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_7159418
_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 H34 N O7'
_chemical_formula_sum            'C34 H34 N O7'
_chemical_formula_weight         568.62
_chemical_name_systematic
1-[2-deoxy-3,5-bis-O-(4-methylbenzoyl)-\b-D-erythro-pentofuranosyl]-(R)-5-benzyloxyazepan-2-one
_space_group_crystal_system      monoclinic
_space_group_IT_number           5
_space_group_name_Hall           'I 2y'
_space_group_name_H-M_alt        'I 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                 98.636(9)
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   19.200(2)
_cell_length_b                   5.3821(5)
_cell_length_c                   32.153(4)
_cell_measurement_reflns_used    4610
_cell_measurement_temperature    293(2)
_cell_measurement_theta_max      66.554
_cell_measurement_theta_min      5.567
_cell_volume                     3284.9(6)
_computing_cell_refinement       'FSProcess in Process-Auto (Rigaku, 1998)'
_computing_data_collection       'CrystalClear (Rigaku, 2005)'
_computing_data_reduction        'FSProcess in Process-Auto (Rigaku, 1998)'
_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 2014/5 (Sheldrick, 2014)'
_diffrn_ambient_temperature      293(2)
_diffrn_detector                 'Image plate'
_diffrn_detector_area_resol_mean 10
_diffrn_measured_fraction_theta_full 0.887
_diffrn_measured_fraction_theta_max 0.887
_diffrn_measurement_device_type  'Rigaku Spider/Rapide'
_diffrn_measurement_method       \w-scans
_diffrn_radiation_monochromator  'Rigaku VariMax-HF Confocal Optical System'
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54187
_diffrn_reflns_av_R_equivalents  0.0442
_diffrn_reflns_av_unetI/netI     0.0735
_diffrn_reflns_Laue_measured_fraction_full 0.887
_diffrn_reflns_Laue_measured_fraction_max 0.887
_diffrn_reflns_limit_h_max       13
_diffrn_reflns_limit_h_min       -22
_diffrn_reflns_limit_k_max       5
_diffrn_reflns_limit_k_min       -4
_diffrn_reflns_limit_l_max       38
_diffrn_reflns_limit_l_min       -38
_diffrn_reflns_number            6980
_diffrn_reflns_point_group_measured_fraction_full 0.735
_diffrn_reflns_point_group_measured_fraction_max 0.735
_diffrn_reflns_theta_full        66.554
_diffrn_reflns_theta_max         66.554
_diffrn_reflns_theta_min         5.567
_diffrn_source                   'Rigaku MM007 microfocus roating anode/'
_exptl_absorpt_coefficient_mu    0.655
_exptl_absorpt_correction_T_max  1
_exptl_absorpt_correction_T_min  0.548
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details   '(ABSCOR; Higashi, 1995)'
_exptl_crystal_colour            colourless
_exptl_crystal_density_diffrn    1.150
_exptl_crystal_density_meas      ?
_exptl_crystal_density_method    'not measured'
_exptl_crystal_description       'flattened needle'
_exptl_crystal_F_000             1284
_exptl_crystal_size_max          0.25
_exptl_crystal_size_mid          0.10
_exptl_crystal_size_min          0.05
_refine_diff_density_max         0.155
_refine_diff_density_min         -0.173
_refine_diff_density_rms         0.043
_refine_ls_abs_structure_details
;
 Flack x determined using 505 quotients [(I+)-(I-)]/[(I+)+(I-)]
 (Parsons, Flack and Wagner, Acta Cryst. B69 (2013) 249-259).
;
_refine_ls_abs_structure_Flack   -0.2(3)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   0.914
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     380
_refine_ls_number_reflns         4270
_refine_ls_number_restraints     187
_refine_ls_restrained_S_all      0.917
_refine_ls_R_factor_all          0.1303
_refine_ls_R_factor_gt           0.0693
_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^)+(0.1410P)^2^] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1842
_refine_ls_wR_factor_ref         0.2434
_reflns_Friedel_coverage         0.485
_reflns_Friedel_fraction_full    0.543
_reflns_Friedel_fraction_max     0.543
_reflns_number_gt                1774
_reflns_number_total             4270
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d3ob00392b2.cif
_cod_data_source_block           hari_se_sx
_cod_depositor_comments
;
The following automatic conversions were performed:

data item '_exptl_crystal_density_meas' value 'not measured' was
changed to '?' -- the value is perceived as not measured.

