Rational design strategies for innovative small-molecule scaffolds inspired by three pivotal protein secondary structures.
Yoo, Jeong Yeon; Kim, Chanwoo; Kwon, Ji Hoon; Cho, Hana; Jeong, Kiyoung; Park, Wonwoo; Kim, Younghun; Lee, Dongwhan; Park, Seung Bum; Chemical communications (Cambridge, England) 61 (2025) 2285–2288; doi:10.1039/d4cc06630h

data_7134127
_publ_section_title
;
 Rational design strategies for innovative small-molecule scaffolds
 inspired by three pivotal protein secondary structures.
;
_journal_issue                   11
_journal_name_full               'Chemical communications (Cambridge, England)'
_journal_page_first              2285
_journal_page_last               2288
_journal_paper_doi               10.1039/d4cc06630h
_journal_volume                  61
_journal_year                    2025
_chemical_absolute_configuration syn
_chemical_formula_moiety         'C31 H38 N6 O4'
_chemical_formula_sum            'C31 H38 N6 O4'
_chemical_formula_weight         558.67
_space_group_crystal_system      orthorhombic
_space_group_IT_number           19
_space_group_name_Hall           'P 2ac 2ab'
_space_group_name_H-M_alt        'P 21 21 21'
_atom_sites_solution_hydrogens   geom
_atom_sites_solution_primary     dual
_audit_creation_date             2024-04-21
_audit_creation_method
;
Olex2 1.5
(compiled 2024.02.16 svn.r378c4104 for OlexSys, GUI svn.r6928)
;
_audit_update_record
;
2024-05-08 deposited with the CCDC.	2025-01-06 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 90
_cell_angle_gamma                90
_cell_formula_units_Z            8
_cell_length_a                   10.14310(10)
_cell_length_b                   25.1649(4)
_cell_length_c                   28.1114(4)
_cell_measurement_reflns_used    24282
_cell_measurement_temperature    93
_cell_measurement_theta_max      78.7280
_cell_measurement_theta_min      4.6910
_cell_volume                     7175.44(17)
_computing_cell_refinement       'CrysAlisPro 1.171.39.29d (Rigaku OD, 2017)'
_computing_data_collection       'CrysAlisPro 1.171.39.29d (Rigaku OD, 2017)'
_computing_data_reduction        'CrysAlisPro 1.171.39.29d (Rigaku OD, 2017)'
_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 2014/5 (Sheldrick, 2014)'
_diffrn_ambient_temperature      93.00
_diffrn_measured_fraction_theta_full 0.983
_diffrn_measured_fraction_theta_max 0.972
_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    -27.00  89.00   0.50   10.29    --    0.00  35.00  33.00  232
  2  \w     16.00 133.00   0.50   44.15    --  105.20 -35.00-123.00  234
  3  \w     78.00 195.00   0.50   44.15    --  105.20  35.00  33.00  234
  4  \w    -89.00  27.00   0.50   10.29    --    0.00 -35.00-123.00  232
  5  \w    -89.00  27.00   0.50   10.29    --    0.00 -38.00 150.00  232
  6  \w    -89.00  27.00   0.50   10.29    --    0.00 -38.00 -30.00  232
  7  \w     16.00 141.00   0.50   44.15    --  105.20 -82.00-120.00  250
  8  \w     79.00 195.00   0.50   44.15    --  105.20  45.00 -90.00  232
  9  \w     16.00 134.00   0.50   44.15    --  105.20 -61.00-150.00  236
 10  \w     23.00 133.00   0.50   44.15    --  105.20 -61.00  90.00  220
 11  \w     72.00  98.00   0.50   44.15    --  105.20 -61.00   0.00   52
 12  \w    104.00 129.00   0.50   44.15    --  105.20 -61.00   0.00   50
 13  \w     78.00 194.00   0.50   44.15    --  105.20  30.00   0.00  232
 14  \w     17.00 131.00   0.50   44.15    --  105.20 -45.00  60.00  228
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'XtaLAB AFC12 (RINC): Kappa dual home/near'
_diffrn_measurement_method       '\w scans'
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54184
_diffrn_reflns_av_R_equivalents  0.0956
_diffrn_reflns_av_unetI/netI     0.0510
_diffrn_reflns_Laue_measured_fraction_full 0.983
_diffrn_reflns_Laue_measured_fraction_max 0.972
_diffrn_reflns_limit_h_max       8
_diffrn_reflns_limit_h_min       -12
_diffrn_reflns_limit_k_max       31
_diffrn_reflns_limit_k_min       -31
_diffrn_reflns_limit_l_max       35
_diffrn_reflns_limit_l_min       -35
_diffrn_reflns_number            68194
_diffrn_reflns_point_group_measured_fraction_full 0.986
_diffrn_reflns_point_group_measured_fraction_max 0.962
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         79.446
_diffrn_reflns_theta_min         3.513
_exptl_absorpt_coefficient_mu    0.565
_exptl_absorpt_correction_T_max  1.000
_exptl_absorpt_correction_T_min  0.455
_exptl_absorpt_correction_type   gaussian
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.39.29d (Rigaku Oxford Diffraction, 2017)
Numerical absorption correction based on gaussian integration over
			a multifaceted crystal model
Empirical absorption correction using spherical harmonics,
 implemented in SCALE3 ABSPACK scaling algorithm.
