Design and application of a non-toxic platinum derivative of the metal chelator Dp44mT for use as a long-term stable lysosome tracker
Sheernaly, Nandan; Steinbrueck, Axel; Ochs, Jasmine; Peeters, Frank; Fiedler, Ronja; Narberhaus, Franz; Heinen-Weiler, Jacqueline; Metzler-Nolte, Nils; Chemical Communications 61 (2025) 9964–9967; doi:10.1039/D5CC01596K

data_7134682
_publ_section_title
;
 Design and application of a non-toxic platinum derivative of the metal
 chelator Dp44mT for use as a long-term stable lysosome tracker
;
_journal_issue                   54
_journal_name_full               'Chemical Communications'
_journal_page_first              9964
_journal_page_last               9967
_journal_paper_doi               10.1039/D5CC01596K
_journal_volume                  61
_journal_year                    2025
_chemical_formula_moiety         'C14 H14 Cl N5 Pt S'
_chemical_formula_sum            'C14 H14 Cl N5 Pt S'
_chemical_formula_weight         514.897
_chemical_properties_physical    Hygroscopic
_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'
_symmetry_Int_Tables_number      14
_atom_sites_solution_primary     dual
_audit_creation_date             2024-11-21
_audit_creation_method
;
Olex2 1.5
(compiled 2023.03.06 svn.rbb2c1857 for OlexSys, GUI svn.r6748)
;
_audit_update_record
;
2025-02-27 deposited with the CCDC.	2025-05-23 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 101.726(1)
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   11.3054(2)
_cell_length_b                   8.7072(1)
_cell_length_c                   15.9931(2)
_cell_measurement_reflns_used    7469
_cell_measurement_temperature    100.00(14)
_cell_measurement_theta_max      76.1620
_cell_measurement_theta_min      4.3840
_cell_volume                     1541.48(4)
_computing_cell_refinement       'CrysAlisPro 1.171.41.93a (Rigaku OD, 2020)'
_computing_data_collection       'CrysAlisPro 1.171.41.93a (Rigaku OD, 2020)'
_computing_data_reduction        'CrysAlisPro 1.171.41.93a (Rigaku OD, 2020)'
_computing_molecular_graphics    'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_structure_refinement  'olex2.refine 1.5 (Bourhis et al., 2015)'
_computing_structure_solution    'SHELXT 2018/2 (Sheldrick, 2018)'
_diffrn_ambient_environment      N~2~
_diffrn_ambient_temperature      100.00(14)
_diffrn_detector                 'Hybrid Pixel Array Detector'
_diffrn_detector_area_resol_mean 10.0000
_diffrn_detector_type            HyPix
_diffrn_measured_fraction_theta_full 0.9979
_diffrn_measured_fraction_theta_max 0.9398
_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     45.00 115.00   0.50    0.05    --   47.28  26.00 -36.00  140
  2  \w    145.00 175.00   0.50    0.08    --  105.91 125.00-180.00   60
  3  \w     96.00 137.00   0.50    0.08    --  105.91 125.00-180.00   82
  4  \w     94.00 171.00   0.50    0.08    --  105.91  26.00 -36.00  154
  5  \w    106.00 175.00   0.50    0.08    --  105.91 125.00 150.00  138
  6  \w    -46.00 -20.00   0.50    0.08    --  -91.75  45.00 120.00   52
  7  \w    -54.00 -19.00   0.50    0.08    --  -91.75  61.00 150.00   70
  8  \w    -63.00 -22.00   0.50    0.08    --  -91.75  61.00 120.00   82
  9  \w    -67.00 -30.00   0.50    0.08    --  -91.75  61.00  60.00   74
 10  \w    -48.00 -21.00   0.50    0.08    --  -91.75  45.00  30.00   54
 11  \w    -46.00 -20.00   0.50    0.08    --  -91.75  45.00  90.00   52
 12  \w    -45.00 -20.00   0.50    0.08    --  -91.75  45.00 -60.00   50
 13  \w    -53.00 -26.00   0.50    0.08    --  -91.75  61.00 -90.00   54
 14  \w    -48.00 -23.00   0.50    0.08    --  -91.75  45.00-150.00   50
 15  \w    -48.00 -20.00   0.50    0.08    --  -91.75  45.00-120.00   56
 16  \w    -48.00 -23.00   0.50    0.08    --  -91.75  45.00 -90.00   50
 17  \w    -47.00 -20.00   0.50    0.08    --  -91.75  45.00 -30.00   54
 18  \w   -113.00 -42.00   0.50    0.05    --  -47.28 -26.00 160.00  142
 19  \w   -120.00 -94.00   0.50    0.08    --  -91.75 -26.00 160.00   52
 20  \w     -1.00  30.00   0.50    0.05    --   47.28 -26.00 160.00   62
 21  \w     37.00  62.00   0.50    0.08    --  105.91 -61.00 120.00   50
 22  \w    -18.00  29.00   0.50    0.05    --   47.28 -19.00  30.00   94
 23  \w     33.00  67.00   0.50    0.08    --  105.91 -61.00-120.00   68
 24  \w     38.00  65.00   0.50    0.08    --  105.91 -61.00-180.00   54
