data_YRP
#

_chem_comp.id                                   YRP
_chem_comp.name                                 "(2R)-N-(4-chlorophenyl)-2-[(1R,3S,5S,6r)-3-(5,6-difluoro-1H-benzimidazol-1-yl)bicyclo[3.1.0]hexan-6-yl]propanamide"
_chem_comp.type                                 non-polymer
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C22 H20 Cl F2 N3 O"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2021-03-29
_chem_comp.pdbx_modified_date                   2021-08-27
_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                       415.864
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    YRP
_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       7M63
_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
YRP  C14   C1   C   0  1  Y  N  N  18.307  4.514  -13.700  -4.041  -1.373   0.445  C14   YRP   1  
YRP  C11   C2   C   0  1  Y  N  N  18.568  2.815  -11.955  -5.747   0.029  -0.543  C11   YRP   2  
YRP  C10   C3   C   0  1  Y  N  N  19.124  3.770  -12.874  -4.420  -0.165  -0.124  C10   YRP   3  
YRP  C13   C4   C   0  1  Y  N  N  20.752  2.762  -11.706  -4.657   1.860  -0.974  C13   YRP   4  
YRP  C01   C5   C   0  1  N  N  N  22.497  3.926  -14.473  -2.186   2.506   0.799  C01   YRP   5  
YRP  C02   C6   C   0  1  N  N  N  21.512  4.554  -13.451  -2.340   1.294  -0.154  C02   YRP   6  
YRP  C03   C7   C   0  1  N  N  N  22.531  5.306  -12.558  -1.635   1.782  -1.444  C03   YRP   7  
YRP  C04   C8   C   0  1  N  N  S  23.431  5.950  -13.636  -0.424   2.589  -0.931  C04   YRP   8  
YRP  C05   C9   C   0  1  N  N  R  23.345  5.153  -14.848  -0.775   3.049   0.494  C05   YRP   9  
YRP  C06   C10  C   0  1  N  N  N  23.066  6.640  -14.940   0.371   2.028   0.249  C06   YRP  10  
YRP  C07   C11  C   0  1  N  N  R  24.137  7.478  -15.767   1.807   2.519   0.442  C07   YRP  11  
YRP  C08   C12  C   0  1  N  N  N  25.056  6.509  -16.622   2.766   1.391   0.160  C08   YRP  12  
YRP  C15   C13  C   0  1  Y  N  N  16.955  4.340  -13.643  -4.970  -2.382   0.597  C15   YRP  13  
YRP  C16   C14  C   0  1  Y  N  N  16.354  3.396  -12.738  -6.286  -2.195   0.183  C16   YRP  14  
YRP  C17   C15  C   0  1  Y  N  N  17.169  2.648  -11.908  -6.677  -1.002  -0.383  C17   YRP  15  
YRP  C22   C16  C   0  1  Y  N  N  27.268  5.184  -17.015   4.981   0.523   0.100  C22   YRP  16  
YRP  C23   C17  C   0  1  Y  N  N  27.091  4.822  -18.384   4.698  -0.477  -0.822  C23   YRP  17  
YRP  C24   C18  C   0  1  Y  N  N  27.944  3.949  -19.067   5.577  -1.529  -0.989  C24   YRP  18  
YRP  C25   C19  C   0  1  Y  N  N  29.025  3.390  -18.400   6.739  -1.588  -0.239  C25   YRP  19  
YRP  C26   C20  C   0  1  Y  N  N  29.247  3.702  -17.072   7.022  -0.593   0.680  C26   YRP  20  
YRP  C27   C21  C   0  1  Y  N  N  28.385  4.576  -16.401   6.147   0.461   0.851  C27   YRP  21  
YRP  C29   C22  C   0  1  N  N  N  25.009  8.352  -14.852   1.993   2.997   1.883  C29   YRP  22  
YRP  F18   F1   F   0  1  N  N  N  16.122  5.041  -14.429  -4.601  -3.557   1.151  F18   YRP  23  
