Uracil derivatives as HIV-1 capsid protein inhibitors: design, in silico, in vitro and cytotoxicity studies
Ramesh, Deepthi; Mohanty, Amaresh Kumar; De, Anirban; Vijayakumar, Balaji Gowrivel; Sethumadhavan, Aiswarya; Muthuvel, Suresh Kumar; Mani, Maheswaran; Kannan, Tharanikkarasu; RSC Advances 12 (2022) 17466–17480; doi:10.1039/D2RA02450K

data_7245071
_publ_section_title
;
 Uracil derivatives as HIV-1 capsid protein inhibitors: design, in silico,
 in vitro and cytotoxicity studies
;
_journal_issue                   27
_journal_name_full               'RSC Advances'
_journal_page_first              17466
_journal_page_last               17480
_journal_paper_doi               10.1039/D2RA02450K
_journal_volume                  12
_journal_year                    2022
_chemical_formula_moiety         'C11 H9 N3 O5'
_chemical_formula_sum            'C11 H9 N3 O5'
_chemical_formula_weight         263.21
_space_group_crystal_system      monoclinic
_space_group_IT_number           14
_space_group_name_Hall           '-P 2yab'
_space_group_name_H-M_alt        'P 1 21/a 1'
_symmetry_Int_Tables_number      14
_atom_sites_solution_primary     direct
_audit_creation_date             2019-08-08
_audit_creation_method
;
Olex2 1.2-ac3
(compiled 2016.03.30 svn.r3266 for Rigaku Oxford Diffraction, GUI svn.r5168)
;
_audit_update_record
;
2022-02-08 deposited with the CCDC.	2022-05-30 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 114.653(18)
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   12.1477(18)
_cell_length_b                   7.4576(8)
_cell_length_c                   13.8322(19)
_cell_measurement_reflns_used    2034
_cell_measurement_temperature    298
_cell_measurement_theta_max      29.3056
_cell_measurement_theta_min      3.2345
_cell_volume                     1138.9(3)
_computing_cell_refinement
;
CrysAlisPro, Agilent Technologies,
Version 1.171.36.21 (release 14-08-2012 CrysAlis171 .NET)
(compiled Sep 14 2012,17:21:16)
;
_computing_data_collection
;
CrysAlisPro, Agilent Technologies,
Version 1.171.36.21 (release 14-08-2012 CrysAlis171 .NET)
(compiled Sep 14 2012,17:21:16)
;
_computing_data_reduction
;
CrysAlisPro, Agilent Technologies,
Version 1.171.36.21 (release 14-08-2012 CrysAlis171 .NET)
(compiled Sep 14 2012,17:21:16)
;
_computing_molecular_graphics    'Olex2 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 (Dolomanov et al., 2009)'
_computing_structure_refinement  'olex2.refine (Bourhis et al., 2015)'
_computing_structure_solution    'ShelXS (Sheldrick, 2008)'
_diffrn_ambient_temperature      298
_diffrn_detector_area_resol_mean 15.9821
_diffrn_measured_fraction_theta_full 0.9722
_diffrn_measured_fraction_theta_max 0.8466
_diffrn_measurement_details
;
  1 omega  -87.00    9.00   1.0000   28.0000
omega____ theta____ kappa____ phi______ frames
    -      -16.9491  -77.0000   30.0000 96

  2 omega  -49.00   36.00   1.0000   28.0000
omega____ theta____ kappa____ phi______ frames
    -       19.6835  -57.0000  120.0000 85

  3 omega   44.00   69.00   1.0000   28.0000
omega____ theta____ kappa____ phi______ frames
    -       19.6835  169.0000  118.0000 25

  4 omega  -38.00    8.00   1.0000   28.0000
omega____ theta____ kappa____ phi______ frames
    -       19.6835  -57.0000 -120.0000 46

