data_IMK # _chem_comp.id IMK _chem_comp.name "2-(BETA-D-GLUCOPYRANOSYL)-5-METHYL-1-BENZIMIDAZOLE" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C14 H18 N2 O5" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "2-(BETA-D-GLUCOPYRANOSYL)-5-METHYL-1,2,3-BENZIMIDAZOLE" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2004-10-05 _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 294.303 _chem_comp.one_letter_code ? _chem_comp.three_letter_code IMK _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag Y _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 1XKX _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 IMK C1 C1 C 0 1 N N S 18.097 12.965 56.274 0.886 -0.121 0.652 C1 IMK 1 IMK C2 C2 C 0 1 N N R 16.623 13.118 56.759 1.399 -1.401 -0.012 C2 IMK 2 IMK O2 O2 O 0 1 N N N 15.837 13.880 55.828 0.840 -2.539 0.647 O2 IMK 3 IMK C3 C3 C 0 1 N N R 16.622 13.814 58.150 2.926 -1.447 0.096 C3 IMK 4 IMK O3 O3 O 0 1 N N N 15.288 13.973 58.639 3.420 -2.602 -0.586 O3 IMK 5 IMK C4 C4 C 0 1 N N S 17.472 12.965 59.135 3.510 -0.185 -0.546 C4 IMK 6 IMK O4 O4 O 0 1 N N N 17.505 13.581 60.440 4.931 -0.181 -0.387 O4 IMK 7 IMK C5 C5 C 0 1 N N R 18.921 12.806 58.566 2.916 1.049 0.139 C5 IMK 8 IMK O5 O5 O 0 1 N N N 18.887 12.194 57.233 1.492 1.013 0.029 O5 IMK 9 IMK C6 C6 C 0 1 N N N 19.784 11.931 59.515 3.449 2.314 -0.536 C6 IMK 10 IMK O6 O6 O 0 1 N N N 21.157 11.969 59.095 2.987 3.464 0.176 O6 IMK 11 IMK C7 C7 C 0 1 Y N N 17.376 9.658 52.685 -3.701 0.003 -1.251 C7 IMK 12 IMK C8 C8 C 0 1 Y N N 17.754 10.801 53.428 -2.583 0.006 -0.414 C8 IMK 13 IMK C9 C9 C 0 1 Y N N 18.433 11.894 52.857 -2.759 0.139 0.974 C9 IMK 14 IMK C10 C10 C 0 1 Y N N 18.787 11.913 51.481 -4.038 0.266 1.499 C10 IMK 15 IMK C11 C11 C 0 1 Y N N 18.420 10.769 50.707 -5.127 0.261 0.653 C11 IMK 16 IMK C12 C12 C 0 1 Y N N 17.728 9.662 51.297 -4.953 0.129 -0.717 C12 IMK 17 IMK N1 N1 N 0 1 Y N N 18.631 12.798 53.843 -1.493 0.106 1.523 N1 IMK 18 IMK C13 C13 C 0 1 Y N N 18.108 12.283 54.929 -0.611 -0.040 0.498 C13 IMK 19 IMK N2 N2 N 0 1 Y N N 17.596 11.135 54.715 -1.247 -0.099 -0.635 N2 IMK 20 IMK C14 C14 C 0 1 N N N ? ? ? -6.155 0.126 -1.625 C14 IMK 21 IMK H1 H1 H 0 1 N N N 18.530 13.971 56.166 1.143 -0.134 1.712 H1 IMK 22 IMK H2 H2 H 0 1 N N N 16.193 12.112 56.876 1.107 -1.409 -1.062 H2 IMK 23 IMK HO2 HO2 H 0 1 N N N 14.947 13.955 56.151 1.122 -3.386 0.277 HO2 IMK 24 IMK H3 H3 H 0 1 N N N 17.101 14.798 58.042 3.216 -1.492 1.146 H3 IMK 25 IMK HO3 HO3 H 0 1 N N N 15.310 14.399 59.488 3.084 -3.438 -0.236 HO3 IMK 26 IMK H4 H4 H 0 1 N N N 17.020 11.965 59.207 3.263 -0.168 -1.607 H4 IMK 27 IMK HO4 HO4 H 0 1 N N N 18.028 13.049 61.028 5.374 -0.939 -0.793 HO4 IMK 28 IMK H5 H5 H 0 1 N N N 19.378 13.804 58.501 3.199 1.051 1.192 H5 IMK 29 IMK H61 H61 H 0 1 N N N 19.705 12.318 60.542 4.539 2.297 -0.530 H61 IMK 30 IMK H62 H62 H 0 1 N N N 19.421 10.893 59.486 3.091 2.355 -1.564 H62 IMK 31 IMK HO6 HO6 H 0 1 N N N 21.682 11.433 59.678 3.287 4.304 -0.197 