data_YKD
#

_chem_comp.id                                   YKD
_chem_comp.name                                 "(1S,2S)-2-((S)-2-((((2-(4,4-difluorocyclohexyl)propan-2-yl)oxy)carbonyl)amino)-4-methylpentanamido)-1-hydroxy-3-((R)-2-oxo-3,4-dihydro-2H-pyrrol-3-yl)propane-1-sulfonic acid"
_chem_comp.type                                 non-polymer
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C23 H37 F2 N3 O8 S"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2021-03-11
_chem_comp.pdbx_modified_date                   2021-03-19
_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                       553.617
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    YKD
_chem_comp.pdbx_model_coordinates_details       ?
_chem_comp.pdbx_model_coordinates_missing_flag  Y
_chem_comp.pdbx_ideal_coordinates_details       Corina
_chem_comp.pdbx_ideal_coordinates_missing_flag  N
_chem_comp.pdbx_model_coordinates_db_code       7M00
_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
YKD  C14  C1   C  0  1  N  N  N  -10.957  -1.992  38.818  -4.704  -1.266  -0.251  C14  YKD   1  
YKD  C15  C2   C  0  1  N  N  R  -11.246  -0.474  38.919  -4.163  -2.473   0.517  C15  YKD   2  
YKD  C16  C3   C  0  1  N  N  N  -10.249   0.426  38.198  -5.229  -3.056   1.422  C16  YKD   3  
YKD  C18  C4   C  0  1  N  N  N  -12.322   0.985  37.162  -4.781  -4.737   0.031  C18  YKD   4  
YKD  C19  C5   C  0  1  N  N  N  -12.566  -0.094  38.258  -3.853  -3.640  -0.445  C19  YKD   5  
YKD  C25  C6   C  0  1  N  N  N  -16.112   3.726  41.376   4.504   1.635   1.757  C25  YKD   6  
YKD  C26  C7   C  0  1  N  N  N  -13.870   4.101  42.486   5.789   0.451  -0.029  C26  YKD   7  
YKD  C28  C8   C  0  1  N  N  N  -13.045   6.436  43.232   8.284   0.373   0.070  C28  YKD   8  
YKD  C01  C9   C  0  1  N  N  N  -14.087   3.026  40.162   4.432  -0.859   1.610  C01  YKD   9  
YKD  C02  C10  C  0  1  N  N  N  -14.673   3.159  41.560   4.505   0.439   0.802  C02  YKD  10  
YKD  C04  C11  C  0  1  N  N  N  -13.826   0.985  42.378   2.139   0.524   0.497  C04  YKD  11  
YKD  C06  C12  C  0  1  N  N  S  -13.263  -1.307  42.993  -0.287   0.715   0.365  C06  YKD  12  
YKD  C07  C13  C  0  1  N  N  N  -13.772  -2.444  43.906  -0.547   2.174   0.742  C07  YKD  13  
YKD  C08  C14  C  0  1  N  N  N  -14.025  -2.065  45.364  -1.824   2.265   1.579  C08  YKD  14  
YKD  C09  C15  C  0  1  N  N  N  -12.820  -1.366  45.990  -1.604   1.564   2.921  C09  YKD  15  
YKD  C10  C16  C  0  1  N  N  N  -14.467  -3.247  46.213  -2.172   3.735   1.823  C10  YKD  16  
YKD  C11  C17  C  0  1  N  N  N  -13.186  -1.817  41.568  -1.347   0.247  -0.598  C11  YKD  17  
YKD  C13  C18  C  0  1  N  N  S  -11.939  -2.882  39.651  -3.574  -0.628  -1.061  C13  YKD  18  
YKD  C21  C19  C  0  1  N  N  S  -11.485  -4.392  39.689  -4.144   0.482  -1.947  C21  YKD  19  
YKD  C27  C20  C  0  1  N  N  N  -13.986   5.640  42.354   7.000   0.361   0.902  C27  YKD  20  
YKD  C29  C21  C  0  1  N  N  N  -13.222   6.062  44.728   8.285  -0.822  -0.884  C29  YKD  21  
YKD  C32  C22  C  0  1  N  N  N  -13.184   4.524  44.905   7.074  -0.733  -1.815  C32  YKD  22  
