2-cyanopyridine derivatives enable N-terminal cysteine bioconjugation and peptide bond cleavage of glutathione under aqueous and mild conditions
Yano, Tetsuya; Yamada, Takahiro; Isida, Hiroaki; Ohashi, Nami; Itoh, Toshimasa; RSC Advances 14 (2024) 6542–6547; doi:10.1039/D4RA00437J

data_7248213
_publ_section_title
;
 2-cyanopyridine derivatives enable N-terminal cysteine bioconjugation and
 peptide bond cleavage of glutathione under aqueous and mild conditions
;
_journal_issue                   10
_journal_name_full               'RSC Advances'
_journal_page_first              6542
_journal_page_last               6547
_journal_paper_doi               10.1039/D4RA00437J
_journal_volume                  14
_journal_year                    2024
_chemical_formula_moiety         'C10 H9 Br N2 O2 S'
_chemical_formula_sum            'C10 H9 Br N2 O2 S'
_chemical_formula_weight         301.16
_chemical_name_systematic
'methyl (R)-2-(5-bromopyridin-2-yl)-4,5-dihydrothiazole-4-carboxylate'
_space_group_crystal_system      monoclinic
_space_group_IT_number           14
_space_group_name_Hall           '-P 2yn'
_space_group_name_H-M_alt        'P 1 21/n 1'
_atom_sites_solution_hydrogens   geom
_atom_sites_solution_primary     dual
_audit_creation_date             2023-08-02
_audit_creation_method
;
Olex2 1.5
(compiled 2022.04.07 svn.rca3783a0 for OlexSys, GUI svn.r6498)
;
_audit_update_record
;
2023-11-27 deposited with the CCDC.	2024-02-13 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 100.6459(8)
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   14.61601(13)
_cell_length_b                   4.09391(4)
_cell_length_c                   18.54407(16)
_cell_measurement_reflns_used    34357
_cell_measurement_temperature    93.15
_cell_measurement_theta_max      77.0370
_cell_measurement_theta_min      2.4170
_cell_volume                     1090.516(17)
_computing_cell_refinement       'CrysAlisPro 1.171.42.72a (Rigaku OD, 2022)'
_computing_data_collection       'CrysAlisPro 1.171.42.72a (Rigaku OD, 2022)'
_computing_data_reduction        'CrysAlisPro 1.171.42.72a (Rigaku OD, 2022)'
_computing_molecular_graphics    'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_structure_refinement  'SHELXL 2018/3 (Sheldrick, 2015)'
_computing_structure_solution    'SHELXT 2018/2 (Sheldrick, 2018)'
_diffrn_ambient_temperature      93.15
_diffrn_detector                 'Image Plate'
_diffrn_detector_area_resol_mean 10.0000
_diffrn_detector_type            'Rigaku IP'
_diffrn_measured_fraction_theta_full 0.998
_diffrn_measured_fraction_theta_max 0.957
_diffrn_measurement_details
;
List of Runs (angles in degrees, time in seconds):

  # Type    Start    End  Width  t~exp~   \w     \q     \k     \f   Frames
  1  \w    -70.00 -24.00   0.50    0.05    --  -97.00  57.00 150.00   92
  2  \w    -70.00 -24.00   0.50    0.05    --  -97.00  57.00  90.00   92
  3  \w    -70.00 -24.00   0.50    0.05    --  -97.00  57.00  60.00   92
  4  \w    -54.00 -25.00   0.50    0.05    --  -97.00  43.00   8.00   58
  5  \w    -54.00  25.00   0.50    0.05    --  -46.95  43.00   8.00  158
  6  \w    -70.00 -24.00   0.50    0.05    --  -97.00  57.00-180.00   92
  7  \w   -108.00 -28.00   0.50    0.05    --  -97.00 112.00-175.12  160
  8  \w   -108.00 -28.00   0.50    0.05    --  -97.00 113.00   5.14  160
  9  \w   -119.00 -47.00   0.50    0.05    --  -46.95 179.00  90.00  144
 10  \w     32.00 118.00   0.50    0.05    --   46.95  57.00  90.00  172
 11  \w     24.00 119.00   0.50    0.05    --   46.95  77.00  60.00  190
 12  \w     35.00 120.00   0.50    0.05    --   46.95  37.00 150.00  170
 13  \w     32.00 118.00   0.50    0.05    --   46.95  57.00  30.00  172
 14  \w     35.00 119.00   0.50    0.05    --   46.95  43.00   8.00  168
