data_GMK # _chem_comp.id GMK _chem_comp.name "(3-Deoxy-3-(3-methoxy-benzamido)-b-D-galactopyranosyl)-(3-deoxy-3-(3-methoxy-benzamido)-2-O-sulfo-b-D-galactopyranosyl)-sulfide" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C28 H36 N2 O15 S2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2013-05-03 _chem_comp.pdbx_modified_date 2014-09-05 _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 704.720 _chem_comp.one_letter_code ? _chem_comp.three_letter_code GMK _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 4bli _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.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 GMK O1 O1G O 0 1 N N N -26.795 7.398 0.554 5.862 -0.210 -1.503 O1 GMK 1 GMK C1 C1F C 0 1 N N N -26.845 8.500 1.235 6.287 -0.088 -0.371 C1 GMK 2 GMK C2 C4F C 0 1 Y N N -27.461 8.485 2.638 7.572 0.605 -0.134 C2 GMK 3 GMK C3 C5F C 0 1 Y N N -28.176 7.340 3.103 8.062 0.747 1.164 C3 GMK 4 GMK C4 C6F C 0 1 Y N N -28.799 7.352 4.364 9.262 1.394 1.381 C4 GMK 5 GMK O2 O1H O 0 1 N N N -27.890 10.917 5.402 10.210 2.269 -2.024 O2 GMK 6 GMK C5 C1H C 0 1 N N N -27.020 12.000 5.046 11.442 2.925 -1.715 C5 GMK 7 GMK C6 C1G C 0 1 Y N N -28.785 8.503 5.174 9.981 1.903 0.315 C6 GMK 8 GMK C7 C2F C 0 1 Y N N -28.118 9.668 4.725 9.500 1.766 -0.980 C7 GMK 9 GMK C8 C3F C 0 1 Y N N -27.503 9.656 3.471 8.301 1.114 -1.210 C8 GMK 10 GMK N1 N1E N 0 1 N N N -25.869 9.454 1.019 5.585 -0.578 0.670 N1 GMK 11 GMK C9 C4D C 0 1 N N S -24.991 9.380 -0.128 4.309 -1.259 0.436 C9 GMK 12 GMK C10 C5D C 0 1 N N R -25.653 9.973 -1.366 4.021 -2.220 1.594 C10 GMK 13 GMK O3 O2D O 0 1 N N N -25.875 11.382 -1.146 4.021 -1.497 2.826 O3 GMK 14 GMK C11 C1D C 0 1 N N R -24.669 9.757 -2.534 2.651 -2.868 1.381 C11 GMK 15 GMK C12 C1E C 0 1 N N N -25.276 10.453 -3.755 2.330 -3.784 2.563 C12 GMK 16 GMK O4 O1F O 0 1 N N N -24.239 10.621 -4.726 1.106 -4.477 2.311 O4 GMK 17 GMK O5 O1D O 0 1 N N N -23.380 10.290 -2.285 1.654 -1.849 1.283 O5 GMK 18 GMK C13 C3D C 0 1 N N R -23.611 9.978 0.095 3.183 -0.224 0.355 C13 GMK 19 GMK O6 O1E O 0 1 N N N -23.092 9.292 1.225 3.403 0.634 -0.767 O6 GMK 20 GMK C14 C2D C 0 1 N N S -22.757 9.695 -1.109 1.844 -0.949 0.190 C14 GMK 21 GMK S1 S1C S 0 1 N N N -21.139 10.314 -0.978 0.498 0.266 0.164 S1 GMK 22 GMK C15 C1C C 0 1 N N S -20.152 8.954 -1.568 -0.963 -0.752 -0.186 C15 GMK 23 GMK C16 C2C C 0 1 N N R -18.676 9.280 -1.526 -2.220 0.119 -0.118 C16 GMK 24 GMK O7 O4K O 0 1 N N N -18.451 10.247 -2.578 -2.369 0.641 1.204 O7 GMK 25 GMK S2 S2K S 0 1 N N N -17.751 11.661 -2.196 -2.273 2.158 1.285 S2 GMK 26 GMK O8 O2K O 0 1 N N N -18.494 12.326 -1.061 -3.563 2.722 0.707 O8 GMK 27 GMK O9 O1K O 0 1 N N N -18.087 12.409 -3.341 -2.274 2.486 