YRP  F19   F2   F   0  1  N  N  N  15.030  3.295  -12.753  -7.185  -3.191   0.338  F19   YRP  24  
YRP  N09   N1   N   0  1  Y  N  N  20.550  3.735  -12.718  -3.755   1.012  -0.410  N09   YRP  25  
YRP  N12   N2   N   0  1  Y  N  N  19.635  2.205  -11.241  -5.822   1.286  -1.052  N12   YRP  26  
YRP  N21   N3   N   0  1  N  N  N  26.393  6.089  -16.267   4.094   1.593   0.267  N21   YRP  27  
YRP  O20   O1   O   0  1  N  N  N  24.549  6.100  -17.619   2.342   0.302  -0.164  O20   YRP  28  
YRP  CL28  CL1  CL  0  0  N  N  N  30.120  2.286  -19.232   7.841  -2.912  -0.451  CL28  YRP  29  
YRP  H1    H1   H   0  1  N  N  N  18.735  5.229  -14.387  -3.020  -1.525   0.763  H1    YRP  30  
YRP  H2    H2   H   0  1  N  N  N  21.733  2.494  -11.342  -4.438   2.863  -1.309  H2    YRP  31  
YRP  H3    H3   H   0  1  N  N  N  21.968  3.517  -15.347  -2.941   3.261   0.580  H3    YRP  32  
YRP  H4    H4   H   0  1  N  N  N  23.109  3.136  -14.013  -2.258   2.186   1.838  H4    YRP  33  
YRP  H5    H5   H   0  1  N  N  N  20.946  5.324  -13.996  -1.840   0.416   0.255  H5    YRP  34  
YRP  H6    H6   H   0  1  N  N  N  23.097  4.614  -11.917  -1.302   0.933  -2.041  H6    YRP  35  
YRP  H7    H7   H   0  1  N  N  N  22.039  6.066  -11.933  -2.302   2.418  -2.026  H7    YRP  36  
YRP  H8    H8   H   0  1  N  N  N  24.452  6.163  -13.287   0.069   3.257  -1.638  H8    YRP  37  
YRP  H9    H9   H   0  1  N  N  N  24.323  4.876  -15.268  -0.540   4.057   0.839  H9    YRP  38  
YRP  H10   H10  H   0  1  N  N  N  22.017  6.947  -15.067   0.188   0.990   0.528  H10   YRP  39  
YRP  H11   H11  H   0  1  N  N  N  23.592  8.133  -16.463   2.004   3.344  -0.243  H11   YRP  40  
YRP  H12   H12  H   0  1  N  N  N  16.733  1.935  -11.223  -7.700  -0.863  -0.701  H12   YRP  41  
YRP  H13   H13  H   0  1  N  N  N  26.254  5.244  -18.921   3.792  -0.431  -1.408  H13   YRP  42  
YRP  H14   H14  H   0  1  N  N  N  27.763  3.712  -20.105   5.358  -2.306  -1.706  H14   YRP  43  
YRP  H15   H15  H   0  1  N  N  N  30.088  3.270  -16.551   7.929  -0.642   1.265  H15   YRP  44  
YRP  H16   H16  H   0  1  N  N  N  28.584  4.797  -15.363   6.370   1.239   1.566  H16   YRP  45  
YRP  H17   H17  H   0  1  N  N  N  24.366  9.022  -14.262   3.016   3.347   2.021  H17   YRP  46  
YRP  H18   H18  H   0  1  N  N  N  25.588  7.708  -14.174   1.300   3.813   2.088  H18   YRP  47  
YRP  H19   H19  H   0  1  N  N  N  25.697  8.952  -15.465   1.796   2.173   2.568  H19   YRP  48  
YRP  H20   H20  H   0  1  N  N  N  26.762  6.458  -15.414   4.436   2.480   0.460  H20   YRP  49  
#   #
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
YRP  CL28  C25  SING  N  N   1  
YRP  C24   C25  DOUB  Y  N   2  
YRP  C24   C23  SING  Y  N   3  
YRP  C25   C26  SING  Y  N   4  
YRP  C23   C22  DOUB  Y  N   5  
YRP  O20   C08  DOUB  N  N   6  
YRP  C26   C27  DOUB  Y  N   7  
YRP  C22   C27  SING  Y  N   8  
YRP  C22   N21  SING  N  N   9  
YRP  C08   N21  SING  N  N  10  
