Caged and clustered structures of endothelin inhibitor BQ123, cyclo(-D-Trp-D-Asp−-Pro-D-Val-Leu-)χdotNa+, forming five and six coordination bonds between sodium ions and peptides
Doi, Mitsunobu; Asano, Akiko; Ishida, Toshimasa; Katsuya, Yoshio; Mezaki, Yoshihiro; Sasaki, Masahiro; Terashima, Akira; Taniguchi, Taizo; Hasegawa, Hiroshi; Shiono, Masaaki; Acta Crystallographica Section D Biological Crystallography 57 (2001) 628–; doi:10.1107/S0907444901002797

data_2019342
_publ_section_title
;
 Caged and clustered structures of endothelin inhibitor BQ123,
 cyclo(-D-Trp-D-Asp&#x2212;-Pro-D-Val-Leu-)\cdotNa+, forming five and six
 coordination bonds between sodium ions and peptides
;
_journal_issue                   5
_journal_name_full
'Acta Crystallographica Section D Biological Crystallography'
_journal_page_first              628
_journal_paper_doi               10.1107/S0907444901002797
_journal_volume                  57
_journal_year                    2001
_chemical_formula_moiety         'C31 H41 N6 O7 Na,2(H2 O),1.41(C3 H7 O H)'
_chemical_formula_sum            'C35.22 H56.26 N6 Na2 O10.41'
_chemical_formula_weight         753.28
_chemical_name_common            bq123
_chemical_name_systematic
; 
 BQ123: cyclo(-D-Trp-D-Asp^-^-Pro-D-Val-Leu-).Na^+^
 an endothelin-1 inhibitor
;
_space_group_IT_number           19
_symmetry_cell_setting           orthorhombic
_symmetry_space_group_name_Hall  'P 2ac 2ab'
_symmetry_space_group_name_H-M   'P 21 21 21'
_atom_sites_solution_hydrogens   geom
_atom_sites_solution_primary     direct
_atom_sites_solution_secondary   difmap
_audit_creation_method           SHELXL-97
_cell_angle_alpha                90.00
_cell_angle_beta                 90.00
_cell_angle_gamma                90.00
_cell_formula_units_Z            16
_cell_length_a                   25.3930(4)
_cell_length_b                   34.7193(3)
_cell_length_c                   25.7201(4)
_cell_measurement_temperature    100(2)
_cell_volume                     22675.5(5)
_computing_cell_refinement       'MOSFLM 6.01 (Leslie, 1999)'
_computing_data_collection       'RIgaku PROCESS'
_computing_data_reduction        'MOSFLM 6.01 (Leslie, 1999)'
_computing_molecular_graphics    'ORTEP-III (Burnett & Johnson,1996)'
_computing_publication_material  'PARST (Nardelli, 1983)'
_computing_structure_refinement  'SHELXL-97 (Sheldrick, 1997)'
_computing_structure_solution    'LODEM (Shiono, 1990)'
_diffrn_ambient_temperature      100(2)
_diffrn_detector_area_resol_mean 10
_diffrn_measured_fraction_theta_full 0.925
_diffrn_measured_fraction_theta_max 0.925
_diffrn_measurement_device_type  'Rigaku RAXIS-IV'
_diffrn_measurement_method       oscillation
_diffrn_radiation_monochromator  diamond
_diffrn_radiation_source         'double monochromated beam'
_diffrn_radiation_type           synchrotron
_diffrn_radiation_wavelength     0.83400
_diffrn_reflns_av_R_equivalents  0.0342
_diffrn_reflns_av_sigmaI/netI    0.0274
_diffrn_reflns_limit_h_max       31
_diffrn_reflns_limit_h_min       -31
_diffrn_reflns_limit_k_max       38
_diffrn_reflns_limit_k_min       -37
_diffrn_reflns_limit_l_max       31
_diffrn_reflns_limit_l_min       0
_diffrn_reflns_number            83268
_diffrn_reflns_theta_full        31.45
_diffrn_reflns_theta_max         31.45
_diffrn_reflns_theta_min         1.49
_exptl_absorpt_coefficient_mu    0.071
_exptl_crystal_colour            colorless
_exptl_crystal_density_diffrn    0.883
_exptl_crystal_density_method    'not measured'
_exptl_crystal_description       block
_exptl_crystal_F_000             6461
_exptl_crystal_size_max          0.08
_exptl_crystal_size_mid          0.04
_exptl_crystal_size_min          0.04
_refine_diff_density_max         0.563
_refine_diff_density_min         -0.263
_refine_diff_density_rms         0.080
_refine_ls_abs_structure_details 'Flack H D (1983), Acta Cryst. A39, 876-881'
_refine_ls_abs_structure_Flack   0(10)
_refine_ls_extinction_coef       2173(12)
_refine_ls_extinction_expression Fc^*^=kFc[1+0.001xFc^2^\l^3^/sin(2\q)]^-1/4^
_refine_ls_extinction_method     SHELXL
_refine_ls_goodness_of_fit_ref   1.072
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     1904
_refine_ls_number_reflns         22865
_refine_ls_number_restraints     36
_refine_ls_restrained_S_all      1.074
_refine_ls_R_factor_all          0.0577
_refine_ls_R_factor_gt           0.0576
_refine_ls_shift/su_max          0.656
_refine_ls_shift/su_mean         0.004
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'calc w=1/[\s^2^(Fo^2^)+(0.1388P)^2^+0.5089P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1642
_refine_ls_wR_factor_ref         0.1642
_reflns_number_gt                22861
_reflns_number_total             22865
_reflns_threshold_expression     >2sigma(I)
_cod_data_source_file            he0271sup1.cif
_cod_data_source_block           bq123
_cod_depositor_comments
;

2023-05-16
Z value and formula fixed to values more according to usual
chemical conventions.                 miguel
;
_cod_original_formula_sum            'C140.88 H225.04 N24 Na4 O41.63'
_cod_original_formula_weight         3013.12
_cod_original_formula_moiety      '4(C31 H41 N6 O7 Na),8(H2 O),5.63(C3 H7 O H)'
_cod_original_formula_units_Z            4
_cod_original_sg_symbol_H-M      P212121
_cod_database_code               2019342