HO6 IMK 32 IMK H7 H7 H 0 1 N N N 16.852 8.830 53.139 -3.577 -0.094 -2.320 H7 IMK 33 IMK H10 H10 H 0 1 N N N 19.308 12.751 51.042 -4.179 0.368 2.565 H10 IMK 34 IMK H11 H11 H 0 1 N N N 18.669 10.738 49.657 -6.122 0.359 1.060 H11 IMK 35 IMK HN1 HN1 H 0 1 N N N 19.086 13.684 53.760 -1.273 0.175 2.466 HN1 IMK 36 IMK H141 H141 H 0 0 N N N -0.904 0.653 -0.023 -6.510 -0.897 -1.754 H141 IMK 37 IMK H142 H142 H 0 0 N N N 0.274 0.003 -1.081 -6.946 0.731 -1.182 H142 IMK 38 IMK H143 H143 H 0 0 N N N -0.360 -1.049 0.110 -5.880 0.541 -2.594 H143 IMK 39 # # 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 IMK C1 C2 SING N N 1 IMK C1 O5 SING N N 2 IMK C1 C13 SING N N 3 IMK C1 H1 SING N N 4 IMK C2 O2 SING N N 5 IMK C2 C3 SING N N 6 IMK C2 H2 SING N N 7 IMK O2 HO2 SING N N 8 IMK C3 O3 SING N N 9 IMK C3 C4 SING N N 10 IMK C3 H3 SING N N 11 IMK O3 HO3 SING N N 12 IMK C4 O4 SING N N 13 IMK C4 C5 SING N N 14 IMK C4 H4 SING N N 15 IMK O4 HO4 SING N N 16 IMK C5 O5 SING N N 17 IMK C5 C6 SING N N 18 IMK C5 H5 SING N N 19 IMK C6 O6 SING N N 20 IMK C6 H61 SING N N 21 IMK C6 H62 SING N N 22 IMK O6 HO6 SING N N 23 IMK C7 C8 DOUB Y N 24 IMK C7 C12 SING Y N 25 IMK C7 H7 SING N N 26 IMK C8 C9 SING Y N 27 IMK C8 N2 SING Y N 28 IMK C9 C10 DOUB Y N 29 IMK C9 N1 SING Y N 30 IMK C10 C11 SING Y N 31 IMK C10 H10 SING N N 32 IMK C11 C12 DOUB Y N 33 IMK C11 H11 SING N N 34 IMK C12 C14 SING N N 35 IMK N1 C13 SING Y N 36 IMK N1 HN1 SING N N 37 IMK C13 N2 DOUB Y N 38 IMK C14 H141 SING N N 39 IMK C14 H142 SING N N 40 IMK C14 H143 SING N N 41 # # 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 IMK SMILES ACDLabs 12.01 "OC1C(O)C(O)C(OC1CO)c3nc2cc(ccc2n3)C" IMK InChI InChI 1.03 "InChI=1S/C14H18N2O5/c1-6-2-3-7-8(4-6)16-14(15-7)13-12(20)11(19)10(18)9(5-17)21-13/h2-4,9-13,17-20H,5H2,1H3,(H,15,16)/t9-,10-,11+,12-,13-/m1/s1" IMK InChIKey InChI 1.03 XIJZORUYQZBFJK-UJPOAAIJSA-N IMK SMILES_CANONICAL CACTVS 3.370 "Cc1ccc2[nH]c(nc2c1)[C@@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3O" IMK SMILES CACTVS 3.370 "Cc1ccc2[nH]c(nc2c1)[CH]3O[CH](CO)[CH](O)[CH](O)[CH]3O" IMK SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "Cc1ccc2c(c1)nc([nH]2)[C@H]3[C@@H]([C@H]([C@@H]([C@H](O3)CO)O)O)O" IMK SMILES "OpenEye OEToolkits" 1.7.6 "Cc1ccc2c(c1)nc([nH]2)C3C(C(C(C(O3)CO)O)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 IMK "SYSTEMATIC NAME" ACDLabs 12.01 "(1S)-1,5-anhydro-1-(5-methyl-1H-benzimidazol-2-yl)-D-glucitol" IMK "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "(2R,3S,4R,5R,6S)-2-(hydroxymethyl)-6-(5-methyl-1H-benzimidazol-2-yl)oxane-3,4,5-triol" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site IMK "Create component" 2004-10-05 RCSB IMK "Modify descriptor" 2011-06-04 RCSB IMK "Modify linking type" 2012-12-21 RCSB IMK "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id IMK _pdbx_chem_comp_synonyms.name "2-(BETA-D-GLUCOPYRANOSYL)-5-METHYL-1,2,3-BENZIMIDAZOLE" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##