YKD  C33  C23  C  0  1  N  N  N  -14.143   3.832  43.964   5.790  -0.745  -0.983  C33  YKD  23  
YKD  F30  F1   F  0  1  N  N  N  -12.275   6.674  45.474   9.459  -0.812  -1.645  F30  YKD  24  
YKD  F31  F2   F  0  1  N  N  N  -14.384   6.541  45.222   8.219  -2.009  -0.145  F31  YKD  25  
YKD  N05  N1   N  0  1  N  N  N  -14.171  -0.193  43.029   1.031   0.601  -0.266  N05  YKD  26  
YKD  N12  N2   N  0  1  N  N  N  -12.053  -2.399  41.042  -2.579  -0.060  -0.147  N12  YKD  27  
YKD  N17  N3   N  0  1  N  N  N  -10.885   1.224  37.247  -5.475  -4.317   1.039  N17  YKD  28  
YKD  O03  O1   O  0  1  N  N  N  -14.840   1.879  42.157   3.355   0.523  -0.081  O03  YKD  29  
YKD  O20  O2   O  0  1  N  N  N   -9.048   0.489  38.424  -5.770  -2.478   2.341  O20  YKD  30  
YKD  O22  O3   O  0  1  N  N  N  -11.344  -4.803  38.362  -5.195  -0.049  -2.756  O22  YKD  31  
YKD  O23  O4   O  0  1  N  N  N  -14.178  -1.686  40.864  -1.092   0.148  -1.780  O23  YKD  32  
YKD  O24  O5   O  0  1  N  N  N  -12.646   1.218  42.051   2.041   0.456   1.706  O24  YKD  33  
YKD  H1   H1   H  0  1  N  N  N  -11.032  -2.289  37.762  -5.496  -1.590  -0.926  H1   YKD  34  
YKD  H2   H2   H  0  1  N  N  N   -9.934  -2.174  39.179  -5.104  -0.536   0.453  H2   YKD  35  
YKD  H3   H3   H  0  1  N  N  N  -11.282  -0.191  39.981  -3.277  -2.199   1.090  H3   YKD  36  
YKD  H4   H4   H  0  1  N  N  N  -13.041   1.445  36.500  -4.854  -5.722  -0.405  H4   YKD  37  
YKD  H5   H5   H  0  1  N  N  N  -13.252   0.308  39.018  -4.083  -3.361  -1.474  H5   YKD  38  
YKD  H6   H6   H  0  1  N  N  N  -13.013  -0.987  37.797  -2.812  -3.951  -0.353  H6   YKD  39  
YKD  H7   H7   H  0  1  N  N  N  -16.589   3.844  42.360   5.366   1.571   2.420  H7   YKD  40  
YKD  H8   H8   H  0  1  N  N  N  -16.059   4.704  40.874   4.555   2.559   1.181  H8   YKD  41  
YKD  H9   H9   H  0  1  N  N  N  -16.704   3.031  40.763   3.589   1.626   2.349  H9   YKD  42  
YKD  H10  H10  H  0  1  N  N  N  -12.810   3.861  42.319   5.840   1.375  -0.605  H10  YKD  43  
YKD  H11  H11  H  0  1  N  N  N  -12.008   6.226  42.930   8.336   1.298  -0.506  H11  YKD  44  
YKD  H12  H12  H  0  1  N  N  N  -13.254   7.508  43.103   9.147   0.310   0.733  H12  YKD  45  
YKD  H13  H13  H  0  1  N  N  N  -13.064   2.627  40.229   3.517  -0.867   2.203  H13  YKD  46  
YKD  H14  H14  H  0  1  N  N  N  -14.709   2.341  39.567   4.433  -1.711   0.931  H14  YKD  47  
YKD  H15  H15  H  0  1  N  N  N  -14.064   4.014  39.679   5.295  -0.922   2.273  H15  YKD  48  
YKD  H16  H16  H  0  1  N  N  N  -12.261  -0.999  43.327  -0.314   0.097   1.263  H16  YKD  49  
YKD  H17  H17  H  0  1  N  N  N  -14.718  -2.816  43.485   0.294   2.556   1.319  H17  YKD  50  
YKD  H18  H18  H  0  1  N  N  N  -13.022  -3.249  43.892  -0.665   2.768  -0.165  H18  YKD  51  
YKD  H19  H19  H  0  1  N  N  N  -14.852  -1.340  45.367  -2.643   1.781   1.047  H19  YKD  52  
YKD  H20  H20  H  0  1  N  N  N  -13.045  -1.112  47.036  -2.533   1.571   3.492  H20  YKD  53  
YKD  H21  H21  H  0  1  N  N  N  -11.949  -2.036  45.955  -1.293   0.534   2.747  H21  YKD  54  