 15  \w     24.00 119.00   0.50    0.05    --   46.95  77.00 -60.00  190
 16  \w     32.00 118.00   0.50    0.05    --   46.95  57.00-150.00  172
 17  \w     36.00  96.00   0.50    0.05    --  108.36 -77.00 -30.00  120
 18  \w    -25.00  44.00   0.50    0.05    --   46.95 -43.00-142.00  138
 19  \w     96.00 175.00   0.50    0.05    --  108.36  37.00 -30.00  158
 20  \w     95.00 175.00   0.50    0.05    --  108.36  43.00   8.00  160
 21  \w    -27.00  26.00   0.50    0.05    --   46.95 -19.00  60.00  106
 22  \w     36.00  96.00   0.50    0.05    --  108.36 -77.00 -60.00  120
 23  \w     38.00 106.00   0.50    0.05    --  108.36 -99.00 -90.00  136
 24  \w     39.00 111.00   0.50    0.05    --  108.36-125.00-150.00  144
 25  \w     38.00 106.00   0.50    0.05    --  108.36 -99.00-150.00  136
 26  \w     38.00 106.00   0.50    0.05    --  108.36 -99.00 -60.00  136
 27  \w     38.00 106.00   0.50    0.05    --  108.36 -99.00  30.00  136
 28  \w   -119.00 -24.00   0.50    0.05    --  -46.95 -77.00 150.00  190
 29  \w   -119.00 -24.00   0.50    0.05    --  -46.95 -77.00 -30.00  190
 30  \w   -118.00 -32.00   0.50    0.05    --  -46.95 -57.00-150.00  172
 31  \w   -119.00 -33.00   0.50    0.05    --  -46.95 -43.00-142.00  172
 32  \w   -120.00 -34.00   0.50    0.05    --  -46.95 -37.00 -30.00  172
 33  \w   -170.00 -74.00   0.50    0.05    --  -97.00 -77.00 150.00  192
 34  \w   -170.00 -74.00   0.50    0.05    --  -97.00 -77.00 120.00  192
 35  \w   -170.00 -74.00   0.50    0.05    --  -97.00 -77.00 106.07  192
 36  \w   -170.00 -74.00   0.50    0.05    --  -97.00 -77.00  90.00  192
 37  \w   -170.00 -74.00   0.50    0.05    --  -97.00 -77.00   7.01  192
 38  \w   -170.00 -75.00   0.50    0.05    --  -97.00 -75.00  25.26  190
 39  \w   -170.00 -75.00   0.50    0.05    --  -97.00 -75.00 -44.88  190
 40  \w   -170.00 -74.00   0.50    0.05    --  -97.00 -77.00-180.00  192
 41  \w   -170.00 -74.00   0.50    0.05    --  -97.00 -76.00-141.70  192
 42  \w   -170.00 -74.00   0.50    0.05    --  -97.00 -77.00 -90.00  192
 43  \w   -170.00 -77.00   0.50    0.05    --  -97.00 -71.00 -34.53  186
 44  \w   -170.00 -77.00   0.50    0.05    --  -97.00 -69.00 -76.59  186
 45  \w   -170.00 -76.00   0.50    0.05    --  -97.00 -72.00  61.36  188
 46  \w   -170.00 -77.00   0.50    0.05    --  -97.00 -69.00 119.17  186
 47  \w   -170.00 -75.00   0.50    0.05    --  -97.00 -75.00 159.89  190
 48  \w   -170.00 -76.00   0.50    0.05    --  -97.00 -72.00 163.76  188
 49  \w   -170.00 -80.00   0.50    0.05    --  -97.00 -63.00 137.73  180
 50  \w   -169.00 -82.00   0.50    0.05    --  -97.00 -58.00  86.04  174
 51  \w   -170.00 -80.00   0.50    0.05    --  -97.00 -62.00  27.26  180
 52  \w   -169.00 -82.00   0.50    0.05    --  -97.00 -57.00  90.00  174
 53  \w   -170.00 -79.00   0.50    0.05    --  -97.00 -64.00 -25.17  182
 54  \w   -169.00 -81.00   0.50    0.05    --  -97.00 -59.00-133.39  176
 55  \w   -169.00 -82.00   0.50    0.05    --  -97.00 -57.00-180.00  174
 56  \w   -169.00 -82.00   0.50    0.05    --  -97.00 -55.00-129.71  174
 57  \w   -170.00 -80.00   0.50    0.05    --  -97.00 -62.00 -38.10  180
 58  \w   -169.00 -83.00   0.50    0.05    --  -97.00 -43.00-142.00  172
 59  \w   -172.00 -84.00   0.50    0.05    --  -97.00 -19.00 150.00  176
 60  \w   -169.00 -82.00   0.50    0.05    --  -97.00 -57.00 140.52  174
 61  \w   -169.00 -82.00   0.50    0.05    --  -97.00 -56.00 117.23  174
 62  \w   -169.00 -83.00   0.50    0.05    --  -97.00 -54.00 110.57  172
 63  \w   -168.00 -91.00   0.50    0.05    --  -97.00 -99.00 -30.00  154
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'Rigaku R-AXIS SPIDER IP'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      0.0086828000
_diffrn_orient_matrix_UB_12      0.0800586000
