data_1C6
# 
_chem_comp.id                                    1C6 
_chem_comp.name                                  "6-methoxy-2-{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfanyl}-1H-benzimidazole" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C17 H19 N3 O2 S" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         "omeprazole; prilosec" 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2013-04-29 
_chem_comp.pdbx_modified_date                    2020-05-26 
_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                        329.417 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     1C6 
_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        4KEW 
_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 
1C6 S   S   S 0 1 N N N 11.743 21.632 8.502  -0.345 0.891  -0.863 S   1C6 1  
1C6 CB  CB  C 0 1 N N N 13.339 21.769 9.107  -1.143 0.176  0.596  CB  1C6 2  
1C6 CG  CG  C 0 1 Y N N 13.660 20.601 10.022 -2.634 0.374  0.501  CG  1C6 3  
1C6 CD1 CD1 C 0 1 Y N N 14.015 20.732 11.472 -3.411 -0.587 -0.112 CD1 1C6 4  
1C6 C3  C3  C 0 1 N N N 14.095 22.089 12.131 -2.779 -1.829 -0.686 C3  1C6 5  
1C6 CE1 CE1 C 0 1 Y N N 14.294 19.466 12.232 -4.787 -0.394 -0.194 CE1 1C6 6  
1C6 O2  O2  O 0 1 N N N 14.630 19.402 13.563 -5.586 -1.316 -0.790 O2  1C6 7  
1C6 C2  C2  C 0 1 N N N 13.924 20.225 14.514 -6.116 -2.349 0.043  C2  1C6 8  
1C6 CZ  CZ  C 0 1 Y N N 14.210 18.180 11.489 -5.325 0.770  0.351  CZ  1C6 9  
1C6 C1  C1  C 0 1 N N N 14.504 16.860 12.203 -6.808 1.028  0.290  C1  1C6 10 
1C6 CE2 CE2 C 0 1 Y N N 13.880 18.203 10.120 -4.480 1.683  0.948  CE2 1C6 11 
1C6 N1  N1  N 0 1 Y N N 13.648 19.365 9.454  -3.181 1.462  1.010  N1  1C6 12 
1C6 CF1 CF1 C 0 1 Y N N 11.573 23.194 7.832  1.340  0.528  -0.499 CF1 1C6 13 
1C6 NV  NV  N 0 1 Y N N 12.467 23.847 7.027  2.404  0.860  -1.290 NV  1C6 14 
1C6 CX2 CX2 C 0 1 Y N N 11.941 25.059 6.708  3.547  0.406  -0.653 CX2 1C6 15 
1C6 CS2 CS2 C 0 1 Y N N 10.659 25.110 7.439  3.117  -0.202 0.537  CS2 1C6 16 
1C6 NE1 NE1 N 0 1 Y N N 10.507 23.922 8.118  1.761  -0.095 0.574  NE1 1C6 17 
1C6 CE3 CE3 C 0 1 Y N N 12.299 26.190 5.943  4.899  0.448  -0.961 CE3 1C6 18 
1C6 CZ3 CZ3 C 0 1 Y N N 11.451 27.304 5.869  5.820  -0.110 -0.091 CZ3 1C6 19 
1C6 O3  O3  O 0 1 N N N 11.795 28.446 5.124  7.146  -0.068 -0.392 O3  1C6 20 
1C6 C4  C4  C 0 1 N N N 10.806 29.331 4.517  8.043  -0.663 0.548  C4  1C6 21 
1C6 CH2 CH2 C 0 1 Y N N 10.257 27.324 6.554  5.396  -0.713 1.088  CH2 1C6 22 
1C6 CZ2 CZ2 C 0 1 Y N N 9.869  26.230 7.314  4.058  -0.762 1.405  CZ2 1C6 23 
1C6 H1  H1  H 0 1 N N N 14.047 21.775 8.265  -0.920 -0.889 0.647  H1  1C6 24 
1C6 H2  H2  H 0 1 N N N 13.433 22.708 9.672  -0.768 0.669  1.493  H2  1C6 25 
1C6 H3  H3  H 0 1 N N N 13.111 22.354 12.546 -2.747 -2.606 0.078  H3  1C6 26 
1C6 H4  H4  H 0 1 N N N 14.839 22.060 12.941 -3.366 -2.177 -1.535 H4  1C6 27 
1C6 H5  H5  H 0 1 N N N 14.394 22.841 11.386 -1.765 -1.601 -1.015 H5  1C6 28 
1C6 H6  H6  H 0 1 N N N 14.323 20.044 15.523 -6.722 -1.904 0.832  H6  1C6 29 
1C6 H7  H7  H 0 1 N N N 14.057 21.285 14.252 -6.735 -3.017 -0.556 H7  1C6 30 
1C6 H8  H8  H 0 1 N N N 12.853 19.974 14.492 -5.297 -2.914 0.488  H8  1C6 31 
1C6 H9  H9  H 0 1 N N N 15.577 16.632 12.125 -7.286 0.612  1.177  H9  1C6 32 
1C6 H10 H10 H 0 1 N N N 14.224 16.946 13.263 -6.989 2.102  0.249  H10 1C6 33 
1C6 H11 H11 H 0 1 N N N 13.922 16.052 11.734 -7.222 0.556  -0.601 H11 1C6 34 
1C6 H12 H12 H 0 1 N N N 13.809 17.269 9.583  -4.888 2.588  1.373  H12 1C6 35 
1C6 H13 H13 H 0 1 N N N 13.353 23.494 6.726  2.366  1.326  -2.140 H13 1C6 36 
1C6 H15 H15 H 0 1 N N N 13.237 26.197 5.408  5.232  0.915  -1.876 H15 1C6 37 
