data_D9M
#

_chem_comp.id                                   D9M
_chem_comp.name                                 "(1S,2S,3S,4R,5R)-4-(morpholin-4-yl)-2-[(pyridin-4-ylmethyl)amino]-6,8-dioxabicyclo[3.2.1]octan-3-ol"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C16 H23 N3 O4"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2017-10-23
_chem_comp.pdbx_modified_date                   2020-04-17
_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                       321.372
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    D9M
_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       5QBM
_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
D9M  O3   O1   O  0  1  N  N  N  -4.307   9.553   4.989   0.672  -3.703  -0.021  O3   D9M   1  
D9M  C4   C1   C  0  1  Y  N  N  -5.088   0.771   6.529   2.609   1.451  -0.064  C4   D9M   2  
D9M  C5   C2   C  0  1  N  N  N  -4.107   1.908   6.497   1.241   2.050  -0.266  C5   D9M   3  
D9M  C6   C3   C  0  1  N  N  S  -3.139   3.872   7.698  -1.095   1.522  -0.620  C6   D9M   4  
D9M  N1   N1   N  0  1  N  N  N  -4.169   2.787   7.709   0.253   0.974  -0.420  N1   D9M   5  
D9M  C7   C4   C  0  1  N  N  S  -2.924   4.497   9.108  -1.717   1.874   0.742  C7   D9M   6  
D9M  C8   C5   C  0  1  N  N  N  -1.466   4.815   9.390  -3.236   2.071   0.529  C8   D9M   7  
D9M  N2   N2   N  0  1  N  N  N  -3.284   7.537   6.181  -0.963  -1.423  -0.129  N2   D9M   8  
D9M  C9   C6   C  0  1  N  N  R  -2.536   6.579   8.405  -2.722  -0.134   1.001  C9   D9M   9  
D9M  C10  C7   C  0  1  N  N  R  -2.683   6.314   6.878  -2.220  -0.693  -0.340  C10  D9M  10  
D9M  C11  C8   C  0  1  N  N  S  -3.528   5.011   6.661  -1.981   0.474  -1.304  C11  D9M  11  
D9M  C12  C9   C  0  1  N  N  N  -2.398   8.749   6.251  -0.531  -2.095  -1.363  C12  D9M  12  
D9M  C13  C10  C  0  1  N  N  N  -2.987   9.866   5.425   0.809  -2.792  -1.115  C13  D9M  13  
D9M  C14  C11  C  0  1  N  N  N  -5.117   9.181   6.092   0.254  -3.082   1.197  C14  D9M  14  
D9M  C15  C12  C  0  1  N  N  N  -4.655   7.878   6.694  -1.092  -2.388   0.973  C15  D9M  15  
D9M  O2   O2   O  0  1  N  N  N  -3.214   4.550   5.346  -3.233   1.066  -1.657  O2   D9M  16  
D9M  O    O3   O  0  1  N  N  N  -1.277   6.143   8.881  -3.811   0.768   0.733  O    D9M  17  
D9M  O1   O4   O  0  1  N  N  N  -3.497   5.823   9.113  -1.664   0.677   1.558  O1   D9M  18  
D9M  C    C13  C  0  1  Y  N  N  -6.290   0.843   5.845   3.074   1.158   1.209  C    D9M  19  
D9M  C3   C14  C  0  1  Y  N  N  -4.793  -0.406   7.192   3.430   1.175  -1.147  C3   D9M  20  
D9M  C2   C15  C  0  1  Y  N  N  -5.692  -1.453   7.136   4.678   0.625  -0.923  C2   D9M  21  
