data_YD4
#

_chem_comp.id                                   YD4
_chem_comp.name                                 "4-({[(3R,4R)-4-{[3-methyl-5-(5-methylpyridin-3-yl)-2-oxo-1,2-dihydro-1,7-naphthyridin-8-yl]amino}piperidin-3-yl]oxy}methyl)-1lambda~6~-thiane-1,1-dione"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C26 H33 N5 O4 S"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2017-12-05
_chem_comp.pdbx_modified_date                   2020-10-23
_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                       511.636
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    YD4
_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       6BSO
_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
YD4  O3   O1   O  0  1  N  N  N  10.732  -37.636  -16.007  -0.723   2.056   3.677  O3   YD4   1  
YD4  C22  C1   C  0  1  N  N  N  11.486  -36.691  -16.709  -1.369   1.544   2.779  C22  YD4   2  
YD4  N3   N1   N  0  1  N  N  N  12.697  -37.035  -17.247  -0.877   0.460   2.153  N3   YD4   3  
YD4  C23  C2   C  0  1  N  N  N  10.975  -35.297  -16.859  -2.619   2.100   2.427  C23  YD4   4  
YD4  C24  C3   C  0  1  N  N  N   9.611  -34.945  -16.215  -3.136   3.312   3.159  C24  YD4   5  
YD4  C25  C4   C  0  1  N  N  N  11.722  -34.348  -17.557  -3.355   1.546   1.430  C25  YD4   6  
YD4  C26  C5   C  0  1  Y  N  N  12.969  -34.703  -18.123  -2.822   0.373   0.743  C26  YD4   7  
YD4  C6   C6   C  0  1  Y  N  N  13.756  -33.792  -18.824  -3.523  -0.264  -0.304  C6   YD4   8  
YD4  C4   C7   C  0  1  Y  N  N  13.350  -32.323  -19.104  -4.840   0.244  -0.755  C4   YD4   9  
YD4  C3   C8   C  0  1  Y  N  N  12.159  -32.096  -19.782  -5.850   0.513   0.168  C3   YD4  10  
YD4  N    N2   N  0  1  Y  N  N  11.745  -30.831  -20.083  -7.021   0.965  -0.233  N    YD4  11  
YD4  C2   C9   C  0  1  Y  N  N  12.532  -29.764  -19.741  -7.285   1.180  -1.507  C2   YD4  12  
YD4  C5   C10  C  0  1  Y  N  N  14.159  -31.246  -18.772  -5.088   0.468  -2.113  C5   YD4  13  
YD4  C1   C11  C  0  1  Y  N  N  13.743  -29.969  -19.078  -6.336   0.938  -2.484  C1   YD4  14  
YD4  C    C12  C  0  1  N  N  N  14.611  -28.752  -18.702  -6.655   1.190  -3.935  C    YD4  15  
YD4  C21  C13  C  0  1  Y  N  N  13.447  -36.070  -17.956  -1.578  -0.147   1.134  C21  YD4  16  
YD4  C9   C14  C  0  1  Y  N  N  14.651  -36.463  -18.487  -1.079  -1.273   0.466  C9   YD4  17  
YD4  N8   N3   N  0  1  Y  N  N  15.426  -35.546  -19.190  -1.771  -1.831  -0.512  N8   YD4  18  
YD4  C7   C15  C  0  1  Y  N  N  14.982  -34.220  -19.365  -2.949  -1.379  -0.901  C7   YD4  19  
YD4  N1   N4   N  0  1  N  N  N  15.115  -37.835  -18.311   0.150  -1.805   0.835  N1   YD4  20  
YD4  C10  C16  C  0  1  N  N  R  16.443  -38.196  -18.702   0.676  -2.983   0.139  C10  YD4  21  
YD4  C14  C17  C  0  1  N  N  R  17.317  -38.201  -17.455   2.203  -3.003   0.251  C14  YD4  22  