2.668 O9 GMK 28 GMK O10 O3K O 0 1 N N N -16.328 11.454 -1.795 -1.233 2.542 0.396 O10 GMK 29 GMK O11 O5C O 0 1 N N N -20.452 7.794 -0.744 -0.847 -1.318 -1.493 O11 GMK 30 GMK C17 C5C C 0 1 N N R -19.727 6.586 -1.169 -1.939 -2.163 -1.862 C17 GMK 31 GMK C18 C6C C 0 1 N N N -20.239 5.461 -0.301 -1.695 -2.732 -3.261 C18 GMK 32 GMK O12 O6C O 0 1 N N N -21.621 5.279 -0.480 -0.549 -3.586 -3.234 O12 GMK 33 GMK C19 C4C C 0 1 N N R -18.273 6.839 -0.957 -3.236 -1.349 -1.861 C19 GMK 34 GMK O13 O4C O 0 1 N N N -17.949 7.119 0.378 -3.147 -0.308 -2.836 O13 GMK 35 GMK C20 C3C C 0 1 N N S -17.869 8.050 -1.803 -3.442 -0.734 -0.474 C20 GMK 36 GMK N2 NA N 0 1 N N N -16.451 8.369 -1.676 -4.641 0.109 -0.484 N2 GMK 37 GMK C21 C1A C 0 1 N N N -15.643 8.043 -2.741 -5.840 -0.422 -0.176 C21 GMK 38 GMK O14 OA O 0 1 N N N -15.939 7.214 -3.701 -5.928 -1.600 0.112 O14 GMK 39 GMK C22 C2A C 0 1 Y N N -14.238 8.477 -2.595 -7.050 0.428 -0.187 C22 GMK 40 GMK C23 C3A C 0 1 Y N N -13.173 7.793 -3.142 -6.953 1.779 -0.522 C23 GMK 41 GMK C24 C4A C 0 1 Y N N -11.882 8.208 -3.022 -8.084 2.570 -0.531 C24 GMK 42 GMK C25 C5A C 0 1 Y N N -11.576 9.348 -2.317 -9.315 2.027 -0.209 C25 GMK 43 GMK C26 C6A C 0 1 Y N N -12.626 10.020 -1.752 -9.421 0.684 0.126 C26 GMK 44 GMK C27 C7A C 0 1 Y N N -13.905 9.649 -1.943 -8.293 -0.119 0.132 C27 GMK 45 GMK O15 O1A O 0 1 N N N -12.430 11.255 -1.095 -10.633 0.157 0.443 O15 GMK 46 GMK C28 C1B C 0 1 N N N -13.556 11.898 -0.430 -11.754 1.042 0.410 C28 GMK 47 GMK H1 H1 H 0 1 N N N -28.239 6.459 2.482 7.503 0.352 1.999 H1 GMK 48 GMK H2 H2 H 0 1 N N N -29.297 6.461 4.717 9.640 1.503 2.387 H2 GMK 49 GMK H3 H3 H 0 1 N N N -27.101 12.799 5.798 12.111 2.225 -1.216 H3 GMK 50 GMK H4 H4 H 0 1 N N N -25.982 11.638 5.006 11.906 3.278 -2.636 H4 GMK 51 GMK H5 H5 H 0 1 N N N -27.309 12.394 4.060 11.247 3.773 -1.058 H5 GMK 52 GMK H6 H6 H 0 1 N N N -29.281 8.497 6.133 10.919 2.408 0.491 H6 GMK 53 GMK H7 H7 H 0 1 N N N -27.040 10.564 3.112 7.928 1.003 -2.217 H7 GMK 54 GMK H8 H8 H 0 1 N N N -25.768 10.209 1.667 5.924 -0.481 1.573 H8 GMK 55 GMK H9 H9 H 0 1 N N N -24.833 8.313 -0.346 4.359 -1.817 -0.499 H9 GMK 56 GMK H10 H10 H 0 1 N N N -26.598 9.450 -1.574 4.790 -2.993 1.625 H10 GMK 57 GMK H11 H11 H 0 1 N N N -26.482 11.499 -0.425 3.845 -2.045 3.603 H11 GMK 58 GMK H12 H12 H 0 1 N N N -24.602 8.679 -2.740 2.664 -3.453 0.461 H12 GMK 59 GMK H13 H13 H 0 1 N N N -25.678 11.435 -3.464 3.136 -4.507 2.692 H13 GMK 60 GMK H14 H14 H 0 1 N N N -26.084 9.835 -4.174 2.230 -3.187 3.469 H14 GMK 61 GMK H15 H15 H 0 1 N N N -24.592 11.052 -5.495 0.840 -5.077 3.021 H15 GMK 62 GMK H16 H16 H 0 1 N N N -23.686 11.061 0.271 3.166 0.369 1.269 H16 GMK 63 GMK H17 H17 H 0 1 N N N -23.635 9.474 