data_XBD
#

_chem_comp.id                                   XBD
_chem_comp.name                                 "2-{[2-methoxy-4-(4-methylpiperazin-1-yl)phenyl]amino}-11-methyl-5-(2,2,2-trifluoroethyl)-5,11-dihydro-6H-pyrimido[4,5-b][1,4]benzodiazepin-6-one"
_chem_comp.type                                 non-polymer
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C26 H28 F3 N7 O2"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2020-12-08
_chem_comp.pdbx_modified_date                   2021-09-17
_chem_comp.pdbx_ambiguous_flag                  N
_chem_comp.pdbx_release_status                  REL
_chem_comp.pdbx_replaced_by                     ?
_chem_comp.pdbx_replaces                        ?
_chem_comp.formula_weight                       527.541
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    XBD
_chem_comp.pdbx_model_coordinates_details       ?
_chem_comp.pdbx_model_coordinates_missing_flag  N
_chem_comp.pdbx_ideal_coordinates_details       Corina
_chem_comp.pdbx_ideal_coordinates_missing_flag  N
_chem_comp.pdbx_model_coordinates_db_code       7KXW
_chem_comp.pdbx_subcomponent_list               ?
_chem_comp.pdbx_processing_site                 RCSB
#   #
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.alt_atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.charge
_chem_comp_atom.pdbx_align
_chem_comp_atom.pdbx_aromatic_flag
_chem_comp_atom.pdbx_leaving_atom_flag
_chem_comp_atom.pdbx_stereo_config
_chem_comp_atom.model_Cartn_x
_chem_comp_atom.model_Cartn_y
_chem_comp_atom.model_Cartn_z
_chem_comp_atom.pdbx_model_Cartn_x_ideal
_chem_comp_atom.pdbx_model_Cartn_y_ideal
_chem_comp_atom.pdbx_model_Cartn_z_ideal
_chem_comp_atom.pdbx_component_atom_id
_chem_comp_atom.pdbx_component_comp_id
_chem_comp_atom.pdbx_ordinal
XBD  N1   N1   N  0  1  Y  N  N  -11.607   -6.804  11.286    1.389  -1.496   0.718  N1   XBD   1  
XBD  C7   C1   C  0  1  Y  N  N  -11.599   -4.092  12.550   -2.385  -0.225  -0.376  C7   XBD   2  
XBD  C8   C2   C  0  1  Y  N  N  -12.049   -3.216  13.517   -3.638   0.292  -0.645  C8   XBD   3  
XBD  N2   N2   N  0  1  N  N  N   -9.761   -5.437  11.605   -0.934  -1.623   0.958  N2   XBD   4  
XBD  C9   C3   C  0  1  Y  N  N  -11.198   -2.753  14.519   -4.722  -0.063   0.148  C9   XBD   5  
XBD  O1   O1   O  0  1  N  N  N   -8.120   -4.521  13.470   -3.121  -2.315   2.523  O1   XBD   6  
XBD  C1   C4   C  0  1  N  N  N  -11.350  -10.752   8.669    3.477   2.609  -0.176  C1   XBD   7  
XBD  C5   C5   C  0  1  Y  N  N  -10.335   -6.501  10.972    0.200  -0.933   0.558  C5   XBD   8  
XBD  C6   C6   C  0  1  Y  N  N  -10.265   -4.536  12.553   -2.207  -1.099   0.685  C6   XBD   9  
XBD  N3   N3   N  0  1  N  N  N  -11.679   -1.943  15.537   -5.990   0.461  -0.126  N3   XBD  10  
XBD  C4   C7   C  0  1  Y  N  N  -12.197   -7.755  10.552    2.495  -0.859   0.348  C4   XBD  11  
XBD  C3   C8   C  0  1  Y  N  N  -11.505   -8.427   9.506    2.393   0.430  -0.177  C3   XBD  12  
XBD  C2   C9   C  0  1  N  N  N  -11.743  -11.673   9.788    4.021   2.826   1.238  C2   XBD  13  
XBD  N4   N4   N  0  1  N  N  N  -12.657   -0.093  17.471   -8.315   0.898  -1.709  N4   XBD  14  