;
_exptl_crystal_colour            'clear whiteish colourless'
_exptl_crystal_colour_lustre     clear
_exptl_crystal_colour_modifier   whiteish
_exptl_crystal_colour_primary    colourless
_exptl_crystal_density_diffrn    1.034
_exptl_crystal_description       plate
_exptl_crystal_F_000             2384
_exptl_crystal_size_max          0.381
_exptl_crystal_size_mid          0.133
_exptl_crystal_size_min          0.101
_refine_diff_density_max         0.270
_refine_diff_density_min         -0.401
_refine_diff_density_rms         0.072
_refine_ls_abs_structure_details
;
 Flack x determined using 3905 quotients [(I+)-(I-)]/[(I+)+(I-)]
 (Parsons, Flack and Wagner, Acta Cryst. B69 (2013) 249-259).
;
_refine_ls_abs_structure_Flack   0.21(12)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.113
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     749
_refine_ls_number_reflns         14962
_refine_ls_number_restraints     0
_refine_ls_restrained_S_all      1.113
_refine_ls_R_factor_all          0.1044
_refine_ls_R_factor_gt           0.0958
_refine_ls_shift/su_max          0.000
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.1902P)^2^+0.2680P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.2794
_refine_ls_wR_factor_ref         0.2911
_reflns_Friedel_coverage         0.800
_reflns_Friedel_fraction_full    0.989
_reflns_Friedel_fraction_max     0.949
_reflns_number_gt                11784
_reflns_number_total             14962
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d4cc06630h2.cif
_cod_data_source_block           jy-01-pww
_cod_depositor_comments
'Adding full bibliography for 7134125--7134127.cif.'
_cod_database_code               7134127
_shelx_shelxl_version_number     2018/3
_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:
 C013(H013), C017(H017), C01C(H01C), C01F(H01F)
2.b Secondary CH2 refined with riding coordinates:
 C00Q(H00C,H00D), C00V(H00A,H00B), C00W(H00E,H00F), C014(H01T,H01V), C01A(H01W,
 H01X), C01B(H01A,H01B), C01G(H01,H), C01K(H01D,H01E), C01O(H01G,H01H),
 C01R(H01I,H01J)
2.c Aromatic/amide H refined with riding coordinates:
 C011(H011), C012(H012), C015(H015), C018(H018), C019(H019), C01D(H01Y),
 C01E(H01Z), C01I(H2), C01L(H01L), C01M(H4), C01N(H5), C01P(H01P), C01Q(H01Q),
 C01T(H6), C01U(H01U), C01V(H7), C01Z(H9), C020(H020), C021(H021), C022(H022),
 C024(H024), C026(H026)
2.d Idealised Me refined as rotating group:
 C01H(H1,HA,HB), C01J(H3,HC,HD), C01S(H01K,H01M,H01N), C01X(H01O,H01R,H01S),
 C01Y(H8,HE,HF), C025(H02A,H02B,H02C), C027(H02D,H02E,H02F), C028(H02G,H02H,
 H02I), C029(H02J,H02K,H02L), C02A(H02M,H02N,H02O)
;
_smtbx_masks_void_probe_radius   1.2
_smtbx_masks_void_truncation_radius 1.2
_shelx_res_checksum              79711
_shelx_hkl_checksum              58421
_shelx_fab_checksum              25349
_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
- B-factor correction
;