Small molecule antagonists of cell-surface heparan sulfate and heparin‒protein interactions
Weiss, Ryan J.; Gordts, Philip L. S. M.; Le, Dzung; Xu, Ding; Esko, Jeffrey D.; Tor, Yitzhak; Chem. Sci. 6 (2015) 5984–; doi:10.1039/C5SC01208B

data_1529302
_publ_section_title
;
 Small molecule antagonists of cell-surface heparan sulfate and
 heparin--protein interactions
;
_journal_issue                   10
_journal_name_full               'Chem. Sci.'
_journal_page_first              5984
_journal_paper_doi               10.1039/C5SC01208B
_journal_volume                  6
_journal_year                    2015
_chemical_formula_moiety         'C24 H25 N6 O3, 2(H2 O), 2(Cl)'
_chemical_formula_sum            'C24 H29 Cl2 N6 O5'
_chemical_formula_weight         552.43
_space_group_crystal_system      monoclinic
_space_group_IT_number           11
_space_group_name_Hall           '-P 2yb'
_space_group_name_H-M_alt        'P 1 21/m 1'
_symmetry_space_group_name_Hall  '-P 2yb'
_symmetry_space_group_name_H-M   'P 1 21/m 1'
_atom_sites_solution_hydrogens   mixed
_atom_sites_solution_primary     direct
_atom_sites_solution_secondary   difmap
_audit_creation_date             2015-02-25
_audit_creation_method
;
Olex2 1.2-beta
(compiled 2015.01.26 svn.r3150 for OlexSys, GUI svn.r4998)
;
_audit_update_record
;
2015-04-01 deposited with the CCDC.
2015-07-22 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 110.533(11)
_cell_angle_gamma                90
_cell_formula_units_Z            2
_cell_length_a                   5.0339(9)
_cell_length_b                   37.994(7)
_cell_length_c                   7.1360(11)
_cell_measurement_reflns_used    2157
_cell_measurement_temperature    100
_cell_measurement_theta_max      26.309
_cell_measurement_theta_min      3.049
_cell_volume                     1278.1(4)
_computing_cell_refinement       'SAINT v8.34A (Bruker, 2013)'
_computing_data_collection       'APEX2 v2013.6-2 (Bruker, 2013)'
_computing_data_reduction        'SAINT v8.34A (Bruker, 2013)'
_computing_molecular_graphics    'Olex2 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 (Dolomanov et al., 2009)'
_computing_structure_refinement  'ShelXL (Sheldrick, 2008)'
_computing_structure_solution    'ShelXT (Sheldrick, 2015)'
_diffrn_ambient_temperature      100.0
_diffrn_detector                 'Bruker APEX-II CCD'
_diffrn_detector_area_resol_mean 7.9
_diffrn_detector_type            'CCD Area Detector'
_diffrn_measured_fraction_theta_full 0.993
_diffrn_measured_fraction_theta_max 0.983
_diffrn_measurement_device       'Kappa Four-Circle Diffractometer'
_diffrn_measurement_device_type  'Bruker APEX II Ultra'
_diffrn_measurement_method       '\f and \w scans'
_diffrn_radiation_monochromator  'Double Bounce Multilayer Mirrors'
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           MoK\a
_diffrn_radiation_wavelength     0.71073
_diffrn_reflns_av_R_equivalents  0.0438
_diffrn_reflns_av_unetI/netI     0.0535
_diffrn_reflns_laue_measured_fraction_full 0.993
_diffrn_reflns_laue_measured_fraction_max 0.983
_diffrn_reflns_limit_h_max       6
_diffrn_reflns_limit_h_min       -6
_diffrn_reflns_limit_k_max       45
_diffrn_reflns_limit_k_min       -47
_diffrn_reflns_limit_l_max       8
_diffrn_reflns_limit_l_min       -8
_diffrn_reflns_number            7858
_diffrn_reflns_point_group_measured_fraction_full 0.993
_diffrn_reflns_point_group_measured_fraction_max 0.983
_diffrn_reflns_theta_full        25.000
_diffrn_reflns_theta_max         26.490
_diffrn_reflns_theta_min         2.144
_diffrn_source                   'Micro Focus Rotating Anode'
_diffrn_source_type              'Bruker TXS'
_diffrn_standards_number         0
_exptl_absorpt_coefficient_mu    0.302
_exptl_absorpt_correction_T_max  0.0932
_exptl_absorpt_correction_T_min  0.0478
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
'SADABS-2014/4 (Bruker,2014/4) was used for absorption correction. wR2(int) was 0.1107 before and 0.0497 after correction. The Ratio of minimum to maximum transmission is 0.5129. The \l/2 correction factor is Not present.'
_exptl_crystal_colour            Colorless
_exptl_crystal_colour_primary    Colorless
_exptl_crystal_density_diffrn    1.435
_exptl_crystal_description       Plate
_exptl_crystal_F_000             578
_exptl_crystal_size_max          0.24
_exptl_crystal_size_mid          0.2
_exptl_crystal_size_min          0.08
_refine_diff_density_max         0.380
_refine_diff_density_min         -0.316
_refine_diff_density_rms         0.079
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.188
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     189
_refine_ls_number_reflns         2635
_refine_ls_number_restraints     3
_refine_ls_restrained_S_all      1.187
_refine_ls_R_factor_all          0.0944
_refine_ls_R_factor_gt           0.0751
_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^)+(0.0615P)^2^+2.1084P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1702
_refine_ls_wR_factor_ref         0.1780
_reflns_Friedel_coverage         0.000
_reflns_number_gt                2065
_reflns_number_total             2635
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            c5sc01208b2.cif
_cod_data_source_block           Tor90
_cod_depositor_comments
;
The following automatic conversions were performed:

'_diffrn_radiation_probe' value 'X-ray' changed to 'x-ray' according
to
/usr/data/users/saulius/crontab/automatic-downloads/rss-feeds/RSC/lib/dictionaries/cif_core.dic
dictionary named 'cif_core.dic' version 2.4.2 from 2011-04-26.

Automatic conversion script
Id: cif_fix_values 3271 2015-04-21 07:52:19Z andrius 

 Adding full bibliography for 1529300--1529303.cif.
;
_cod_database_code               1529302
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All C(H,H) groups, All N(H) groups, All N(H,H) groups
 At 1.5 times of:
  All C(H,H,H) groups, All O(H,H) groups
2. Restrained distances
 H1SB-H1SA
 1.42 with sigma of 0.02
 O1S-H1SB = O1S-H1SA
 0.9 with sigma of 0.02
3. Others
 Fixed Sof: H1(0.5) O2S(0.5) H2SA(0.5) H2SB(0.5) Cl2(0.5)
4.a Free rotating group:
 O2S(H2SA,H2SB)
4.b Secondary CH2 refined with riding coordinates:
 C12(H12A,H12B)
4.c Aromatic/amide H refined with riding coordinates:
 N1(H1), N3(H3), C2(H2), C6(H6), C7(H7), C9(H9)
4.d X=CH2 refined with riding coordinates:
 N2(H2A,H2B)
4.e Idealised Me refined as rotating group:
 C10(H10A,H10B,H10C)
;
_shelx_res_checksum              28300
_shelx_shelxl_version_number     2014/7
_olex2_submission_special_instructions 'No special instructions were received'