XBD  N    N5   N  0  1  N  N  N  -12.096   -9.482   8.764    3.523   1.181  -0.502  N    XBD  15  
XBD  C    C10  C  0  1  N  N  N  -13.311   -9.430   8.126    4.633   0.737  -1.075  C    XBD  16  
XBD  O    O2   O  0  1  N  N  N  -13.661  -10.292   7.347    5.507   1.553  -1.293  O    XBD  17  
XBD  C10  C11  C  0  1  N  N  N  -13.066   -1.466  15.477   -6.971  -0.613  -0.330  C10  XBD  18  
XBD  C11  C12  C  0  1  N  N  N  -13.561   -1.063  16.859   -8.357  -0.000  -0.548  C11  XBD  19  
XBD  C12  C13  C  0  1  N  N  N  -13.176    0.358  18.766   -9.647   1.449  -1.997  C12  XBD  20  
XBD  C13  C14  C  0  1  N  N  N  -11.337   -0.698  17.624   -7.334   1.973  -1.506  C13  XBD  21  
XBD  C14  C15  C  0  1  N  N  N  -10.759   -1.072  16.272   -5.948   1.360  -1.288  C14  XBD  22  
XBD  C15  C16  C  0  1  Y  N  N   -9.857   -3.169  14.512   -4.548  -0.939   1.211  C15  XBD  23  
XBD  C16  C17  C  0  1  Y  N  N   -9.424   -4.040  13.554   -3.293  -1.457   1.482  C16  XBD  24  
XBD  C17  C18  C  0  1  N  N  N   -7.219   -4.121  14.502   -4.278  -2.637   3.296  C17  XBD  25  
XBD  C18  C19  C  0  1  Y  N  N  -10.197   -8.013   9.287    1.128   0.974  -0.347  C18  XBD  26  
XBD  C19  C20  C  0  1  N  N  N  -14.005   -7.680  12.130    4.220  -1.889   1.798  C19  XBD  27  
XBD  C20  C21  C  0  1  Y  N  N  -14.354   -7.641   9.661    4.484  -1.719  -0.663  C20  XBD  28  
XBD  C21  C22  C  0  1  Y  N  N  -14.239   -8.289   8.425    4.901  -0.651  -1.469  C21  XBD  29  
XBD  C22  C23  C  0  1  Y  N  N  -15.045   -7.884   7.360    5.592  -0.916  -2.655  C22  XBD  30  
XBD  C23  C24  C  0  1  Y  N  N  -15.952   -6.855   7.533    5.884  -2.215  -3.008  C23  XBD  31  
XBD  C24  C25  C  0  1  Y  N  N  -16.067   -6.222   8.752    5.497  -3.266  -2.192  C24  XBD  32  
XBD  C25  C26  C  0  1  Y  N  N  -15.271   -6.610   9.821    4.796  -3.022  -1.028  C25  XBD  33  
XBD  F    F1   F  0  1  N  N  N  -13.062  -11.641  10.021    5.343   2.374   1.304  F    XBD  34  
XBD  F1   F2   F  0  1  N  N  N  -11.430  -12.950   9.524    3.977   4.190   1.549  F1   XBD  35  
XBD  F2   F3   F  0  1  N  N  N  -11.122  -11.344  10.937    3.238   2.114   2.153  F2   XBD  36  
XBD  N5   N6   N  0  1  Y  N  N   -9.594   -7.060  10.004    0.067   0.273   0.027  N5   XBD  37  
XBD  N6   N7   N  0  1  N  N  N  -13.553   -8.025  10.783    3.726  -1.484   0.479  N6   XBD  38  
XBD  H1   H1   H  0  1  N  N  N  -12.277   -4.439  11.785   -1.544   0.049  -0.996  H1   XBD  39  
XBD  H2   H2   H  0  1  N  N  N  -13.077   -2.884  13.497   -3.775   0.972  -1.472  H2   XBD  40  
XBD  H3   H3   H  0  1  N  N  N   -8.810   -5.270  11.346   -0.847  -2.469   1.426  H3   XBD  41  
XBD  H4   H4   H  0  1  N  N  N  -11.576  -11.234   7.706    2.447   2.961  -0.227  H4   XBD  42  
XBD  H5   H5   H  0  1  N  N  N  -10.272  -10.545   8.732    4.087   3.163  -0.889  H5   XBD  43  
XBD  H7   H7   H  0  1  N  N  N  -13.119   -0.595  14.807   -6.692  -1.200  -1.205  H7   XBD  44  
XBD  H8   H8   H  0  1  N  N  N  -13.707   -2.270  15.085   -6.993  -1.258   0.549  H8   XBD  45  
XBD  H9   H9   H  0  1  N  N  N  -14.562   -0.616  16.767   -8.648   0.564   0.338  H9   XBD  46  
