R 54.006 -2.539 -8.131 -1.457 -0.000 1.196 CAT EDS 4 EDS CAU C5 C 0 1 N N S 55.130 -3.186 -7.353 -1.043 -1.123 2.149 CAU EDS 5 EDS CAV C6 C 0 1 N N N 55.478 -2.317 -6.139 0.057 -1.964 1.498 CAV EDS 6 EDS CAW C7 C 0 1 N N R 51.844 -0.072 -4.337 1.952 1.480 -1.329 CAW EDS 7 EDS CAX C8 C 0 1 N N R 49.469 -0.854 -3.780 3.562 3.240 -0.592 CAX EDS 8 EDS CAY C9 C 0 1 N N R 50.841 -0.404 -3.219 3.307 2.132 -1.619 CAY EDS 9 EDS CAZ C10 C 0 1 N N R 49.006 0.150 -4.826 2.409 4.246 -0.645 CAZ EDS 10 EDS CBA C11 C 0 1 N N N 50.109 0.385 -5.854 1.089 3.513 -0.393 CBA EDS 11 EDS CBB C12 C 0 1 N N S 53.169 -2.796 -10.504 -3.543 1.147 0.914 CBB EDS 12 EDS CBC C13 C 0 1 N N N 47.770 -0.424 -5.526 2.614 5.316 0.429 CBC EDS 13 EDS CBD C14 C 0 1 N N R 52.723 -3.596 -11.648 -4.428 2.216 1.570 CBD EDS 14 EDS CBE C15 C 0 1 N N N 55.321 -1.829 -3.012 3.182 -2.577 1.345 CBE EDS 15 EDS CBF C16 C 0 1 N N N 52.248 -2.545 -12.686 -5.517 2.615 0.568 CBF EDS 16 EDS CBG C17 C 0 1 N N S 55.811 -0.849 -1.970 4.265 -3.406 0.704 CBG EDS 17 EDS CBH C18 C 0 1 N N N 47.539 -0.157 -2.227 5.969 3.206 -0.327 CBH EDS 18 EDS CBI C19 C 0 1 N N N 54.213 -1.290 -11.994 -5.544 0.207 0.032 CBI EDS 19 EDS CBJ C20 C 0 1 N N N 53.370 -1.750 -13.018 -6.127 1.376 -0.029 CBJ EDS 20 EDS CBK C21 C 0 1 N N N 55.042 -0.879 -0.640 3.630 -4.548 -0.092 CBK EDS 21 EDS CBL C22 C 0 1 N N N 55.271 -0.483 -12.402 -6.234 -0.970 -0.607 CBL EDS 22 EDS CBM C23 C 0 1 N N N 55.702 0.176 0.254 4.721 -5.314 -0.843 CBM EDS 23 EDS CBN C24 C 0 1 N N N 56.697 -2.348 -13.002 -6.070 -2.610 -2.380 CBN EDS 24 EDS CBO C25 C 0 1 N N N 58.054 -3.025 -12.818 -5.201 -3.091 -3.544 CBO EDS 25 EDS NAK N1 N 0 1 N N N 54.784 -1.283 -4.115 2.320 -1.884 0.575 NAK EDS 26 EDS NAL N2 N 0 1 N N N 56.273 -3.481 -8.222 -2.205 -1.974 2.437 NAL EDS 27 EDS NAM N3 N 0 1 N N N 48.477 -1.182 -2.715 4.824 3.921 -0.908 NAM EDS 28 EDS NAN N4 N 0 1 N N N 53.787 -4.484 -12.144 -5.047 1.670 2.785 NAN EDS 29 EDS NAO N5 N 0 1 N N N 56.585 -1.120 -12.198 -5.426 -1.460 -1.732 NAO EDS 30 EDS NAP N6 N 0 1 N N N 55.095 0.270 1.588 4.111 -6.411 -1.607 NAP EDS 31 EDS OAA O1 O 0 1 N N N 52.040 -1.245 -5.153 1.983 0.873 -0.036 OAA EDS 32 EDS OAB O2 O 0 1 N N N 53.668 -3.360 -9.275 -2.484 0.786 1.804 OAB EDS 33 EDS OAC O3 O 0 1 N N N 51.335 0.893 -5.290 0.928 2.476 -1.363 OAC EDS 34 EDS OAD O4 O 0 1 N N N 51.704 -1.682 -7.915 -0.634 1.935 0.005 OAD EDS 35 EDS OAE O5 O 0 1 N N N 51.420 -1.382 -2.329 4.339 1.149 -1.528 OAE EDS 36 EDS OAF O6 O 0 1 N N N 48.689 1.429 -4.250 2.373 4.863 -1.934 OAF EDS 37 EDS OAG O7 O 0 1 N N N 54.335 -1.945 -10.818 -4.353 0.002 0.637 OAG EDS 38 EDS OAH O8 O 0 1 N N N 55.211 -3.045 -2.755 3.086 -2.535 2.553 