D9M  N    N3   N  0  1  Y  N  N  -6.850  -1.399   6.471   5.089   0.363   0.303  N    D9M  22  
D9M  C1   C16  C  0  1  Y  N  N  -7.129  -0.253   5.841   4.331   0.603   1.355  C1   D9M  23  
D9M  H1   H1   H  0  1  N  N  N  -3.092   1.490   6.422   0.981   2.662   0.598  H1   D9M  24  
D9M  H2   H2   H  0  1  N  N  N  -4.317   2.523   5.610   1.245   2.671  -1.163  H2   D9M  25  
D9M  H3   H3   H  0  1  N  N  N  -2.181   3.442   7.371  -1.039   2.418  -1.239  H3   D9M  26  
D9M  H4   H4   H  0  1  N  N  N  -5.075   3.208   7.751   0.507   0.355  -1.175  H4   D9M  27  
D9M  H6   H6   H  0  1  N  N  N  -3.351   3.852   9.890  -1.232   2.728   1.215  H6   D9M  28  
D9M  H7   H7   H  0  1  N  N  N  -0.807   4.103   8.871  -3.632   2.779   1.258  H7   D9M  29  
D9M  H8   H8   H  0  1  N  N  N  -1.264   4.782  10.471  -3.435   2.421  -0.484  H8   D9M  30  
D9M  H10  H10  H  0  1  N  N  N  -2.671   7.655   8.592  -3.021  -0.925   1.688  H10  D9M  31  
D9M  H11  H11  H  0  1  N  N  N  -1.679   6.138   6.465  -2.968  -1.367  -0.758  H11  D9M  32  
D9M  H12  H12  H  0  1  N  N  N  -4.598   5.245   6.763  -1.484   0.108  -2.202  H12  D9M  33  
D9M  H13  H13  H  0  1  N  N  N  -1.401   8.495   5.862  -1.277  -2.835  -1.655  H13  D9M  34  
D9M  H14  H14  H  0  1  N  N  N  -2.311   9.077   7.297  -0.418  -1.359  -2.158  H14  D9M  35  
D9M  H15  H15  H  0  1  N  N  N  -2.350  10.033   4.544   1.568  -2.047  -0.876  H15  D9M  36  
D9M  H16  H16  H  0  1  N  N  N  -3.019  10.782   6.034   1.105  -3.340  -2.010  H16  D9M  37  
D9M  H17  H17  H  0  1  N  N  N  -5.064   9.969   6.858   0.148  -3.838   1.974  H17  D9M  38  
D9M  H18  H18  H  0  1  N  N  N  -6.157   9.070   5.752   0.996  -2.345   1.503  H18  D9M  39  
D9M  H19  H19  H  0  1  N  N  N  -4.622   7.973   7.789  -1.388  -1.864   1.882  H19  D9M  40  
D9M  H20  H20  H  0  1  N  N  N  -5.358   7.078   6.417  -1.847  -3.131   0.718  H20  D9M  41  
D9M  H21  H21  H  0  1  N  N  N  -3.703   3.757   5.163  -3.157   1.812  -2.267  H21  D9M  42  
D9M  H22  H22  H  0  1  N  N  N  -6.568   1.746   5.321   2.461   1.360   2.075  H22  D9M  43  
D9M  H23  H23  H  0  1  N  N  N  -3.872  -0.505   7.746   3.098   1.387  -2.152  H23  D9M  44  
D9M  H24  H24  H  0  1  N  N  N  -5.446  -2.366   7.658   5.323   0.407  -1.760  H24  D9M  45  
D9M  H25  H25  H  0  1  N  N  N  -8.061  -0.181   5.300   4.701   0.372   2.343  H25  D9M  46  
#   #
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
D9M  O3   C13  SING  N  N   1  
D9M  O3   C14  SING  N  N   2  
D9M  O2   C11  SING  N  N   3  
D9M  C13  C12  SING  N  N   4  
D9M  C1   C    DOUB  Y  N   5  
D9M  C1   N    SING  Y  N   6  
D9M  C    C4   SING  Y  N   7  
D9M  C14  C15  SING  N  N   8  
D9M  N2   C12  SING  N  N   9  