  5 omega  -87.00  -48.00   1.0000   28.0000
omega____ theta____ kappa____ phi______ frames
    -      -16.9491  -77.0000 -150.0000 39
;
_diffrn_measurement_device_type  'Xcalibur, Eos'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_UB_11      0.0045516000
_diffrn_orient_matrix_UB_12      0.0312646000
_diffrn_orient_matrix_UB_13      0.0499253000
_diffrn_orient_matrix_UB_21      -0.0122210000
_diffrn_orient_matrix_UB_22      0.0885391000
_diffrn_orient_matrix_UB_23      -0.0203550000
_diffrn_orient_matrix_UB_31      -0.0629661000
_diffrn_orient_matrix_UB_32      -0.0150437000
_diffrn_orient_matrix_UB_33      -0.0163662000
_diffrn_radiation_monochromator  graphite
_diffrn_radiation_type           'Mo K\a'
_diffrn_radiation_wavelength     0.71073
_diffrn_reflns_av_R_equivalents  0.0196
_diffrn_reflns_av_unetI/netI     0.0245
_diffrn_reflns_limit_h_max       16
_diffrn_reflns_limit_h_min       -13
_diffrn_reflns_limit_k_max       9
_diffrn_reflns_limit_k_min       -9
_diffrn_reflns_limit_l_max       19
_diffrn_reflns_limit_l_min       -18
_diffrn_reflns_number            6480
_diffrn_reflns_theta_full        29.3705
_diffrn_reflns_theta_max         29.37
_diffrn_reflns_theta_min         3.24
_diffrn_source                   'Enhance (Mo) X-ray Source'
_exptl_absorpt_coefficient_mu    0.124
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.80219
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro, Agilent Technologies,
Version 1.171.36.21 (release 14-08-2012 CrysAlis171 .NET)
(compiled Sep 14 2012,17:21:16)
Empirical absorption correction using spherical harmonics,
 implemented in SCALE3 ABSPACK scaling algorithm.
;
_exptl_crystal_colour            colourless
_exptl_crystal_colour_primary    colourless
_exptl_crystal_density_diffrn    1.5350
_exptl_crystal_description       block
_exptl_crystal_F_000             544.3489
_exptl_crystal_size_max          0.24
_exptl_crystal_size_mid          0.22
_exptl_crystal_size_min          0.16
_refine_diff_density_max         0.3438
_refine_diff_density_min         -0.3776
_refine_diff_density_rms         0.0602
_refine_ls_d_res_high            0.7246
_refine_ls_d_res_low             6.2857
_refine_ls_goodness_of_fit_ref   1.0715
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_constraints    18
_refine_ls_number_parameters     172
_refine_ls_number_reflns         2654
_refine_ls_number_restraints     0
_refine_ls_restrained_S_all      1.0715
_refine_ls_R_factor_all          0.0753
_refine_ls_R_factor_gt           0.0537
_refine_ls_shift/su_max          0.0000
_refine_ls_shift/su_mean         0.0000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.0930P)^2^+0.2997P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1600
_refine_ls_wR_factor_ref         0.1805
_reflns_Friedel_coverage         0.0
_reflns_limit_h_max              16
_reflns_limit_h_min              0
_reflns_limit_k_max              9
_reflns_limit_k_min              0
_reflns_limit_l_max              16
_reflns_limit_l_min              -19
_reflns_number_gt                1930
_reflns_number_total             2654
_reflns_threshold_expression     I>=2u(I)
_cod_data_source_file            d2ra02450k2.cif
_cod_data_source_block           KT-DR-AD-2I-AS
_cod_depositor_comments
;

2025-04-02
Z value and formula fixed to values more according to usual
chemical conventions.                 miguel
;
_cod_original_formula_sum            'C22 H18 N6 O10'
_cod_original_formula_weight         526.42
_cod_original_formula_moiety         '2(C11 H9 N3 O5)'
_cod_original_formula_units_Z            2
_cod_original_sg_symbol_Hall     '-P 2ybc (z,y,-x)'
_cod_database_code               7245071
_chemical_oxdiff_formula         'C20 H18 N3 O5'
_chemical_oxdiff_usercomment     ' COLOURLESS BLOCK, 298K, 0.24 0.22 0.16'
_reflns_odcompleteness_completeness 99.72
_reflns_odcompleteness_iscentric 1
_reflns_odcompleteness_theta     26.32
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All N(H) groups
 At 1.5 times of:
  All O(H) groups
2.a Ternary CH refined with riding coordinates:
 C7(H7)
2.b Aromatic/amide H refined with riding coordinates:
 N2(H2), N3(H3), C10(H10), C5(H5), C3(H3b), C6(H6), C2(H2a)
2.c Idealised tetrahedral OH refined as rotating group:
 O3(H3a)
;
_olex2_submission_special_instructions 'No special instructions were received'