YKD  H22  H22  H  0  1  N  N  N  -12.598  -0.446  45.429  -0.830   2.087   3.482  H22  YKD  55  
YKD  H23  H23  H  0  1  N  N  N  -14.633  -2.914  47.248  -2.328   4.234   0.866  H23  YKD  56  
YKD  H24  H24  H  0  1  N  N  N  -15.402  -3.661  45.807  -3.081   3.799   2.420  H24  YKD  57  
YKD  H25  H25  H  0  1  N  N  N  -13.686  -4.021  46.198  -1.353   4.218   2.355  H25  YKD  58  
YKD  H26  H26  H  0  1  N  N  N  -12.928  -2.838  39.172  -3.102  -1.385  -1.686  H26  YKD  59  
YKD  S1   S1   S  0  1  N  Y  N  -10.561  -4.497  40.219  -4.798   1.813  -0.902  S1   YKD  60  
YKD  H28  H28  H  0  1  N  N  N  -12.322  -4.950  40.134  -3.356   0.876  -2.588  H28  YKD  61  
YKD  H29  H29  H  0  1  N  N  N  -13.782   5.908  41.307   6.999   1.214   1.581  H29  YKD  62  
YKD  H30  H30  H  0  1  N  N  N  -15.016   5.927  42.612   6.948  -0.563   1.477  H30  YKD  63  
YKD  H31  H31  H  0  1  N  N  N  -13.460   4.277  45.941   7.126   0.191  -2.391  H31  YKD  64  
YKD  H32  H32  H  0  1  N  N  N  -12.164   4.166  44.702   7.075  -1.585  -2.495  H32  YKD  65  
YKD  H33  H33  H  0  1  N  N  N  -15.162   4.176  44.195   5.738  -1.669  -0.408  H33  YKD  66  
YKD  H34  H34  H  0  1  N  N  N  -14.074   2.748  44.136   4.927  -0.682  -1.646  H34  YKD  67  
YKD  H35  H35  H  0  1  N  N  N  -15.041  -0.265  43.517   1.105   0.581  -1.233  H35  YKD  68  
YKD  H36  H36  H  0  1  N  N  N  -11.258  -2.501  41.640  -2.808   0.095   0.783  H36  YKD  69  
YKD  H37  H37  H  0  1  N  N  N  -11.070  -5.712  38.339  -5.933  -0.418  -2.251  H37  YKD  70  
YKD  O1   O6   O  0  1  N  Y  N        ?       ?       ?  -5.881   1.341  -0.112  O1   YKD  71  
YKD  O2   O7   O  0  1  N  Y  N        ?       ?       ?  -3.737   2.558  -0.321  O2   YKD  72  
YKD  O3   O8   O  0  1  N  Y  N        ?       ?       ?  -5.443   2.782  -1.883  O3   YKD  73  
YKD  H27  H27  H  0  1  N  N  N        ?       ?       ?  -5.842   3.557  -1.464  H27  YKD  74  
#   #
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
YKD  C18  N17  DOUB  N  N   1  
YKD  C18  C19  SING  N  N   2  
YKD  N17  C16  SING  N  N   3  
YKD  C16  O20  DOUB  N  N   4  
YKD  C16  C15  SING  N  N   5  
YKD  C19  C15  SING  N  N   6  
YKD  O22  C21  SING  N  N   7  
YKD  C14  C15  SING  N  N   8  
YKD  C14  C13  SING  N  N   9  
YKD  C13  C21  SING  N  N  10  
YKD  C13  N12  SING  N  N  11  
YKD  C01  C02  SING  N  N  12  
YKD  O23  C11  DOUB  N  N  13  
YKD  N12  C11  SING  N  N  14  
YKD  C25  C02  SING  N  N  15  
YKD  C02  O03  SING  N  N  16  
YKD  C02  C26  SING  N  N  17  
YKD  C11  C06  SING  N  N  18  
YKD  O24  C04  DOUB  N  N  19  
YKD  O03  C04  SING  N  N  20  
YKD  C27  C26  SING  N  N  21  
YKD  C27  C28  SING  N  N  22  
YKD  C04  N05  SING  N  N  23  
YKD  C26  C33  SING  N  N  24  
YKD  C06  N05  SING  N  N  25  
YKD  C06  C07  SING  N  N  26  
YKD  C28  C29  SING  N  N  27  
YKD  C07  C08  SING  N  N  28  
YKD  C33  C32  SING  N  N  29  
YKD  C29  C32  SING  N  N  30  
YKD  C29  F31  SING  N  N  31  
YKD  C29  F30  SING  N  N  32  
YKD  C08  C09  SING  N  N  33  
YKD  C08  C10  SING  N  N  34  
