data_D9Y
#

_chem_comp.id                                   D9Y
_chem_comp.name                                 "1-cyclohexyl-3-[(1S,2S,3S,4R,5R)-3-hydroxy-4-(piperidin-1-yl)-6,8-dioxabicyclo[3.2.1]octan-2-yl]urea"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C18 H31 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                       353.456
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    D9Y
_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       5QBP
_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
D9Y  O3   O1   O  0  1  N  N  N  -4.217   3.386   8.166   3.405   1.743   1.603  O3   D9Y   1  
D9Y  C4   C1   C  0  1  N  N  N  -3.421   7.579   6.459  -4.448  -0.882   0.808  C4   D9Y   2  
D9Y  C5   C2   C  0  1  N  N  N  -4.072   8.902   6.077  -5.915  -0.450   0.756  C5   D9Y   3  
D9Y  C6   C3   C  0  1  N  N  N  -2.212   5.663   8.677  -1.184   0.788   0.552  C6   D9Y   4  
D9Y  N1   N1   N  0  1  N  N  N  -1.605   4.474   8.778   0.108   0.407   0.598  N1   D9Y   5  
D9Y  C7   C4   C  0  1  N  N  S  -2.225   3.446   9.591   1.163   1.411   0.756  C7   D9Y   6  
D9Y  C8   C5   C  0  1  N  N  S  -1.308   2.449  10.285   1.474   2.052  -0.607  C8   D9Y   7  
D9Y  N2   N2   N  0  1  N  N  N  -4.753   0.616   8.584   2.097  -1.328   0.011  N2   D9Y   8  
D9Y  C9   C6   C  0  1  N  N  N  -1.794   2.083  11.681   2.822   2.800  -0.478  C9   D9Y   9  
D9Y  C10  C7   C  0  1  N  N  R  -2.636   0.671  10.115   3.128   0.597  -1.112  C10  D9Y  10  
D9Y  C11  C8   C  0  1  N  N  R  -3.836   1.459   9.500   3.003  -0.188   0.203  C11  D9Y  11  
D9Y  C12  C9   C  0  1  N  N  S  -3.163   2.603   8.726   2.438   0.742   1.282  C12  D9Y  12  
D9Y  C13  C10  C  0  1  N  N  N  -5.026  -0.750   9.153   2.090  -2.199   1.193  C13  D9Y  13  
D9Y  C14  C11  C  0  1  N  N  N  -6.235  -1.368   8.491   1.031  -3.291   1.017  C14  D9Y  14  
D9Y  C15  C12  C  0  1  N  N  N  -6.244  -1.109   6.998   1.349  -4.106  -0.239  C15  D9Y  15  
D9Y  O    O2   O  0  1  N  N  N  -3.065   6.034   9.484  -1.474   1.965   0.642  O    D9Y  16  
D9Y  N    N3   N  0  1  N  N  N  -1.672   6.496   7.772  -2.154  -0.137   0.407  N    D9Y  17  
D9Y  C3   C13  C  0  1  N  N  N  -2.295   7.784   7.465  -3.558   0.277   0.357  C3   D9Y  18  
D9Y  C2   C14  C  0  1  N  N  N  -1.276   8.773   6.936  -3.923   0.672  -1.076  C2   D9Y  19  
D9Y  C1   C15  C  0  1  N  N  N  -1.940  10.093   6.549  -5.390   1.104  -1.128  C1   D9Y  20  
D9Y  C    C16  C  0  1  N  N  N  -3.050   9.876   5.541  -6.280  -0.055  -0.677  C    D9Y  21  
D9Y  O1   O3   O  0  1  N  N  N  -2.567   0.882  11.503   3.821   1.829  -0.837  O1   D9Y  22  
D9Y  O2   O4   O  0  1  N  N  N  -1.424   1.179   9.605   1.796   0.975  -1.522  O2   D9Y  23  
D9Y  C17  C17  C  0  1  N  N  N  -4.319   0.495   7.152   2.446  -2.080  -1.201  C17  D9Y  24  
D9Y  C16  C18  C  0  1  N  N  N  -4.860  -0.763   6.498   1.398  -3.168  -1.448  C16  D9Y  25  
D9Y  H1   H1   H  0  1  N  N  N  -3.847   4.110   7.675   3.114   2.368   2.281  H1   D9Y  26  
D9Y  H2   H2   H  0  1  N  N  N  -4.182   6.920   6.903  -4.188  -1.164   1.829  H2   D9Y  27  
