Sesquiterpenoids and hexanorcucurbitacin from Aquilaria malaccensis agarwood with anti-inflammatory effects by inhibiting the STAT1/AKT/MAPK/NLRP3 pathway
Ma, Chi Thanh; Huang, Tianqi; Yu, Jae Sik; Ly, Tu Loan; Vu Huynh, Kim Long; Kwon, Sung Won; Park, Jeong Hill; Yang, Hyun Ok; RSC Advances 14 (2024) 9391–9405; doi:10.1039/D3RA08686K

data_7248375
_publ_section_title
;
 Sesquiterpenoids and hexanorcucurbitacin from Aquilaria malaccensis
 agarwood with anti-inflammatory effects by inhibiting the
 STAT1/AKT/MAPK/NLRP3 pathway
;
_journal_issue                   13
_journal_name_full               'RSC Advances'
_journal_page_first              9391
_journal_page_last               9405
_journal_paper_doi               10.1039/D3RA08686K
_journal_volume                  14
_journal_year                    2024
_chemical_absolute_configuration unk
_chemical_formula_moiety         'C24 H30 O4, C H4 O'
_chemical_formula_sum            'C25 H34 O5'
_chemical_formula_weight         414.52
_chemical_name_systematic        'Compound 19'
_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     direct
_audit_creation_date             2017-03-17
_audit_creation_method
;
Olex2 1.2
(compiled 2017.03.02 svn.r3394 for OlexSys, GUI svn.r5324)
;
_audit_update_record
;
2020-09-24 deposited with the CCDC.	2024-03-28 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 90
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   10.0589(2)
_cell_length_b                   14.2921(3)
_cell_length_c                   15.1181(3)
_cell_measurement_reflns_used    12450
_cell_measurement_temperature    99.8(7)
_cell_measurement_theta_max      73.6990
_cell_measurement_theta_min      4.2240
_cell_volume                     2173.42(8)
_computing_cell_refinement       'CrysAlisPro 1.171.38.44a (Rigaku OD, 2015)'
_computing_data_collection       'CrysAlisPro 1.171.38.44a (Rigaku OD, 2015)'
_computing_data_reduction        'CrysAlisPro 1.171.38.44a (Rigaku OD, 2015)'
_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 (Sheldrick, 2015)'
_diffrn_ambient_environment      N~2~
_diffrn_ambient_temperature      99.8(7)
_diffrn_detector                 'CCD plate'
_diffrn_detector_area_resol_mean 5.2262
_diffrn_detector_type            AtlasS2
_diffrn_measured_fraction_theta_full 1.000
_diffrn_measured_fraction_theta_max 0.995
_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   -113.00 -13.00   1.00    6.50    --  -41.24 -57.00   0.00  100
  2  \w   -113.00 -13.00   1.00    6.50    --  -41.24 -57.00  90.00  100
  3  \w     23.00  97.00   1.00    6.50    --   41.24-125.00  60.00   74
  4  \w     36.00 116.00   1.00   25.00    --  112.00-111.00  30.00   80
  5  \w     86.00 178.00   1.00   25.00    --  112.00  45.00-180.00   92
  6  \w     86.00 178.00   1.00   25.00    --  112.00  45.00   0.00   92
  7  \w    100.00 178.00   1.00   25.00    --  112.00 111.00-150.00   78
  8  \w     29.00 109.00   1.00   25.00    --  112.00 -94.00 -30.00   80
  9  \w     29.00 109.00   1.00   25.00    --  112.00 -94.00-150.00   80
 10  \w     57.00 135.00   1.00   25.00    --  112.00 178.00   0.00   78
 11  \w     41.00 132.00   1.00   25.00    --  112.00 -45.00  90.00   91
 12  \w     33.00 106.00   1.00   25.00    --  112.00 -94.00  60.00   73
 13  \w   -115.00 -64.00   1.00   39.51    --  -41.49-140.00  32.00   51
 14  \w   -115.00 -13.00   1.00   39.51    --  -41.49 -57.00-120.00  102
 15  \w     84.00 178.00   1.00   50.84    --  112.00  30.00 120.00   94
 16  \w     86.00 178.00   1.00   50.84    --  112.00  45.00  60.00   92
 17  \w     83.00 178.00   1.00   50.84    --  112.00  61.00 -60.00   95
 18  \w     83.00 178.00   1.00   50.84    --  112.00  61.00-150.00   95
 19  \w     86.00 161.00   1.00   50.84    --  112.00  45.00 150.00   75
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'SuperNova, Dual, Cu at zero, AtlasS2'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      -0.1306933000
_diffrn_orient_matrix_UB_12      -0.0269419000
_diffrn_orient_matrix_UB_13      -0.0465782000
_diffrn_orient_matrix_UB_21      0.0653821000