YD4  C13  C18  C  0  1  N  N  N  18.666  -38.884  -17.690   2.742  -4.267  -0.424  C13  YD4  23  
YD4  N2   N5   N  0  1  N  N  N  18.632  -40.157  -18.401   2.170  -5.453   0.226  N2   YD4  24  
YD4  C12  C19  C  0  1  N  N  N  17.290  -40.618  -18.684   0.708  -5.479   0.090  C12  YD4  25  
YD4  C11  C20  C  0  1  N  N  N  16.439  -39.570  -19.406   0.108  -4.252   0.781  C11  YD4  26  
YD4  O    O2   O  0  1  N  N  N  17.527  -36.848  -17.064   2.744  -1.849  -0.394  O    YD4  27  
YD4  C15  C21  C  0  1  N  N  N  17.967  -36.681  -15.687   3.972  -1.388   0.173  C15  YD4  28  
YD4  C16  C22  C  0  1  N  N  N  17.783  -35.197  -15.248   4.457  -0.156  -0.593  C16  YD4  29  
YD4  C20  C23  C  0  1  N  N  N  18.383  -35.008  -13.854   5.828   0.258  -0.065  C20  YD4  30  
YD4  C19  C24  C  0  1  N  N  N  18.442  -33.555  -13.412   6.441   1.321  -0.979  C19  YD4  31  
YD4  S    S1   S  0  1  N  N  N  16.786  -32.949  -13.628   5.402   2.810  -0.934  S    YD4  32  
YD4  O1   O3   O  0  1  N  N  N  16.786  -31.528  -13.457   5.819   3.687  -1.971  O1   YD4  33  
YD4  O2   O4   O  0  1  N  N  N  15.953  -33.551  -12.637   5.351   3.289   0.403  O2   YD4  34  
YD4  C18  C25  C  0  1  N  N  N  16.082  -33.384  -15.204   3.778   2.125  -1.371  C18  YD4  35  
YD4  C17  C26  C  0  1  N  N  N  16.338  -34.877  -15.264   3.448   0.975  -0.415  C17  YD4  36  
YD4  H1   H1   H  0  1  N  N  N  13.049  -37.965  -17.139  -0.017   0.100   2.422  H1   YD4  37  
YD4  H2   H2   H  0  1  N  N  N   9.199  -35.836  -15.719  -2.414   3.612   3.918  H2   YD4  38  
YD4  H3   H3   H  0  1  N  N  N   9.751  -34.144  -15.474  -3.281   4.129   2.452  H3   YD4  39  
YD4  H4   H4   H  0  1  N  N  N   8.914  -34.604  -16.995  -4.086   3.071   3.635  H4   YD4  40  
YD4  H5   H5   H  0  1  N  N  N  11.348  -33.341  -17.665  -4.312   1.963   1.152  H5   YD4  41  
YD4  H6   H6   H  0  1  N  N  N  11.549  -32.937  -20.077  -5.672   0.348   1.220  H6   YD4  42  
YD4  H7   H7   H  0  1  N  N  N  12.215  -28.761  -19.985  -8.258   1.551  -1.793  H7   YD4  43  
YD4  H8   H8   H  0  1  N  N  N  15.106  -31.407  -18.278  -4.326   0.275  -2.855  H8   YD4  44  
YD4  H9   H9   H  0  1  N  N  N  14.332  -28.398  -17.699  -6.391   2.215  -4.193  H9   YD4  45  
YD4  H10  H10  H  0  1  N  N  N  15.672  -29.043  -18.706  -6.085   0.500  -4.557  H10  YD4  46  
YD4  H11  H11  H  0  1  N  N  N  14.449  -27.946  -19.433  -7.721   1.035  -4.104  H11  YD4  47  
YD4  H12  H12  H  0  1  N  N  N  15.591  -33.523  -19.922  -3.468  -1.876  -1.707  H12  YD4  48  
YD4  H13  H13  H  0  1  N  N  N  14.492  -38.420  -18.831   0.660  -1.398   1.552  H13  YD4  49  
YD4  H14  H14  H  0  1  N  N  N  16.840  -37.449  -19.405   0.388  -2.944  -0.911  H14  YD4  50  
YD4  H15  H15  H  0  1  N  N  N  16.787  -38.743  -16.658   2.491  -3.001   1.303  H15  YD4  51  
YD4  H16  H16  H  0  1  N  N  N  19.127  -39.062  -16.707   2.466  -4.261  -1.478  H16  YD4  52  