D9M  N2   C15  SING  N  N  10  
D9M  N2   C10  SING  N  N  11  
D9M  N    C2   DOUB  Y  N  12  
D9M  C5   C4   SING  N  N  13  
D9M  C5   N1   SING  N  N  14  
D9M  C4   C3   DOUB  Y  N  15  
D9M  C11  C10  SING  N  N  16  
D9M  C11  C6   SING  N  N  17  
D9M  C10  C9   SING  N  N  18  
D9M  C2   C3   SING  Y  N  19  
D9M  C6   N1   SING  N  N  20  
D9M  C6   C7   SING  N  N  21  
D9M  C9   O    SING  N  N  22  
D9M  C9   O1   SING  N  N  23  
D9M  O    C8   SING  N  N  24  
D9M  C7   O1   SING  N  N  25  
D9M  C7   C8   SING  N  N  26  
D9M  C5   H1   SING  N  N  27  
D9M  C5   H2   SING  N  N  28  
D9M  C6   H3   SING  N  N  29  
D9M  N1   H4   SING  N  N  30  
D9M  C7   H6   SING  N  N  31  
D9M  C8   H7   SING  N  N  32  
D9M  C8   H8   SING  N  N  33  
D9M  C9   H10  SING  N  N  34  
D9M  C10  H11  SING  N  N  35  
D9M  C11  H12  SING  N  N  36  
D9M  C12  H13  SING  N  N  37  
D9M  C12  H14  SING  N  N  38  
D9M  C13  H15  SING  N  N  39  
D9M  C13  H16  SING  N  N  40  
D9M  C14  H17  SING  N  N  41  
D9M  C14  H18  SING  N  N  42  
D9M  C15  H19  SING  N  N  43  
D9M  C15  H20  SING  N  N  44  
D9M  O2   H21  SING  N  N  45  
D9M  C    H22  SING  N  N  46  
D9M  C3   H23  SING  N  N  47  
D9M  C2   H24  SING  N  N  48  
D9M  C1   H25  SING  N  N  49  
#   #
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
D9M  SMILES            ACDLabs               12.01  "O1CCN(CC1)C3C4OCC(C(NCc2ccncc2)C3O)O4"  
D9M  InChI             InChI                 1.03   "InChI=1S/C16H23N3O4/c20-15-13(18-9-11-1-3-17-4-2-11)12-10-22-16(23-12)14(15)19-5-7-21-8-6-19/h1-4,12-16,18,20H,5-10H2/t12-,13-,14-,15+,16-/m1/s1"  
D9M  InChIKey          InChI                 1.03   RCXMXLJCXLGFHQ-DGXTUMSLSA-N  
D9M  SMILES_CANONICAL  CACTVS                3.385  "O[C@H]1[C@H](NCc2ccncc2)[C@H]3CO[C@H](O3)[C@@H]1N4CCOCC4"  
D9M  SMILES            CACTVS                3.385  "O[CH]1[CH](NCc2ccncc2)[CH]3CO[CH](O3)[CH]1N4CCOCC4"  
D9M  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.6  "c1cnccc1CN[C@@H]2[C@H]3CO[C@H](O3)[C@@H]([C@H]2O)N4CCOCC4"  
D9M  SMILES            "OpenEye OEToolkits"  2.0.6  "c1cnccc1CNC2C3COC(O3)C(C2O)N4CCOCC4"  
#   #
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
D9M  "SYSTEMATIC NAME"  ACDLabs               12.01  "(1S,2S,3S,4R,5R)-4-(morpholin-4-yl)-2-[(pyridin-4-ylmethyl)amino]-6,8-dioxabicyclo[3.2.1]octan-3-ol (non-preferred name)"  
D9M  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  2.0.6  "(1~{S},2~{S},3~{S},4~{R},5~{R})-4-morpholin-4-yl-2-(pyridin-4-ylmethylamino)-6,8-dioxabicyclo[3.2.1]octan-3-ol"  
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
D9M  "Create component"  2017-10-23  RCSB  
D9M  "Initial release"   2020-04-22  RCSB  
##