YKD  C14  H1   SING  N  N  35  
YKD  C14  H2   SING  N  N  36  
YKD  C15  H3   SING  N  N  37  
YKD  C18  H4   SING  N  N  38  
YKD  C19  H5   SING  N  N  39  
YKD  C19  H6   SING  N  N  40  
YKD  C25  H7   SING  N  N  41  
YKD  C25  H8   SING  N  N  42  
YKD  C25  H9   SING  N  N  43  
YKD  C26  H10  SING  N  N  44  
YKD  C28  H11  SING  N  N  45  
YKD  C28  H12  SING  N  N  46  
YKD  C01  H13  SING  N  N  47  
YKD  C01  H14  SING  N  N  48  
YKD  C01  H15  SING  N  N  49  
YKD  C06  H16  SING  N  N  50  
YKD  C07  H17  SING  N  N  51  
YKD  C07  H18  SING  N  N  52  
YKD  C08  H19  SING  N  N  53  
YKD  C09  H20  SING  N  N  54  
YKD  C09  H21  SING  N  N  55  
YKD  C09  H22  SING  N  N  56  
YKD  C10  H23  SING  N  N  57  
YKD  C10  H24  SING  N  N  58  
YKD  C10  H25  SING  N  N  59  
YKD  C13  H26  SING  N  N  60  
YKD  C21  S1   SING  N  N  61  
YKD  C21  H28  SING  N  N  62  
YKD  C27  H29  SING  N  N  63  
YKD  C27  H30  SING  N  N  64  
YKD  C32  H31  SING  N  N  65  
YKD  C32  H32  SING  N  N  66  
YKD  C33  H33  SING  N  N  67  
YKD  C33  H34  SING  N  N  68  
YKD  N05  H35  SING  N  N  69  
YKD  N12  H36  SING  N  N  70  
YKD  O22  H37  SING  N  N  71  
YKD  S1   O1   DOUB  N  N  72  
YKD  S1   O2   DOUB  N  N  73  
YKD  S1   O3   SING  N  N  74  
YKD  O3   H27  SING  N  N  75  
#   #
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
YKD  SMILES            ACDLabs               12.01  "O=C1N=CCC1CC(NC(=O)C(CC(C)C)NC(=O)OC(C)(C)C1CCC(F)(F)CC1)C(O)S(=O)(=O)O"  
YKD  InChI             InChI                 1.03   "InChI=1S/C23H37F2N3O8S/c1-13(2)11-16(28-21(32)36-22(3,4)15-5-8-23(24,25)9-6-15)19(30)27-17(20(31)37(33,34)35)12-14-7-10-26-18(14)29/h10,13-17,20,31H,5-9,11-12H2,1-4H3,(H,27,30)(H,28,32)(H,33,34,35)/t14-,16-,17-,20-/m0/s1"  
YKD  InChIKey          InChI                 1.03   AFVXFMYQWMALEA-VERUCKTNSA-N  
YKD  SMILES_CANONICAL  CACTVS                3.385  "CC(C)C[C@H](NC(=O)OC(C)(C)C1CCC(F)(F)CC1)C(=O)N[C@@H](C[C@@H]2CC=NC2=O)[C@@H](O)[S](O)(=O)=O"  
YKD  SMILES            CACTVS                3.385  "CC(C)C[CH](NC(=O)OC(C)(C)C1CCC(F)(F)CC1)C(=O)N[CH](C[CH]2CC=NC2=O)[CH](O)[S](O)(=O)=O"  
YKD  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "CC(C)C[C@@H](C(=O)N[C@@H](C[C@@H]1CC=NC1=O)C(O)S(=O)(=O)O)NC(=O)OC(C)(C)C2CCC(CC2)(F)F"  
YKD  SMILES            "OpenEye OEToolkits"  2.0.7  "CC(C)CC(C(=O)NC(CC1CC=NC1=O)C(O)S(=O)(=O)O)NC(=O)OC(C)(C)C2CCC(CC2)(F)F"  
#   #
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
YKD  "SYSTEMATIC NAME"  ACDLabs               12.01  "(1S,2S)-2-{[N-({[2-(4,4-difluorocyclohexyl)propan-2-yl]oxy}carbonyl)-L-leucyl]amino}-1-hydroxy-3-[(3R)-2-oxo-3,4-dihydro-2H-pyrrol-3-yl]propane-1-sulfonic acid"  
YKD  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  2.0.7  "(2~{S})-2-[[(2~{S})-2-[2-[4,4-bis(fluoranyl)cyclohexyl]propan-2-yloxycarbonylamino]-4-methyl-pentanoyl]amino]-1-oxidanyl-3-[(3~{R})-2-oxidanylidene-3,4-dihydropyrrol-3-yl]propane-1-sulfonic acid"  
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
YKD  "Create component"  2021-03-11  RCSB  
YKD  "Initial release"   2021-03-24  RCSB  
##