YD4  H17  H17  H  0  1  N  N  N  19.295  -38.193  -18.271   3.828  -4.292  -0.333  H17  YD4  53  
YD4  H18  H18  H  0  1  N  N  N  19.093  -40.846  -17.841   2.444  -5.501   1.196  H18  YD4  54  
YD4  H20  H20  H  0  1  N  N  N  16.799  -40.874  -17.733   0.441  -5.468  -0.967  H20  YD4  55  
YD4  H21  H21  H  0  1  N  N  N  17.353  -41.515  -19.317   0.316  -6.384   0.554  H21  YD4  56  
YD4  H22  H22  H  0  1  N  N  N  15.402  -39.935  -19.456   0.363  -4.270   1.840  H22  YD4  57  
YD4  H23  H23  H  0  1  N  N  N  16.832  -39.442  -20.425  -0.976  -4.263   0.666  H23  YD4  58  
YD4  H24  H24  H  0  1  N  N  N  17.370  -37.332  -15.032   3.814  -1.127   1.219  H24  YD4  59  
YD4  H25  H25  H  0  1  N  N  N  19.029  -36.956  -15.608   4.722  -2.176   0.105  H25  YD4  60  
YD4  H26  H26  H  0  1  N  N  N  18.315  -34.549  -15.960   4.539  -0.400  -1.652  H26  YD4  61  
YD4  H27  H27  H  0  1  N  N  N  17.770  -35.567  -13.132   5.720   0.663   0.941  H27  YD4  62  
YD4  H28  H28  H  0  1  N  N  N  19.406  -35.413  -13.857   6.481  -0.614  -0.034  H28  YD4  63  
YD4  H29  H29  H  0  1  N  N  N  18.747  -33.483  -12.358   7.445   1.566  -0.631  H29  YD4  64  
YD4  H30  H30  H  0  1  N  N  N  19.147  -32.988  -14.037   6.492   0.940  -1.999  H30  YD4  65  
YD4  H31  H31  H  0  1  N  N  N  16.589  -32.858  -16.027   3.018   2.901  -1.282  H31  YD4  66  
YD4  H32  H32  H  0  1  N  N  N  15.005  -33.162  -15.235   3.802   1.753  -2.395  H32  YD4  67  
YD4  H33  H33  H  0  1  N  N  N  15.897  -35.275  -16.190   2.446   0.604  -0.628  H33  YD4  68  
YD4  H34  H34  H  0  1  N  N  N  15.860  -35.354  -14.396   3.488   1.337   0.613  H34  YD4  69  
#   #
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
YD4  N    C3   DOUB  Y  N   1  
YD4  N    C2   SING  Y  N   2  
YD4  C3   C4   SING  Y  N   3  
YD4  C2   C1   DOUB  Y  N   4  
YD4  C11  C10  SING  N  N   5  
YD4  C11  C12  SING  N  N   6  
YD4  C7   N8   DOUB  Y  N   7  
YD4  C7   C6   SING  Y  N   8  
YD4  N8   C9   SING  Y  N   9  
YD4  C4   C6   SING  N  N  10  
YD4  C4   C5   DOUB  Y  N  11  
YD4  C1   C5   SING  Y  N  12  
YD4  C1   C    SING  N  N  13  
YD4  C6   C26  DOUB  Y  N  14  
YD4  C10  N1   SING  N  N  15  
YD4  C10  C14  SING  N  N  16  
YD4  C12  N2   SING  N  N  17  
YD4  C9   N1   SING  N  N  18  
YD4  C9   C21  DOUB  Y  N  19  
YD4  N2   C13  SING  N  N  20  
YD4  C26  C21  SING  Y  N  21  
YD4  C26  C25  SING  N  N  22  
YD4  C21  N3   SING  N  N  23  
YD4  C13  C14  SING  N  N  24  
YD4  C25  C23  DOUB  N  N  25  
YD4  C14  O    SING  N  N  26  
YD4  N3   C22  SING  N  N  27  
YD4  O    C15  SING  N  N  28  
YD4  C23  C22  SING  N  N  29  
YD4  C23  C24  SING  N  N  30  
YD4  C22  O3   DOUB  N  N  31  
YD4  C15  C16  SING  N  N  32  
YD4  C17  C16  SING  N  N  33  
YD4  C17  C18  SING  N  N  34  
YD4  C16  C20  SING  N  N  35  