XBD  H10  H10  H  0  1  N  N  N  -13.616   -1.957  17.497   -9.082  -0.794  -0.728  H10  XBD  47  
XBD  H11  H11  H  0  1  N  N  N  -12.480    1.087  19.207   -9.601   2.057  -2.901  H11  XBD  48  
XBD  H12  H12  H  0  1  N  N  N  -14.159    0.831  18.622  -10.354   0.632  -2.144  H12  XBD  49  
XBD  H13  H13  H  0  1  N  N  N  -13.279   -0.505  19.440   -9.973   2.066  -1.160  H13  XBD  50  
XBD  H14  H14  H  0  1  N  N  N  -11.424   -1.603  18.242   -7.312   2.618  -2.385  H14  XBD  51  
XBD  H15  H15  H  0  1  N  N  N  -10.666    0.020  18.118   -7.613   2.560  -0.631  H15  XBD  52  
XBD  H16  H16  H  0  1  N  N  N   -9.805   -1.599  16.421   -5.224   2.154  -1.108  H16  XBD  53  
XBD  H17  H17  H  0  1  N  N  N  -10.585   -0.156  15.688   -5.657   0.796  -2.174  H17  XBD  54  
XBD  H18  H18  H  0  1  N  N  N   -9.171   -2.802  15.261   -5.391  -1.215   1.827  H18  XBD  55  
XBD  H19  H19  H  0  1  N  N  N   -6.230   -4.566  14.319   -5.026  -3.103   2.655  H19  XBD  56  
XBD  H20  H20  H  0  1  N  N  N   -7.132   -3.024  14.508   -4.002  -3.329   4.093  H20  XBD  57  
XBD  H21  H21  H  0  1  N  N  N   -7.601   -4.464  15.475   -4.689  -1.727   3.732  H21  XBD  58  
XBD  H22  H22  H  0  1  N  N  N   -9.637   -8.487   8.494    1.009   1.957  -0.779  H22  XBD  59  
XBD  H23  H23  H  0  1  N  N  N  -13.276   -8.048  12.867    3.487  -1.620   2.559  H23  XBD  60  
XBD  H24  H24  H  0  1  N  N  N  -14.095   -6.587  12.218    4.378  -2.968   1.811  H24  XBD  61  
XBD  H25  H25  H  0  1  N  N  N  -14.984   -8.145  12.319    5.161  -1.382   2.005  H25  XBD  62  
XBD  H26  H26  H  0  1  N  N  N  -14.960   -8.374   6.401    5.896  -0.101  -3.296  H26  XBD  63  
XBD  H27  H27  H  0  1  N  N  N  -16.575   -6.545   6.707    6.418  -2.416  -3.925  H27  XBD  64  
XBD  H28  H28  H  0  1  N  N  N  -16.780   -5.420   8.876    5.744  -4.281  -2.468  H28  XBD  65  
XBD  H29  H29  H  0  1  N  N  N  -15.364   -6.112  10.775    4.489  -3.846  -0.401  H29  XBD  66  
#   #
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_aromatic_flag
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_ordinal
XBD  O    C    DOUB  N  N   1  
XBD  C22  C23  DOUB  Y  N   2  
XBD  C22  C21  SING  Y  N   3  
XBD  C23  C24  SING  Y  N   4  
XBD  C    C21  SING  N  N   5  
XBD  C    N    SING  N  N   6  
XBD  C21  C20  DOUB  Y  N   7  
XBD  C1   N    SING  N  N   8  
XBD  C1   C2   SING  N  N   9  
XBD  C24  C25  DOUB  Y  N  10  
XBD  N    C3   SING  N  N  11  
XBD  C18  C3   DOUB  Y  N  12  
XBD  C18  N5   SING  Y  N  13  
XBD  C3   C4   SING  Y  N  14  
XBD  F1   C2   SING  N  N  15  
XBD  C20  C25  SING  Y  N  16  
XBD  C20  N6   SING  N  N  17  
XBD  C2   F    SING  N  N  18  
XBD  C2   F2   SING  N  N  19  
XBD  N5   C5   DOUB  Y  N  20  
XBD  C4   N6   SING  N  N  21  
XBD  C4   N1   DOUB  Y  N  22  
XBD  N6   C19  SING  N  N  23  
XBD  C5   N1   SING  Y  N  24  
XBD  C5   N2   SING  N  N  25  
XBD  N2   C6   SING  N  N  26  
XBD  C7   C6   DOUB  Y  N  27  
XBD  C7   C8   SING  Y  N  28  
XBD  C6   C16  SING  Y  N  29  
XBD  O1   C16  SING  N  N  30  