YRP  C08   C07  SING  N  N  11  
YRP  C07   C06  SING  N  N  12  
YRP  C07   C29  SING  N  N  13  
YRP  C06   C05  SING  N  N  14  
YRP  C06   C04  SING  N  N  15  
YRP  C05   C01  SING  N  N  16  
YRP  C05   C04  SING  N  N  17  
YRP  C01   C02  SING  N  N  18  
YRP  F18   C15  SING  N  N  19  
YRP  C14   C15  DOUB  Y  N  20  
YRP  C14   C10  SING  Y  N  21  
YRP  C15   C16  SING  Y  N  22  
YRP  C04   C03  SING  N  N  23  
YRP  C02   N09  SING  N  N  24  
YRP  C02   C03  SING  N  N  25  
YRP  C10   N09  SING  Y  N  26  
YRP  C10   C11  DOUB  Y  N  27  
YRP  F19   C16  SING  N  N  28  
YRP  C16   C17  DOUB  Y  N  29  
YRP  N09   C13  SING  Y  N  30  
YRP  C11   C17  SING  Y  N  31  
YRP  C11   N12  SING  Y  N  32  
YRP  C13   N12  DOUB  Y  N  33  
YRP  C14   H1   SING  N  N  34  
YRP  C13   H2   SING  N  N  35  
YRP  C01   H3   SING  N  N  36  
YRP  C01   H4   SING  N  N  37  
YRP  C02   H5   SING  N  N  38  
YRP  C03   H6   SING  N  N  39  
YRP  C03   H7   SING  N  N  40  
YRP  C04   H8   SING  N  N  41  
YRP  C05   H9   SING  N  N  42  
YRP  C06   H10  SING  N  N  43  
YRP  C07   H11  SING  N  N  44  
YRP  C17   H12  SING  N  N  45  
YRP  C23   H13  SING  N  N  46  
YRP  C24   H14  SING  N  N  47  
YRP  C26   H15  SING  N  N  48  
YRP  C27   H16  SING  N  N  49  
YRP  C29   H17  SING  N  N  50  
YRP  C29   H18  SING  N  N  51  
YRP  C29   H19  SING  N  N  52  
YRP  N21   H20  SING  N  N  53  
#   #
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
YRP  SMILES            ACDLabs               12.01  "Clc1ccc(cc1)NC(=O)C(C)C1C2CC(CC21)n1cnc2cc(F)c(F)cc21"  
YRP  InChI             InChI                 1.03   "InChI=1S/C22H20ClF2N3O/c1-11(22(29)27-13-4-2-12(23)3-5-13)21-15-6-14(7-16(15)21)28-10-26-19-8-17(24)18(25)9-20(19)28/h2-5,8-11,14-16,21H,6-7H2,1H3,(H,27,29)/t11-,14-,15-,16+,21+/m1/s1"  
YRP  InChIKey          InChI                 1.03   FVIXADGZFNVGRM-IDJJVQAESA-N  
YRP  SMILES_CANONICAL  CACTVS                3.385  "C[C@H]([C@H]1[C@@H]2C[C@H](C[C@H]12)n3cnc4cc(F)c(F)cc34)C(=O)Nc5ccc(Cl)cc5"  
YRP  SMILES            CACTVS                3.385  "C[CH]([CH]1[CH]2C[CH](C[CH]12)n3cnc4cc(F)c(F)cc34)C(=O)Nc5ccc(Cl)cc5"  
YRP  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "C[C@H](C1[C@H]2[C@@H]1CC(C2)n3cnc4c3cc(c(c4)F)F)C(=O)Nc5ccc(cc5)Cl"  
YRP  SMILES            "OpenEye OEToolkits"  2.0.7  "CC(C1C2C1CC(C2)n3cnc4c3cc(c(c4)F)F)C(=O)Nc5ccc(cc5)Cl"  
#   #
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
YRP  "SYSTEMATIC NAME"  ACDLabs               12.01  "(2R)-N-(4-chlorophenyl)-2-[(1R,3S,5S,6r)-3-(5,6-difluoro-1H-benzimidazol-1-yl)bicyclo[3.1.0]hexan-6-yl]propanamide"  
YRP  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  2.0.7  "(2~{R})-2-[(1~{R},5~{S})-3-[5,6-bis(fluoranyl)benzimidazol-1-yl]-6-bicyclo[3.1.0]hexanyl]-~{N}-(4-chlorophenyl)propanamide"  
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
YRP  "Create component"  2021-03-29  RCSB  
YRP  "Initial release"   2021-09-01  RCSB  
##