1.983 2.726 1.315 -0.879 H17 GMK 64 GMK H18 H18 H 0 1 N N N -22.667 8.607 -1.243 1.847 -1.509 -0.746 H18 GMK 65 GMK H19 H19 H 0 1 N N N -20.459 8.774 -2.609 -1.034 -1.551 0.551 H19 GMK 66 GMK H20 H20 H 0 1 N N N -18.410 9.697 -0.544 -2.132 0.942 -0.827 H20 GMK 67 GMK H21 H21 H 0 1 N N N -19.927 6.367 -2.228 -2.023 -2.981 -1.146 H21 GMK 68 GMK H22 H22 H 0 1 N N N -19.715 4.532 -0.570 -2.567 -3.303 -3.578 H22 GMK 69 GMK H23 H23 H 0 1 N N N -20.041 5.701 0.754 -1.522 -1.914 -3.960 H23 GMK 70 GMK H24 H24 H 0 1 N N N -21.922 4.568 0.074 -0.335 -3.983 -4.090 H24 GMK 71 GMK H25 H25 H 0 1 N N N -17.705 5.965 -1.309 -4.076 -2.001 -2.100 H25 GMK 72 GMK H26 H26 H 0 1 N N N -18.191 6.381 0.925 -3.010 -0.626 -3.739 H26 GMK 73 GMK H27 H27 H 0 1 N N N -18.052 7.775 -2.852 -3.561 -1.527 0.265 H27 GMK 74 GMK H28 H28 H 0 1 N N N -16.084 8.804 -0.854 -4.571 1.048 -0.714 H28 GMK 75 GMK H29 H29 H 0 1 N N N -13.372 6.885 -3.692 -5.994 2.206 -0.774 H29 GMK 76 GMK H30 H30 H 0 1 N N N -11.091 7.637 -3.485 -8.008 3.615 -0.791 H30 GMK 77 GMK H31 H31 H 0 1 N N N -10.559 9.696 -2.214 -10.197 2.651 -0.217 H31 GMK 78 GMK H32 H32 H 0 1 N N N -14.696 10.287 -1.576 -8.375 -1.166 0.389 H32 GMK 79 GMK H33 H33 H 0 1 N N N -13.223 12.843 0.025 -11.595 1.856 1.118 H33 GMK 80 GMK H34 H34 H 0 1 N N N -14.347 12.104 -1.166 -11.866 1.450 -0.594 H34 GMK 81 GMK H35 H35 H 0 1 N N N -13.948 11.232 0.353 -12.657 0.495 0.683 H35 GMK 82 GMK H36 H36 H 0 1 N N N -18.990 13.064 -1.396 -3.606 3.688 0.711 H36 GMK 83 # 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 GMK O4 C12 SING N N 1 GMK C12 C11 SING N N 2 GMK O14 C21 DOUB N N 3 GMK O9 S2 DOUB N N 4 GMK C23 C24 DOUB Y N 5 GMK C23 C22 SING Y N 6 GMK C24 C25 SING Y N 7 GMK C21 C22 SING N N 8 GMK C21 N2 SING N N 9 GMK C22 C27 DOUB Y N 10 GMK O7 S2 SING N N 11 GMK O7 C16 SING N N 12 GMK C11 O5 SING N N 13 GMK C11 C10 SING N N 14 GMK C25 C26 DOUB Y N 15 GMK O5 C14 SING N N 16 GMK S2 O10 DOUB N N 17 GMK S2 O8 SING N N 18 GMK C27 C26 SING Y N 19 GMK C20 N2 SING N N 20 GMK C20 C16 SING N N 21 GMK C20 C19 SING N N 22 GMK C26 O15 SING N N 23 GMK C15 C16 SING N N 24 GMK C15 S1 SING N N 25 GMK C15 O11 SING N N 26 GMK C10 O3 SING N N 27 GMK C10 C9 SING N N 28 GMK C17 C19 SING N N 29 GMK C17 O11 SING N N 30 GMK C17 C18 SING N N 31 GMK C14 S1 SING N N 32 GMK C14 C13 SING N N 33 GMK O15 C28 SING N N 34 GMK C19 O13 SING N N 35 GMK O12 C18 SING N N 36 GMK C9 C13 SING N N 37 GMK C9 N1 SING N N 38 GMK C13 O6 SING N N 39 GMK O1 C1 DOUB N N 40 GMK N1 C1 SING N N 41 GMK C1 C2 SING N N 42 GMK C2 C3 DOUB Y N 43 GMK C2 C8 SING Y N 44 GMK C3 C4 SING Y N 45 GMK C8 C7 DOUB Y N 46 GMK C4 C6 DOUB Y N 47 GMK C7 C6 SING Y N 48 GMK C7 O2 SING N N 49 GMK C5 O2 