_diffrn_orient_matrix_UB_22      0.0179770000
_diffrn_orient_matrix_UB_23      -0.0905822000
_diffrn_orient_matrix_UB_31      0.0459652000
_diffrn_orient_matrix_UB_32      -0.1027624000
_diffrn_orient_matrix_UB_33      -0.0035965000
_diffrn_radiation_collimation    '0.2 mm sinlge-pinhole'
_diffrn_radiation_monochromator  mirror
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54184
_diffrn_reflns_av_R_equivalents  0.0390
_diffrn_reflns_av_unetI/netI     0.0242
_diffrn_reflns_Laue_measured_fraction_full 1.000
_diffrn_reflns_Laue_measured_fraction_max 0.995
_diffrn_reflns_limit_h_max       12
_diffrn_reflns_limit_h_min       -12
_diffrn_reflns_limit_k_max       15
_diffrn_reflns_limit_k_min       -17
_diffrn_reflns_limit_l_max       19
_diffrn_reflns_limit_l_min       -19
_diffrn_reflns_number            21475
_diffrn_reflns_point_group_measured_fraction_full 1.000
_diffrn_reflns_point_group_measured_fraction_max 0.992
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         76.678
_diffrn_reflns_theta_min         4.257
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'SuperNova (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    0.697
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.81985
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.38.44a (Rigaku Oxford Diffraction, 2015)
Empirical absorption correction using spherical harmonics,
 implemented in SCALE3 ABSPACK scaling algorithm.
;
_exptl_crystal_colour            'clear light colourless'
_exptl_crystal_colour_lustre     clear
_exptl_crystal_colour_modifier   light
_exptl_crystal_colour_primary    colourless
_exptl_crystal_density_diffrn    1.267
_exptl_crystal_description       block
_exptl_crystal_F_000             896
_exptl_crystal_size_max          0.15
_exptl_crystal_size_mid          0.04
_exptl_crystal_size_min          0.02
_refine_diff_density_max         0.219
_refine_diff_density_min         -0.236
_refine_diff_density_rms         0.056
_refine_ls_abs_structure_details
;
 Flack x determined using 1822 quotients [(I+)-(I-)]/[(I+)+(I-)]
 (Parsons, Flack and Wagner, Acta Cryst. B69 (2013) 249-259).
;
_refine_ls_abs_structure_Flack   -0.01(8)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.067
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     280
_refine_ls_number_reflns         4530
_refine_ls_number_restraints     0
_refine_ls_restrained_S_all      1.067
_refine_ls_R_factor_all          0.0382
_refine_ls_R_factor_gt           0.0369
_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^)+(0.0589P)^2^+0.3557P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.0976
_refine_ls_wR_factor_ref         0.0987
_reflns_Friedel_coverage         0.759
_reflns_Friedel_fraction_full    1.000
_reflns_Friedel_fraction_max     0.989
_reflns_number_gt                4390
_reflns_number_total             4530
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d3ra08686k3.cif
_cod_data_source_block           exp_823
_cod_original_cell_volume        2173.43(8)
_cod_database_code               7248375
_shelx_shelxl_version_number     2014/7
_chemical_oxdiff_formula         C24H30O4
_reflns_odcompleteness_completeness 100.00
_reflns_odcompleteness_iscentric 1
_reflns_odcompleteness_theta     74.33
_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, All O(H) groups
2.a Ternary CH refined with riding coordinates:
 C8(H8), C10(H10)
2.b Secondary CH2 refined with riding coordinates:
 C7(H7A,H7B), C12(H12A,H12B), C15(H15A,H15B)
2.c Aromatic/amide H refined with riding coordinates:
 C1(H1), C6(H6), C16(H16)
2.d Idealised Me refined as rotating group:
 C18(H18A,H18B,H18C), C19(H19A,H19B,H19C), C20(H20A,H20B,H20C), C22(H22A,H22B,
 H22C), C23(H23B,H23A,H23C), C24(H24A,H24B,H24C), C25(H25A,H25B,H25C)
2.e Idealised tetrahedral OH refined as rotating group:
 O2(H2), O25(H25)
;
_shelx_res_checksum              21790
_shelx_hkl_checksum              41412
_olex2_date_sample_data_collection 2017-03-16
_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 2.310
_oxdiff_exptl_absorpt_empirical_full_min 0.654