D9Y  H3   H3   H  0  1  N  N  N  -3.011   7.107   5.554  -4.297  -1.735   0.147  H3   D9Y  28  
D9Y  H4   H4   H  0  1  N  N  N  -4.551   9.337   6.967  -6.549  -1.276   1.078  H4   D9Y  29  
D9Y  H5   H5   H  0  1  N  N  N  -4.833   8.718   5.304  -6.066   0.403   1.418  H5   D9Y  30  
D9Y  H6   H6   H  0  1  N  N  N  -0.743   4.299   8.303   0.340  -0.532   0.527  H6   D9Y  31  
D9Y  H7   H7   H  0  1  N  N  N  -2.836   3.933  10.366   0.835   2.180   1.456  H7   D9Y  32  
D9Y  H8   H8   H  0  1  N  N  N  -0.271   2.816  10.310   0.668   2.695  -0.961  H8   D9Y  33  
D9Y  H10  H10  H  0  1  N  N  N  -0.941   1.898  12.351   2.852   3.646  -1.165  H10  D9Y  34  
D9Y  H11  H11  H  0  1  N  N  N  -2.419   2.887  12.096   2.971   3.139   0.547  H11  D9Y  35  
D9Y  H12  H12  H  0  1  N  N  N  -2.750  -0.397   9.879   3.634   0.021  -1.887  H12  D9Y  36  
D9Y  H13  H13  H  0  1  N  N  N  -4.438   1.882  10.317   3.985  -0.549   0.507  H13  D9Y  37  
D9Y  H14  H14  H  0  1  N  N  N  -2.569   2.158   7.914   2.203   0.163   2.175  H14  D9Y  38  
D9Y  H15  H15  H  0  1  N  N  N  -5.211  -0.661  10.234   3.070  -2.660   1.310  H15  D9Y  39  
D9Y  H16  H16  H  0  1  N  N  N  -4.151  -1.394   8.982   1.858  -1.608   2.079  H16  D9Y  40  
D9Y  H17  H17  H  0  1  N  N  N  -7.145  -0.937   8.934   1.037  -3.947   1.888  H17  D9Y  41  
D9Y  H18  H18  H  0  1  N  N  N  -6.222  -2.454   8.665   0.048  -2.831   0.914  H18  D9Y  42  
D9Y  H19  H19  H  0  1  N  N  N  -6.924  -0.271   6.783   2.315  -4.597  -0.120  H19  D9Y  43  
D9Y  H20  H20  H  0  1  N  N  N  -6.598  -2.012   6.479   0.574  -4.858  -0.391  H20  D9Y  44  
D9Y  H21  H21  H  0  1  N  N  N  -0.831   6.232   7.300  -1.922  -1.076   0.335  H21  D9Y  45  
D9Y  H22  H22  H  0  1  N  N  N  -2.730   8.198   8.386  -3.710   1.130   1.018  H22  D9Y  46  
D9Y  H23  H23  H  0  1  N  N  N  -0.786   8.344   6.050  -3.289   1.498  -1.398  H23  D9Y  47  
D9Y  H24  H24  H  0  1  N  N  N  -0.523   8.964   7.715  -3.772  -0.181  -1.737  H24  D9Y  48  
D9Y  H25  H25  H  0  1  N  N  N  -1.183  10.760   6.110  -5.541   1.957  -0.466  H25  D9Y  49  
D9Y  H26  H26  H  0  1  N  N  N  -2.362  10.560   7.451  -5.649   1.386  -2.148  H26  D9Y  50  
D9Y  H27  H27  H  0  1  N  N  N  -2.621   9.474   4.611  -6.128  -0.908  -1.338  H27  D9Y  51  
D9Y  H28  H28  H  0  1  N  N  N  -3.542  10.838   5.332  -7.324   0.252  -0.714  H28  D9Y  52  
D9Y  H29  H29  H  0  1  N  N  N  -3.220   0.470   7.115   2.473  -1.402  -2.054  H29  D9Y  53  
D9Y  H30  H30  H  0  1  N  N  N  -4.685   1.370   6.595   3.425  -2.542  -1.073  H30  D9Y  54  
D9Y  H31  H31  H  0  1  N  N  N  -4.182  -1.600   6.722   1.666  -3.736  -2.339  H31  D9Y  55  
D9Y  H32  H32  H  0  1  N  N  N  -4.904  -0.607   5.410   0.421  -2.706  -1.590  H32  D9Y  56  
#   #
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
D9Y  C    C5   SING  N  N   1  
D9Y  C    C1   SING  N  N   2  
D9Y  C5   C4   SING  N  N   3  
D9Y  C4   C3   SING  N  N   4  
D9Y  C16  C15  SING  N  N   5  
D9Y  C16  C17  SING  N  N   6  
D9Y  C1   C2   SING  N  N   7  
D9Y  C2   C3   SING  N  N   8  