1C6 H16 H16 H 0 1 N N N 11.319 30.149 3.990  9.067  -0.561 0.187  H16 1C6 38 
1C6 H17 H17 H 0 1 N N N 10.194 28.761 3.802  7.945  -0.162 1.510  H17 1C6 39 
1C6 H18 H18 H 0 1 N N N 10.159 29.750 5.301  7.802  -1.720 0.662  H18 1C6 40 
1C6 H19 H19 H 0 1 N N N 9.620  28.194 6.500  6.123  -1.146 1.760  H19 1C6 41 
1C6 H20 H20 H 0 1 N N N 8.917  26.258 7.824  3.735  -1.231 2.323  H20 1C6 42 
# 
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 
1C6 C4  O3  SING N N 1  
1C6 O3  CZ3 SING N N 2  
1C6 CZ3 CE3 DOUB Y N 3  
1C6 CZ3 CH2 SING Y N 4  
1C6 CE3 CX2 SING Y N 5  
1C6 CH2 CZ2 DOUB Y N 6  
1C6 CX2 NV  SING Y N 7  
1C6 CX2 CS2 DOUB Y N 8  
1C6 NV  CF1 SING Y N 9  
1C6 CZ2 CS2 SING Y N 10 
1C6 CS2 NE1 SING Y N 11 
1C6 CF1 NE1 DOUB Y N 12 
1C6 CF1 S   SING N N 13 
1C6 S   CB  SING N N 14 
1C6 CB  CG  SING N N 15 
1C6 N1  CG  DOUB Y N 16 
1C6 N1  CE2 SING Y N 17 
1C6 CG  CD1 SING Y N 18 
1C6 CE2 CZ  DOUB Y N 19 
1C6 CD1 C3  SING N N 20 
1C6 CD1 CE1 DOUB Y N 21 
1C6 CZ  C1  SING N N 22 
1C6 CZ  CE1 SING Y N 23 
1C6 CE1 O2  SING N N 24 
1C6 O2  C2  SING N N 25 
1C6 CB  H1  SING N N 26 
1C6 CB  H2  SING N N 27 
1C6 C3  H3  SING N N 28 
1C6 C3  H4  SING N N 29 
1C6 C3  H5  SING N N 30 
1C6 C2  H6  SING N N 31 
1C6 C2  H7  SING N N 32 
1C6 C2  H8  SING N N 33 
1C6 C1  H9  SING N N 34 
1C6 C1  H10 SING N N 35 
1C6 C1  H11 SING N N 36 
1C6 CE2 H12 SING N N 37 
1C6 NV  H13 SING N N 38 
1C6 CE3 H15 SING N N 39 
1C6 C4  H16 SING N N 40 
1C6 C4  H17 SING N N 41 
1C6 C4  H18 SING N N 42 
1C6 CH2 H19 SING N N 43 
1C6 CZ2 H20 SING N N 44 
# 
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 
1C6 SMILES           ACDLabs              12.01 "n2c1ccc(OC)cc1nc2SCc3ncc(c(OC)c3C)C"                                                                                  
1C6 InChI            InChI                1.03  "InChI=1S/C17H19N3O2S/c1-10-8-18-15(11(2)16(10)22-4)9-23-17-19-13-6-5-12(21-3)7-14(13)20-17/h5-8H,9H2,1-4H3,(H,19,20)" 
1C6 InChIKey         InChI                1.03  XURCIPRUUASYLR-UHFFFAOYSA-N                                                                                            
1C6 SMILES_CANONICAL CACTVS               3.370 "COc1ccc2nc([nH]c2c1)SCc3ncc(C)c(OC)c3C"                                                                               
1C6 SMILES           CACTVS               3.370 "COc1ccc2nc([nH]c2c1)SCc3ncc(C)c(OC)c3C"                                                                               
1C6 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "Cc1cnc(c(c1OC)C)CSc2[nH]c3cc(ccc3n2)OC"                                                                               
1C6 SMILES           "OpenEye OEToolkits" 1.7.6 "Cc1cnc(c(c1OC)C)CSc2[nH]c3cc(ccc3n2)OC"                                                                               
# 
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 
1C6 "SYSTEMATIC NAME" ACDLabs              12.01 "6-methoxy-2-{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfanyl}-1H-benzimidazole" 
1C6 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "6-methoxy-2-[(4-methoxy-3,5-dimethyl-pyridin-2-yl)methylsulfanyl]-1H-benzimidazole"  
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
1C6 "Create component" 2013-04-29 RCSB 
1C6 "Modify synonyms"  2013-04-29 RCSB 
1C6 "Initial release"  2013-07-10 RCSB 
1C6 "Modify synonyms"  2020-05-26 PDBE 
# 
loop_
_pdbx_chem_comp_synonyms.ordinal 
_pdbx_chem_comp_synonyms.comp_id 
_pdbx_chem_comp_synonyms.name 
_pdbx_chem_comp_synonyms.provenance 
_pdbx_chem_comp_synonyms.type 
1 1C6 omeprazole ? ? 
2 1C6 prilosec   ? ? 
# 