Automatic conversion script
Id: cif_fix_values 8170 2020-07-09 18:12:32Z antanas 
;
_cod_database_code               7159418
_shelx_shelxl_version_number     2017/1
_shelx_estimated_absorpt_t_max   0.968
_shelx_estimated_absorpt_t_min   0.877
_exptl_absorpt_special_details
;
Note that the experimental absorption process corrects not only for absorption but for mis-alignment.
;
_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. Restrained distances
 C22T-C28T = C27T-C25T = C24T-C23T
 1.392 with sigma of 0.01
 C2T-C7T = C6T-C5T = C4T-C3T
 1.392 with sigma of 0.01
 C15T-C12T = C17T-C13T = C18T-C14T
 2.784 with sigma of 0.01
 C12T-C18T = C17T-C15T = C14T-C13T
 1.392 with sigma of 0.01
 C15T-C12T
 2.784 with sigma of 0.01
 C17T-C13T
 2.784 with sigma of 0.01
 C18T-C14T
 2.784 with sigma of 0.01
3. Restrained planarity
 O3', O11T, C11T, C12T
 with sigma of 0.1
 C21T, C22T, C28T, C27T, C25T, C26T, C24T, C23T
 with sigma of 0.1
 C22T, C21T, O21T, O5'
 with sigma of 0.1
 C11T, C12T, C13T, C14T, C15T, C16T, C17T, C18T
 with sigma of 0.1
 C1T, C2T, C7T, C6T, C5T, C4T, C3T
 with sigma of 0.1
 C1', N1, C2, O2, C3
 with sigma of 0.1
4. Rigid bond restraints
 C11T, C12T, C18T, C17T, C15T, C16T, C14T, C13T
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.01
 C1T, C2T, C7T, C6T, C5T, C4T, C3T
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.01
5. Uiso/Uaniso restraints and constraints
C12T \\sim C18T \\sim C17T \\sim C15T \\sim C16T \\sim C14T \\sim C13T: within
2A with sigma of 0.1 and sigma for terminal atoms of 0.1
C1T \\sim C2T \\sim C7T \\sim C6T \\sim C5T \\sim C4T \\sim C3T: within 2A with
sigma of 0.1 and sigma for terminal atoms of 0.1
Uanis(C16T) \\sim Ueq, Uanis(C18T) \\sim Ueq, Uanis(C13T) \\sim Ueq,
Uanis(C14T) \\sim Ueq, Uanis(C17T) \\sim Ueq, Uanis(C15T) \\sim Ueq: with sigma
of 0.1 and sigma for terminal atoms of 0.2
6.a Ternary CH refined with riding coordinates:
 C1'(H1'), C4'(H4'), C3'(H3'), C5(H5)
6.b Secondary CH2 refined with riding coordinates:
 C3(H3A,H3B), C7(H7A,H7B), C5'(H5'A,H5'B), C6(H6A,H6B), C2'(H2'A,H2'B), C4(H4A,
 H4B), C1T(H1TA,H1TB)
6.c Aromatic/amide H refined with riding coordinates:
 C28T(H28T), C23T(H23T), C24T(H24T), C27T(H27T), C7T(H7T), C3T(H3T),
 C17T(H17T), C6T(H6T), C13T(H13T), C18T(H18T), C4T(H4T), C5T(H5T), C14T(H14T)
6.d Idealised Me refined as rotating group:
 C26T(H26A,H26B,H26C)
;
_shelx_res_checksum              54903
_shelx_hkl_checksum              71952
_shelx_fab_checksum              86115
_olex2_submission_special_instructions 'No special instructions were received'