 25  \w     54.00 105.00   0.50    0.08    --  105.91 -94.00 -30.00  102
 26  \w    -28.00   0.00   0.50    0.05    --  -47.28  26.00 -36.00   56
 27  \w    -10.00  25.00   0.50    0.05    --  -47.28  19.00  90.00   70
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'XtaLAB Synergy, Dualflex, HyPix'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      0.0677199000
_diffrn_orient_matrix_UB_12      -0.0283153000
_diffrn_orient_matrix_UB_13      -0.0730201000
_diffrn_orient_matrix_UB_21      0.1117918000
_diffrn_orient_matrix_UB_22      -0.0537166000
_diffrn_orient_matrix_UB_23      0.0653878000
_diffrn_orient_matrix_UB_31      -0.0478395000
_diffrn_orient_matrix_UB_32      -0.1661123000
_diffrn_orient_matrix_UB_33      -0.0088141000
_diffrn_radiation_monochromator  mirror
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           'Cu K\a'
_diffrn_radiation_wavelength     1.54184
_diffrn_reflns_av_R_equivalents  0.0416
_diffrn_reflns_av_unetI/netI     0.0348
_diffrn_reflns_Laue_measured_fraction_full 0.9979
_diffrn_reflns_Laue_measured_fraction_max 0.9398
_diffrn_reflns_limit_h_max       14
_diffrn_reflns_limit_h_min       -13
_diffrn_reflns_limit_k_max       4
_diffrn_reflns_limit_k_min       -10
_diffrn_reflns_limit_l_max       20
_diffrn_reflns_limit_l_min       -18
_diffrn_reflns_number            11035
_diffrn_reflns_point_group_measured_fraction_full 0.9979
_diffrn_reflns_point_group_measured_fraction_max 0.9398
_diffrn_reflns_theta_full        67.6840
_diffrn_reflns_theta_max         76.81
_diffrn_reflns_theta_min         4.40
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'PhotonJet (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    19.913
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.46492
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.41.93a (Rigaku Oxford Diffraction, 2020)
Empirical absorption correction using spherical harmonics,
implemented in SCALE3 ABSPACK scaling algorithm.
;
_exptl_crystal_colour            'clear reddish orange'
_exptl_crystal_colour_lustre     clear
_exptl_crystal_colour_modifier   reddish
_exptl_crystal_colour_primary    orange
_exptl_crystal_density_diffrn    2.219
_exptl_crystal_description       block
_exptl_crystal_F_000             964.729
_exptl_crystal_recrystallization_method
'grown by slow evaporation of pentane into acetonitrile'
_exptl_crystal_size_max          0.1
_exptl_crystal_size_mid          0.1
_exptl_crystal_size_min          0.1
_refine_diff_density_max         1.2683
_refine_diff_density_min         -1.5460
_refine_diff_density_rms         0.2037
_refine_ls_d_res_high            0.7918
_refine_ls_d_res_low             10.0533
_refine_ls_goodness_of_fit_ref   1.0439
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_constraints    23
_refine_ls_number_parameters     204
_refine_ls_number_reflns         3046
_refine_ls_number_restraints     0
_refine_ls_restrained_S_all      1.0439
_refine_ls_R_factor_all          0.0282
_refine_ls_R_factor_gt           0.0267
_refine_ls_shift/su_max          0.0009
_refine_ls_shift/su_mean         0.0000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.0470P)^2^+1.2568P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.0725
_refine_ls_wR_factor_ref         0.0740
_reflns_Friedel_coverage         0.0
_reflns_limit_h_max              10
_reflns_limit_h_min              -14
_reflns_limit_k_max              10
_reflns_limit_k_min              0
_reflns_limit_l_max              20
_reflns_limit_l_min              -9
_reflns_number_gt                2881
_reflns_number_total             3046
_reflns_threshold_expression     I>=2u(I)
_cod_data_source_file            d5cc01596k2.cif
_cod_data_source_block           NMN-JO-NS-184_auto_a
_cod_depositor_comments          'Adding full bibliography for 7134682.cif.'
_cod_database_code               7134682
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.5 times of:
  All C(H,H,H) groups, H1 of C1
 At 1.2 times of:
  H10 of C10, H9 of C9, H11 of C11, H8 of C8, H2 of C2, H4 of C4, H3 of C3
2.a Aromatic/amide H refined with riding coordinates:
 C8(H8), C9(H9), C10(H10), C11(H11), C2(H2), C3(H3), C4(H4)
2.b Idealised Me refined as rotating group:
 C13(H13a,H13b,H13c), C14(H14a,H14b,H14c)
;
_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 1.892
_oxdiff_exptl_absorpt_empirical_full_min 0.767