OAH EDS 39 EDS OAI O9 O 0 1 N N N 55.755 0.473 -2.527 5.114 -3.947 1.719 OAI EDS 40 EDS OAJ O10 O 0 1 N N N 58.228 -3.378 -11.444 -3.960 -3.588 -3.039 OAJ EDS 41 EDS H1 H1 H 0 1 N N N 53.560 -0.480 -6.390 0.479 -0.386 -0.684 H1 EDS 42 EDS H2 H2 H 0 1 N N N 53.933 -3.085 -4.820 1.641 -0.647 2.127 H2 EDS 43 EDS H3 H3 H 0 1 N N N 52.461 -3.293 -6.833 0.127 1.318 1.824 H3 EDS 44 EDS H4 H4 H 0 1 N N N 54.351 -1.556 -8.483 -1.831 -0.431 0.267 H4 EDS 45 EDS H5 H5 H 0 1 N N N 54.748 -4.142 -6.965 -0.669 -0.692 3.078 H5 EDS 46 EDS H6 H6 H 0 1 N N N 56.290 -2.804 -5.578 -0.317 -2.396 0.570 H6 EDS 47 EDS H7 H7 H 0 1 N N N 55.817 -1.333 -6.496 0.352 -2.764 2.178 H7 EDS 48 EDS H8 H8 H 0 1 N N N 52.793 0.269 -3.897 1.746 0.720 -2.082 H8 EDS 49 EDS H9 H9 H 0 1 N N N 49.662 -1.791 -4.323 3.622 2.805 0.406 H9 EDS 50 EDS H10 H10 H 0 1 N N N 50.669 0.522 -2.651 3.297 2.560 -2.621 H10 EDS 51 EDS H11 H11 H 0 1 N N N 49.742 1.110 -6.596 1.101 3.076 0.606 H11 EDS 52 EDS H12 H12 H 0 1 N N N 50.327 -0.571 -6.353 0.261 4.217 -0.472 H12 EDS 53 EDS H13 H13 H 0 1 N N N 52.342 -2.120 -10.242 -3.125 1.535 -0.015 H13 EDS 54 EDS H14 H14 H 0 1 N N N 46.974 -0.594 -4.786 1.792 6.031 0.391 H14 EDS 55 EDS H15 H15 H 0 1 N N N 47.417 0.287 -6.287 2.641 4.845 1.411 H15 EDS 56 EDS H16 H16 H 0 1 N N N 48.032 -1.378 -6.008 3.556 5.836 0.249 H16 EDS 57 EDS H17 H17 H 0 1 N N N 51.855 -4.202 -11.351 -3.825 3.088 1.824 H17 EDS 58 EDS H18 H18 H 0 1 N N N 51.456 -1.917 -12.252 -6.289 3.190 1.080 H18 EDS 59 EDS H19 H19 H 0 1 N N N 51.864 -3.050 -13.585 -5.078 3.221 -0.224 H19 EDS 60 EDS H20 H20 H 0 1 N N N 56.860 -1.093 -1.749 4.854 -2.780 0.034 H20 EDS 61 EDS H21 H21 H 0 1 N N N 46.894 -0.590 -1.449 6.890 3.732 -0.576 H21 EDS 62 EDS H22 H22 H 0 1 N N N 48.105 0.687 -1.806 5.857 3.161 0.757 H22 EDS 63 EDS H23 H23 H 0 1 N N N 46.918 0.199 -3.062 6.007 2.194 -0.730 H23 EDS 64 EDS H25 H25 H 0 1 N N N 53.576 -1.500 -14.048 -7.082 1.454 -0.525 H25 EDS 65 EDS H27 H27 H 0 1 N N N 53.983 -0.631 -0.805 3.115 -5.224 0.590 H27 EDS 66 EDS H28 H28 H 0 1 N N N 55.118 -1.874 -0.177 2.915 -4.139 -0.806 H28 EDS 67 EDS H29 H29 H 0 1 N N N 55.241 0.454 -11.826 -6.353 -1.765 0.129 H29 EDS 68 EDS H30 H30 H 0 1 N N N 55.151 -0.260 -13.472 -7.215 -0.662 -0.971 H30 EDS 69 EDS H31 H31 H 0 1 N N N 56.765 -0.082 0.372 5.236 -4.638 -1.525 H31 EDS 70 EDS H32 H32 H 0 1 N N N 55.615 1.155 -0.239 5.435 -5.723 -0.128 H32 EDS 71 EDS H33 H33 H 0 1 N N N 56.568 -2.091 -14.064 -7.049 -2.314 -2.756 H33 EDS 72 EDS H34 H34 H 0 1 N N N 55.906 -3.048 -12.695 -6.187 -3.417 -1.657 H34 EDS 73 EDS H35 H35 H 0 1 N N N 58.098 -3.932 -13.438 -5.719 -3.886 -4.080 H35 EDS 74 EDS H36 H36 H 0 1 N N N 58.853 -2.333 -13.123 -5.010 -2.260 -4.223 H36 EDS 75 EDS H37 H37 H 0 1 N N N 54.728 -0.288 -4.193 2.397 -1.918 -0.391 H37 EDS 76 EDS H38 H38 H 0 1 N N N 57.000 -3.907 -7.684 -1.957 -2.724 3.066 H38 EDS 77 EDS H39 H39 H 0 1 N N N 55.987 -4.105 -8.949 -2.969 -1.429 2.808 H39 EDS 78 EDS H41 H41 H 0 1 N N N 47.921 -1.937 -3.064 4.936 4.032 -1.905 H41 EDS 79 EDS H43 H43 H 0 1 N N N 54.042 -5.132 -11.426 -5.634 2.358 3.232 H43 EDS 80 EDS H44 H44 H 0 1 N N N 53.457 -4.985 -12.944 -5.566 0.830 2.580 H44 EDS 81 EDS H46 H46 H 0 1 N N N 56.692 -1.350 -11.231 -4.491 -1.690 -1.431 H46 EDS 82 EDS H48 H48 H 0 1 N N N 55.567 0.972 2.121 4.811 -6.932 -2.113 H48 EDS 83 EDS H49 H49 H 0 1 N N N 54.129 0.513 1.498 3.573 -7.016 -1.005 H49 EDS 84 EDS H51 H51 H 0 1 N N N 50.972 -1.558 -7.322 -1.315 2.522 0.361 H51 EDS 85 EDS H52 H52 H 0 1 N N N 50.801 -1.588 -1.638 4.238 0.414 -2.148 H52 EDS 86 EDS H53 H53 H 0 1 N N N 48.003 1.324 -3.602 1.665 5.514 -2.039 H53 EDS 87 EDS H54 H54 H 0 1 N N N 56.060 1.102 -1.883 4.656 -4.517 2.352 H54 EDS 88 EDS H55 H55 H 0 1 N N N 59.072 -3.799 -11.329 -3.358 -3.910 -3.723 H55 EDS 89 # # 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 EDS CBJ CBF SING N N 1 EDS CBJ CBI DOUB N N 2 EDS CBN CBO SING N N 3 EDS CBN NAO SING N N 4 EDS CBO OAJ SING N N 5 EDS CBF CBD SING N N 6 EDS CBL NAO SING N N 7 EDS CBL CBI SING N N 8 EDS NAN CBD SING N N 9 EDS CBI OAG SING N N 10 EDS CBD CBB SING N N 11 EDS OAG CBB SING N N 12 EDS CBB OAB SING N N 13 EDS OAB CAT SING N N 14 EDS NAL CAU SING N N 15 EDS CAT CAU SING N N 16 EDS CAT CAS SING N N 17 EDS OAD CAS SING N N 18 EDS CAU CAV SING N N 19 EDS CAS CAQ SING N N 20 EDS CAV CAR SING N N 21 EDS CAQ CAR SING N N 22 EDS CAQ OAA SING N N 23 EDS CBA OAC SING N N 24 EDS CBA CAZ SING N N 25 EDS CBC CAZ SING N N 26 EDS OAC CAW SING N N 27 EDS CAR NAK SING N N 28 EDS OAA CAW SING N N 29 EDS CAZ OAF SING N N 30 EDS CAZ CAX SING N N 31 EDS CAW CAY SING N N 32 EDS NAK CBE SING N N 33 EDS CAX CAY SING N N 34 EDS CAX NAM SING N N 35 EDS CAY OAE SING N N 36 EDS CBE OAH DOUB N N 37 EDS CBE CBG SING N N 38 EDS NAM CBH SING N N 39 EDS OAI CBG SING N N 40 EDS CBG CBK SING N N 41 EDS CBK CBM SING N N 42 EDS CBM NAP SING N N 43 EDS CAQ H1 SING N N 44 EDS CAR H2 SING N N 45 EDS CAS H3 SING N N 46 EDS CAT H4 SING N N 47 EDS CAU H5 SING N N 48 EDS CAV H6 SING N N 49 EDS CAV H7 SING N N 50 EDS CAW H8 SING N N 51 EDS CAX H9 SING N N 52 EDS CAY H10 SING N N 53 EDS CBA H11 SING N N 54 EDS CBA H12 SING N N 55 EDS CBB H13 SING N N 56 EDS CBC H14 SING N N 57 EDS CBC H15 SING N N 58 EDS CBC H16 SING N N 59 EDS CBD H17 SING N N 60 EDS CBF H18 SING N N 61 EDS CBF H19 SING N N 62 EDS CBG H20 SING N N 63 EDS