SING N N 50 GMK C3 H1 SING N N 51 GMK C4 H2 SING N N 52 GMK C5 H3 SING N N 53 GMK C5 H4 SING N N 54 GMK C5 H5 SING N N 55 GMK C6 H6 SING N N 56 GMK C8 H7 SING N N 57 GMK N1 H8 SING N N 58 GMK C9 H9 SING N N 59 GMK C10 H10 SING N N 60 GMK O3 H11 SING N N 61 GMK C11 H12 SING N N 62 GMK C12 H13 SING N N 63 GMK C12 H14 SING N N 64 GMK O4 H15 SING N N 65 GMK C13 H16 SING N N 66 GMK O6 H17 SING N N 67 GMK C14 H18 SING N N 68 GMK C15 H19 SING N N 69 GMK C16 H20 SING N N 70 GMK C17 H21 SING N N 71 GMK C18 H22 SING N N 72 GMK C18 H23 SING N N 73 GMK O12 H24 SING N N 74 GMK C19 H25 SING N N 75 GMK O13 H26 SING N N 76 GMK C20 H27 SING N N 77 GMK N2 H28 SING N N 78 GMK C23 H29 SING N N 79 GMK C24 H30 SING N N 80 GMK C25 H31 SING N N 81 GMK C27 H32 SING N N 82 GMK C28 H33 SING N N 83 GMK C28 H34 SING N N 84 GMK C28 H35 SING N N 85 GMK O8 H36 SING N N 86 # 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 GMK SMILES ACDLabs 12.01 "O=S(=O)(O)OC4C(NC(=O)c1cccc(OC)c1)C(O)C(OC4SC3OC(CO)C(O)C(NC(=O)c2cccc(OC)c2)C3O)CO" GMK InChI InChI 1.03 ;InChI=1S/C28H36N2O15S2/c1-41-15-7-3-5-13(9-15)25(36)29-19-21(33)17(11-31)43-27(23(19)35)46-28-24(45-47(38,39)40)20(22(34)18(12-32)44-28)30-26(37)14-6-4-8-16(10-14)42-2/h3-10,17-24,27-28,31-35H,11-12H2,1-2H3,(H,29,36)(H,30,37)(H,38,39,40)/t17-,18-,19+,20+,21+,22+,23-,24-,27+,28+/m1/s1 ; GMK InChIKey InChI 1.03 CNUFQRWWCPUUQG-CWKIZLMASA-N GMK SMILES_CANONICAL CACTVS 3.385 "COc1cccc(c1)C(=O)N[C@H]2[C@@H](O)[C@@H](CO)O[C@@H](S[C@@H]3O[C@H](CO)[C@H](O)[C@H](NC(=O)c4cccc(OC)c4)[C@H]3O[S](O)(=O)=O)[C@@H]2O" GMK SMILES CACTVS 3.385 "COc1cccc(c1)C(=O)N[CH]2[CH](O)[CH](CO)O[CH](S[CH]3O[CH](CO)[CH](O)[CH](NC(=O)c4cccc(OC)c4)[CH]3O[S](O)(=O)=O)[CH]2O" GMK SMILES_CANONICAL "OpenEye OEToolkits" 1.9.2 "COc1cccc(c1)C(=O)N[C@H]2[C@H]([C@H](O[C@H]([C@@H]2O)S[C@H]3[C@@H]([C@H]([C@H]([C@H](O3)CO)O)NC(=O)c4cccc(c4)OC)OS(=O)(=O)O)CO)O" GMK SMILES "OpenEye OEToolkits" 1.9.2 "COc1cccc(c1)C(=O)NC2C(C(OC(C2O)SC3C(C(C(C(O3)CO)O)NC(=O)c4cccc(c4)OC)OS(=O)(=O)O)CO)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 GMK "SYSTEMATIC NAME" ACDLabs 12.01 "3-deoxy-3-[(3-methoxybenzoyl)amino]-beta-D-galactopyranosyl 3-deoxy-3-[(3-methoxybenzoyl)amino]-2-O-sulfo-1-thio-beta-D-galactopyranoside" GMK "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.9.2 "[(2S,3R,4S,5R,6R)-6-(hydroxymethyl)-2-[(2S,3R,4S,5R,6R)-6-(hydroxymethyl)-4-[(3-methoxyphenyl)carbonylamino]-3,5-bis(oxidanyl)oxan-2-yl]sulfanyl-4-[(3-methoxyphenyl)carbonylamino]-5-oxidanyl-oxan-3-yl] hydrogen sulfate" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site GMK "Create component" 2013-05-03 EBI GMK "Initial release" 2014-05-21 RCSB GMK "Modify descriptor" 2014-09-05 RCSB #