YD4  C18  S    SING  N  N  36  
YD4  C20  C19  SING  N  N  37  
YD4  S    O1   DOUB  N  N  38  
YD4  S    C19  SING  N  N  39  
YD4  S    O2   DOUB  N  N  40  
YD4  N3   H1   SING  N  N  41  
YD4  C24  H2   SING  N  N  42  
YD4  C24  H3   SING  N  N  43  
YD4  C24  H4   SING  N  N  44  
YD4  C25  H5   SING  N  N  45  
YD4  C3   H6   SING  N  N  46  
YD4  C2   H7   SING  N  N  47  
YD4  C5   H8   SING  N  N  48  
YD4  C    H9   SING  N  N  49  
YD4  C    H10  SING  N  N  50  
YD4  C    H11  SING  N  N  51  
YD4  C7   H12  SING  N  N  52  
YD4  N1   H13  SING  N  N  53  
YD4  C10  H14  SING  N  N  54  
YD4  C14  H15  SING  N  N  55  
YD4  C13  H16  SING  N  N  56  
YD4  C13  H17  SING  N  N  57  
YD4  N2   H18  SING  N  N  58  
YD4  C12  H20  SING  N  N  59  
YD4  C12  H21  SING  N  N  60  
YD4  C11  H22  SING  N  N  61  
YD4  C11  H23  SING  N  N  62  
YD4  C15  H24  SING  N  N  63  
YD4  C15  H25  SING  N  N  64  
YD4  C16  H26  SING  N  N  65  
YD4  C20  H27  SING  N  N  66  
YD4  C20  H28  SING  N  N  67  
YD4  C19  H29  SING  N  N  68  
YD4  C19  H30  SING  N  N  69  
YD4  C18  H31  SING  N  N  70  
YD4  C18  H32  SING  N  N  71  
YD4  C17  H33  SING  N  N  72  
YD4  C17  H34  SING  N  N  73  
#   #
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
YD4  SMILES            ACDLabs               12.01  "O=C1Nc3c(C=C1C)c(c2cc(cnc2)C)cnc3NC5C(OCC4CCS(=O)(=O)CC4)CNCC5"  
YD4  InChI             InChI                 1.03   "InChI=1S/C26H33N5O4S/c1-16-9-19(12-28-11-16)21-13-29-25(24-20(21)10-17(2)26(32)31-24)30-22-3-6-27-14-23(22)35-15-18-4-7-36(33,34)8-5-18/h9-13,18,22-23,27H,3-8,14-15H2,1-2H3,(H,29,30)(H,31,32)/t22-,23-/m1/s1"  
YD4  InChIKey          InChI                 1.03   ZIRMKCLZUOCUSC-DHIUTWEWSA-N  
YD4  SMILES_CANONICAL  CACTVS                3.385  "Cc1cncc(c1)c2cnc(N[C@@H]3CCNC[C@H]3OCC4CC[S](=O)(=O)CC4)c5NC(=O)C(=Cc25)C"  
YD4  SMILES            CACTVS                3.385  "Cc1cncc(c1)c2cnc(N[CH]3CCNC[CH]3OCC4CC[S](=O)(=O)CC4)c5NC(=O)C(=Cc25)C"  
YD4  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.6  "Cc1cc(cnc1)c2cnc(c3c2C=C(C(=O)N3)C)N[C@@H]4CCNC[C@H]4OCC5CCS(=O)(=O)CC5"  
YD4  SMILES            "OpenEye OEToolkits"  2.0.6  "Cc1cc(cnc1)c2cnc(c3c2C=C(C(=O)N3)C)NC4CCNCC4OCC5CCS(=O)(=O)CC5"  
#   #
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
YD4  "SYSTEMATIC NAME"  ACDLabs               12.01  "4-({[(3R,4R)-4-{[3-methyl-5-(5-methylpyridin-3-yl)-2-oxo-1,2-dihydro-1,7-naphthyridin-8-yl]amino}piperidin-3-yl]oxy}methyl)-1lambda~6~-thiane-1,1-dione"  
YD4  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  2.0.6  "8-[[(3~{R},4~{R})-3-[[1,1-bis(oxidanylidene)thian-4-yl]methoxy]piperidin-4-yl]amino]-3-methyl-5-(5-methylpyridin-3-yl)-1~{H}-1,7-naphthyridin-2-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
YD4  "Create component"  2017-12-05  RCSB  
YD4  "Initial release"   2020-10-28  RCSB  
##
