Seven-membered ring nucleobases as inhibitors of human cytidine deaminase and APOBEC3A.
Kurup, Harikrishnan M.; Kvach, Maksim V.; Harjes, Stefan; Jameson, Geoffrey B.; Harjes, Elena; Filichev, Vyacheslav V.; Organic & biomolecular chemistry 21 (2023) 5117–5128; doi:10.1039/d3ob00392b

data_7159419
_publ_section_title
;
 Seven-membered ring nucleobases as inhibitors of human cytidine deaminase
 and APOBEC3A.
;
_journal_issue                   24
_journal_name_full               'Organic &amp; biomolecular chemistry'
_journal_page_first              5117
_journal_page_last               5128
_journal_paper_doi               10.1039/d3ob00392b
_journal_volume                  21
_journal_year                    2023
_chemical_absolute_configuration rmad
_chemical_formula_moiety         'C34 H37 N O7'
_chemical_formula_sum            'C34 H37 N O7'
_chemical_formula_weight         571.64
_chemical_name_systematic
'1-[2-deoxy-3,5-bis-O-(4-methylbenzoyl)-\b-D-erythro-pentofuranosyl]-(S)-5-benzyloxyazepan-2-one '
_space_group_crystal_system      monoclinic
_space_group_IT_number           5
_space_group_name_Hall           'C 2y'
_space_group_name_H-M_alt        'C 1 2 1'
_atom_sites_solution_hydrogens   geom
_audit_creation_date             2022-09-07
_audit_creation_method
;
Olex2 1.2
(compiled 2018.05.29 svn.r3508 for OlexSys, GUI svn.r5506)
;
_audit_update_record
;
2022-09-14 deposited with the CCDC.	2023-05-23 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 106.418(2)
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   33.3058(16)
_cell_length_b                   5.5217(3)
_cell_length_c                   17.9538(8)
_cell_measurement_reflns_used    9873
_cell_measurement_temperature    150.0
_cell_measurement_theta_max      58.810
_cell_measurement_theta_min      2.566
_cell_volume                     3167.2(3)
_computing_cell_refinement       'SAINT V8.40B (?, 2016)'
_computing_data_reduction        'SAINT V8.40B (?, 2016)'
_computing_molecular_graphics    'Olex2 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 (Dolomanov et al., 2009)'
_computing_structure_refinement  'ShelXL (Sheldrick, 2015)'
_computing_structure_solution    'SHELXT 2018/2 (Sheldrick, 2018)'
_diffrn_ambient_temperature      150.0
_diffrn_measured_fraction_theta_full 0.986
_diffrn_measured_fraction_theta_max 0.986
_diffrn_measurement_device_type  'Bruker D8 Venture'
_diffrn_measurement_method       '\f and \w scans'
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54178
_diffrn_reflns_av_R_equivalents  0.0320
_diffrn_reflns_av_unetI/netI     0.0332
_diffrn_reflns_Laue_measured_fraction_full 0.986
_diffrn_reflns_Laue_measured_fraction_max 0.986
_diffrn_reflns_limit_h_max       36
_diffrn_reflns_limit_h_min       -36
_diffrn_reflns_limit_k_max       5
_diffrn_reflns_limit_k_min       -5
_diffrn_reflns_limit_l_max       20
_diffrn_reflns_limit_l_min       -20
_diffrn_reflns_number            18253
_diffrn_reflns_point_group_measured_fraction_full 0.968
_diffrn_reflns_point_group_measured_fraction_max 0.968
_diffrn_reflns_theta_full        59.414
_diffrn_reflns_theta_max         59.414
_diffrn_reflns_theta_min         2.566
_diffrn_source                   'Micro-focus sealed source'
_exptl_absorpt_coefficient_mu    0.680
_exptl_absorpt_correction_T_max  0.7516
_exptl_absorpt_correction_T_min  0.6311
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
SADABS-2016/2 (Bruker,2016/2) was used for absorption correction.
wR2(int) was 0.1035 before and 0.0444 after correction.
The Ratio of minimum to maximum transmission is 0.8397.
The \l/2 correction factor is Not present.
;
_exptl_crystal_colour            'clear colourless'
_exptl_crystal_colour_lustre     clear
_exptl_crystal_colour_primary    colourless
_exptl_crystal_density_diffrn    1.199
_exptl_crystal_description       needle
_exptl_crystal_F_000             1216
_exptl_crystal_size_max          0.2
_exptl_crystal_size_mid          0.05
_exptl_crystal_size_min          0.01
_refine_diff_density_max         0.765
_refine_diff_density_min         -0.374
_refine_diff_density_rms         0.059
_refine_ls_abs_structure_details
;
 Flack x determined using 1573 quotients [(I+)-(I-)]/[(I+)+(I-)]
 (Parsons, Flack and Wagner, Acta Cryst. B69 (2013) 249-259).
;
_refine_ls_abs_structure_Flack   -0.02(9)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.078
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     381
_refine_ls_number_reflns         4471
_refine_ls_number_restraints     1
_refine_ls_restrained_S_all      1.078
_refine_ls_R_factor_all          0.0582
_refine_ls_R_factor_gt           0.0536
_refine_ls_shift/su_max          0.001
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.0935P)^2^+2.5551P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1439
_refine_ls_wR_factor_ref         0.1481
_reflns_Friedel_coverage         0.751
_reflns_Friedel_fraction_full    0.945
_reflns_Friedel_fraction_max     0.945
_reflns_number_gt                4102
_reflns_number_total             4471
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d3ob00392b2.cif
_cod_data_source_block           hari_0m
_cod_database_code               7159419
_shelx_shelxl_version_number     2017/1
_shelx_estimated_absorpt_t_max   0.993
_shelx_estimated_absorpt_t_min   0.876
_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:
 C3'(H3'), C4'(H4'), C1'(H1'), C5(H5)
2.b Secondary CH2 refined with riding coordinates:
 C2'(H2'A,H2'B), C7(H7A,H7B), C4(H4A,H4B), C6(H6A,H6B), C5'(H5'A,H5'B), C3(H3A,
 H3B), C1T(H1TA,H1TB)
2.c Aromatic/amide H refined with riding coordinates:
 C18T(H18T), C17T(H17T), C13T(H13T), C28T(H28T), C14T(H14T), C23T(H23T),
 C24T(H24T), C27T(H27T), C7T(H7T), C4T(H4T), C5T(H5T), C3T(H3T), C6T(H6T)
2.d Idealised Me refined as rotating group:
 C16T(H16A,H16B,H16C), C26T(H26A,H26B,H26C)
;
_smtbx_masks_void_probe_radius   1.2
_smtbx_masks_void_truncation_radius 1.2
_shelx_res_checksum              28778
_shelx_hkl_checksum              96010
_shelx_fab_checksum              41211
_olex2_submission_special_instructions 'No special instructions were received'