_diffrn_orient_matrix_UB_13      -0.0796284000
_diffrn_orient_matrix_UB_21      0.0930307000
_diffrn_orient_matrix_UB_22      -0.1866719000
_diffrn_orient_matrix_UB_23      0.0105599000
_diffrn_orient_matrix_UB_31      -0.0526463000
_diffrn_orient_matrix_UB_32      -0.3167596000
_diffrn_orient_matrix_UB_33      -0.0263732000
_diffrn_radiation_monochromator  graphite
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           'Cu K\a'
_diffrn_radiation_wavelength     1.54184
_diffrn_reflns_av_R_equivalents  0.0407
_diffrn_reflns_av_unetI/netI     0.0112
_diffrn_reflns_Laue_measured_fraction_full 0.998
_diffrn_reflns_Laue_measured_fraction_max 0.957
_diffrn_reflns_limit_h_max       18
_diffrn_reflns_limit_h_min       -18
_diffrn_reflns_limit_k_max       5
_diffrn_reflns_limit_k_min       -4
_diffrn_reflns_limit_l_max       23
_diffrn_reflns_limit_l_min       -22
_diffrn_reflns_number            37570
_diffrn_reflns_point_group_measured_fraction_full 0.998
_diffrn_reflns_point_group_measured_fraction_max 0.957
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         77.250
_diffrn_reflns_theta_min         3.549
_diffrn_source                   'sealed X-ray tube'
_diffrn_source_target            Mo
_diffrn_source_type              'Rigaku (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    6.833
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.40517
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.42.72a (Rigaku Oxford Diffraction, 2022)
Empirical absorption correction using spherical harmonics,
implemented in SCALE3 ABSPACK scaling algorithm.
;
_exptl_crystal_colour            'clear colourless'
_exptl_crystal_colour_lustre     clear
_exptl_crystal_colour_primary    colourless
_exptl_crystal_density_diffrn    1.834
_exptl_crystal_description       needle
_exptl_crystal_F_000             600
_exptl_crystal_recrystallization_method n-hexane
_exptl_crystal_size_max          0.5
_exptl_crystal_size_mid          0.1
_exptl_crystal_size_min          0.05
_refine_diff_density_max         0.371
_refine_diff_density_min         -0.501
_refine_diff_density_rms         0.074
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.132
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     146
_refine_ls_number_reflns         2211
_refine_ls_number_restraints     0
_refine_ls_restrained_S_all      1.132
_refine_ls_R_factor_all          0.0218
_refine_ls_R_factor_gt           0.0218
_refine_ls_shift/su_max          0.002
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.0232P)^2^+1.6806P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.0563
_refine_ls_wR_factor_ref         0.0563
_reflns_Friedel_coverage         0.000
_reflns_number_gt                2205
_reflns_number_total             2211
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d4ra00437j2.cif
_cod_data_source_block           20230727_4_auto
_cod_database_code               7248213
_shelx_shelxl_version_number     2018/3
_chemical_oxdiff_formula         C10H9N2O2S1Br1
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All C(H,H) groups
 At 1.5 times of:
  All C(H,H,H) groups
2.a Ternary CH refined with riding coordinates:
 C00C(H00C)
2.b Secondary CH2 refined with riding coordinates:
 C00F(H00B,H00E)
2.c Aromatic/amide H refined with riding coordinates:
 C009(H009), C00A(H00A), C00D(H00D)
2.d Idealised Me refined as rotating group:
 C00G(H00F,H00G,H00H)
;
_olex2_submission_original_sample_id yts-5-Br
_olex2_submission_special_instructions 'No special instructions were received'
_oxdiff_exptl_absorpt_empirical_details
;
Empirical correction (ABSPACK) includes:
- Absorption correction using spherical harmonics
- Frame scaling
;
_oxdiff_exptl_absorpt_empirical_full_max 2.335
_oxdiff_exptl_absorpt_empirical_full_min 0.540