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        ?
##