D9Y  C15  C14  SING  N  N   9  
D9Y  C17  N2   SING  N  N  10  
D9Y  C3   N    SING  N  N  11  
D9Y  N    C6   SING  N  N  12  
D9Y  O3   C12  SING  N  N  13  
D9Y  C14  C13  SING  N  N  14  
D9Y  N2   C13  SING  N  N  15  
D9Y  N2   C11  SING  N  N  16  
D9Y  C6   N1   SING  N  N  17  
D9Y  C6   O    DOUB  N  N  18  
D9Y  C12  C11  SING  N  N  19  
D9Y  C12  C7   SING  N  N  20  
D9Y  N1   C7   SING  N  N  21  
D9Y  C11  C10  SING  N  N  22  
D9Y  C7   C8   SING  N  N  23  
D9Y  O2   C10  SING  N  N  24  
D9Y  O2   C8   SING  N  N  25  
D9Y  C10  O1   SING  N  N  26  
D9Y  C8   C9   SING  N  N  27  
D9Y  O1   C9   SING  N  N  28  
D9Y  O3   H1   SING  N  N  29  
D9Y  C4   H2   SING  N  N  30  
D9Y  C4   H3   SING  N  N  31  
D9Y  C5   H4   SING  N  N  32  
D9Y  C5   H5   SING  N  N  33  
D9Y  N1   H6   SING  N  N  34  
D9Y  C7   H7   SING  N  N  35  
D9Y  C8   H8   SING  N  N  36  
D9Y  C9   H10  SING  N  N  37  
D9Y  C9   H11  SING  N  N  38  
D9Y  C10  H12  SING  N  N  39  
D9Y  C11  H13  SING  N  N  40  
D9Y  C12  H14  SING  N  N  41  
D9Y  C13  H15  SING  N  N  42  
D9Y  C13  H16  SING  N  N  43  
D9Y  C14  H17  SING  N  N  44  
D9Y  C14  H18  SING  N  N  45  
D9Y  C15  H19  SING  N  N  46  
D9Y  C15  H20  SING  N  N  47  
D9Y  N    H21  SING  N  N  48  
D9Y  C3   H22  SING  N  N  49  
D9Y  C2   H23  SING  N  N  50  
D9Y  C2   H24  SING  N  N  51  
D9Y  C1   H25  SING  N  N  52  
D9Y  C1   H26  SING  N  N  53  
D9Y  C    H27  SING  N  N  54  
D9Y  C    H28  SING  N  N  55  
D9Y  C17  H29  SING  N  N  56  
D9Y  C17  H30  SING  N  N  57  
D9Y  C16  H31  SING  N  N  58  
D9Y  C16  H32  SING  N  N  59  
#   #
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
D9Y  SMILES            ACDLabs               12.01  "OC3C(NC(=O)NC1CCCCC1)C4COC(C3N2CCCCC2)O4"  
D9Y  InChI             InChI                 1.03   "InChI=1S/C18H31N3O4/c22-16-14(20-18(23)19-12-7-3-1-4-8-12)13-11-24-17(25-13)15(16)21-9-5-2-6-10-21/h12-17,22H,1-11H2,(H2,19,20,23)/t13-,14-,15-,16+,17-/m1/s1"  
D9Y  InChIKey          InChI                 1.03   NLUHIVDPQQPQPD-OVYGPGRDSA-N  
D9Y  SMILES_CANONICAL  CACTVS                3.385  "O[C@H]1[C@H](NC(=O)NC2CCCCC2)[C@H]3CO[C@H](O3)[C@@H]1N4CCCCC4"  
D9Y  SMILES            CACTVS                3.385  "O[CH]1[CH](NC(=O)NC2CCCCC2)[CH]3CO[CH](O3)[CH]1N4CCCCC4"  
D9Y  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.6  "C1CCC(CC1)NC(=O)N[C@@H]2[C@H]3CO[C@H](O3)[C@@H]([C@H]2O)N4CCCCC4"  
D9Y  SMILES            "OpenEye OEToolkits"  2.0.6  "C1CCC(CC1)NC(=O)NC2C3COC(O3)C(C2O)N4CCCCC4"  
#   #
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
D9Y  "SYSTEMATIC NAME"  ACDLabs               12.01  "1-cyclohexyl-3-[(1S,2S,3S,4R,5R)-3-hydroxy-4-(piperidin-1-yl)-6,8-dioxabicyclo[3.2.1]octan-2-yl]urea (non-preferred name)"  
D9Y  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  2.0.6  "1-cyclohexyl-3-[(1~{S},2~{S},3~{S},4~{R},5~{R})-3-oxidanyl-4-piperidin-1-yl-6,8-dioxabicyclo[3.2.1]octan-2-yl]urea"  
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
D9Y  "Create component"  2017-10-23  RCSB  
D9Y  "Initial release"   2020-04-22  RCSB  
##