CBH H21 SING N N 64 EDS CBH H22 SING N N 65 EDS CBH H23 SING N N 66 EDS CBJ H25 SING N N 67 EDS CBK H27 SING N N 68 EDS CBK H28 SING N N 69 EDS CBL H29 SING N N 70 EDS CBL H30 SING N N 71 EDS CBM H31 SING N N 72 EDS CBM H32 SING N N 73 EDS CBN H33 SING N N 74 EDS CBN H34 SING N N 75 EDS CBO H35 SING N N 76 EDS CBO H36 SING N N 77 EDS NAK H37 SING N N 78 EDS NAL H38 SING N N 79 EDS NAL H39 SING N N 80 EDS NAM H41 SING N N 81 EDS NAN H43 SING N N 82 EDS NAN H44 SING N N 83 EDS NAO H46 SING N N 84 EDS NAP H48 SING N N 85 EDS NAP H49 SING N N 86 EDS OAD H51 SING N N 87 EDS OAE H52 SING N N 88 EDS OAF H53 SING N N 89 EDS OAI H54 SING N N 90 EDS OAJ H55 SING N N 91 # # 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 EDS SMILES ACDLabs 12.01 "C1(C(NC(=O)C(CCN)O)CC(C(C1O)OC2C(CC=C(O2)CNCCO)N)N)OC3C(C(NC)C(O)(CO3)C)O" EDS InChI InChI 1.03 "InChI=1S/C25H48N6O10/c1-25(37)11-38-24(18(35)21(25)29-2)41-20-15(31-22(36)16(33)5-6-26)9-14(28)19(17(20)34)40-23-13(27)4-3-12(39-23)10-30-7-8-32/h3,13-21,23-24,29-30,32-35,37H,4-11,26-28H2,1-2H3,(H,31,36)/t13-,14+,15-,16+,17+,18-,19-,20+,21-,23-,24-,25+/m1/s1" EDS InChIKey InChI 1.03 IYDYFVUFSPQPPV-PEXOCOHZSA-N EDS 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](O)[C@H](O[C@H]3OC(=CC[C@H]3N)CNCCO)[C@@H](N)C[C@H]2NC(=O)[C@@H](O)CCN" EDS SMILES CACTVS 3.385 "CN[CH]1[CH](O)[CH](OC[C]1(C)O)O[CH]2[CH](O)[CH](O[CH]3OC(=CC[CH]3N)CNCCO)[CH](N)C[CH]2NC(=O)[CH](O)CCN" EDS SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "C[C@@]1(CO[C@@H]([C@@H]([C@H]1NC)O)O[C@H]2[C@@H](C[C@@H]([C@H]([C@@H]2O)O[C@@H]3[C@@H](CC=C(O3)CNCCO)N)N)NC(=O)[C@H](CCN)O)O" EDS SMILES "OpenEye OEToolkits" 2.0.6 "CC1(COC(C(C1NC)O)OC2C(CC(C(C2O)OC3C(CC=C(O3)CNCCO)N)N)NC(=O)C(CCN)O)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 EDS "SYSTEMATIC NAME" ACDLabs 12.01 "(2S)-4-amino-N-[(1R,2S,3S,4R,5S)-5-amino-4-{[(2S,3R)-3-amino-6-{[(2-hydroxyethyl)amino]methyl}-3,4-dihydro-2H-pyran-2-yl]oxy}-2-{[3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranosyl]oxy}-3-hydroxycyclohexyl]-2-hydroxybutanamide" EDS "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "(2~{S})-4-azanyl-~{N}-[(1~{R},2~{S},3~{S},4~{R},5~{S})-5-azanyl-4-[[(2~{S},3~{R})-3-azanyl-6-[(2-hydroxyethylamino)methyl]-3,4-dihydro-2~{H}-pyran-2-yl]oxy]-2-[(2~{R},3~{R},4~{R},5~{R})-5-methyl-4-(methylamino)-3,5-bis(oxidanyl)oxan-2-yl]oxy-3-oxidanyl-cyclohexyl]-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 EDS "Create component" 2018-01-02 RCSB EDS "Initial release" 2018-01-31 RCSB EDS "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id EDS _pdbx_chem_comp_synonyms.name plazomicin _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##