XBD  O1   C17  SING  N  N  31  
XBD  C8   C9   DOUB  Y  N  32  
XBD  C16  C15  DOUB  Y  N  33  
XBD  C15  C9   SING  Y  N  34  
XBD  C9   N3   SING  N  N  35  
XBD  C10  N3   SING  N  N  36  
XBD  C10  C11  SING  N  N  37  
XBD  N3   C14  SING  N  N  38  
XBD  C14  C13  SING  N  N  39  
XBD  C11  N4   SING  N  N  40  
XBD  N4   C13  SING  N  N  41  
XBD  N4   C12  SING  N  N  42  
XBD  C7   H1   SING  N  N  43  
XBD  C8   H2   SING  N  N  44  
XBD  N2   H3   SING  N  N  45  
XBD  C1   H4   SING  N  N  46  
XBD  C1   H5   SING  N  N  47  
XBD  C10  H7   SING  N  N  48  
XBD  C10  H8   SING  N  N  49  
XBD  C11  H9   SING  N  N  50  
XBD  C11  H10  SING  N  N  51  
XBD  C12  H11  SING  N  N  52  
XBD  C12  H12  SING  N  N  53  
XBD  C12  H13  SING  N  N  54  
XBD  C13  H14  SING  N  N  55  
XBD  C13  H15  SING  N  N  56  
XBD  C14  H16  SING  N  N  57  
XBD  C14  H17  SING  N  N  58  
XBD  C15  H18  SING  N  N  59  
XBD  C17  H19  SING  N  N  60  
XBD  C17  H20  SING  N  N  61  
XBD  C17  H21  SING  N  N  62  
XBD  C18  H22  SING  N  N  63  
XBD  C19  H23  SING  N  N  64  
XBD  C19  H24  SING  N  N  65  
XBD  C19  H25  SING  N  N  66  
XBD  C22  H26  SING  N  N  67  
XBD  C23  H27  SING  N  N  68  
XBD  C24  H28  SING  N  N  69  
XBD  C25  H29  SING  N  N  70  
#   #
loop_
_pdbx_chem_comp_descriptor.comp_id
_pdbx_chem_comp_descriptor.type
_pdbx_chem_comp_descriptor.program
_pdbx_chem_comp_descriptor.program_version
_pdbx_chem_comp_descriptor.descriptor
XBD  SMILES            ACDLabs               12.01  "n3c(Nc2ccc(N1CCN(C)CC1)cc2OC)ncc4c3N(C)c5ccccc5C(N4CC(F)(F)F)=O"  
XBD  InChI             InChI                 1.03   "InChI=1S/C26H28F3N7O2/c1-33-10-12-35(13-11-33)17-8-9-19(22(14-17)38-3)31-25-30-15-21-23(32-25)34(2)20-7-5-4-6-18(20)24(37)36(21)16-26(27,28)29/h4-9,14-15H,10-13,16H2,1-3H3,(H,30,31,32)"  
XBD  InChIKey          InChI                 1.03   OQFCHSFVWSLDAO-UHFFFAOYSA-N  
XBD  SMILES_CANONICAL  CACTVS                3.385  "COc1cc(ccc1Nc2ncc3N(CC(F)(F)F)C(=O)c4ccccc4N(C)c3n2)N5CCN(C)CC5"  
XBD  SMILES            CACTVS                3.385  "COc1cc(ccc1Nc2ncc3N(CC(F)(F)F)C(=O)c4ccccc4N(C)c3n2)N5CCN(C)CC5"  
XBD  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "CN1CCN(CC1)c2ccc(c(c2)OC)Nc3ncc4c(n3)N(c5ccccc5C(=O)N4CC(F)(F)F)C"  
XBD  SMILES            "OpenEye OEToolkits"  2.0.7  "CN1CCN(CC1)c2ccc(c(c2)OC)Nc3ncc4c(n3)N(c5ccccc5C(=O)N4CC(F)(F)F)C"  
#   #
loop_
_pdbx_chem_comp_identifier.comp_id
_pdbx_chem_comp_identifier.type
_pdbx_chem_comp_identifier.program
_pdbx_chem_comp_identifier.program_version
_pdbx_chem_comp_identifier.identifier
XBD  "SYSTEMATIC NAME"  ACDLabs               12.01  "2-{[2-methoxy-4-(4-methylpiperazin-1-yl)phenyl]amino}-11-methyl-5-(2,2,2-trifluoroethyl)-5,11-dihydro-6H-pyrimido[4,5-b][1,4]benzodiazepin-6-one"  
XBD  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  2.0.7  "2-[[2-methoxy-4-(4-methylpiperazin-1-yl)phenyl]amino]-11-methyl-5-[2,2,2-tris(fluoranyl)ethyl]pyrimido[4,5-b][1,4]benzodiazepin-6-one"  
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
XBD  "Create component"  2020-12-08  RCSB  
XBD  "Initial release"   2021-09-22  RCSB  
##
