data_Y1T
# 
_chem_comp.id                                    Y1T 
_chem_comp.name                                  "(pentafluorophenyl)methyl (2R,3S)-2-(carbamimidamidomethyl)-3-[2-(4-chloro-3-fluoroanilino)(oxo)acetamido]-6-[(methylamino)methyl]-2,3-dihydro-1H-indole-1-carboxylate" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C28 H24 Cl F6 N7 O4" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2022-12-27 
_chem_comp.pdbx_modified_date                    2023-03-31 
_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                        671.978 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     Y1T 
_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        8FM8 
_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 
Y1T C10  C1  C  0 1 Y N N -24.096 6.234  -75.279 7.902  2.104  -1.052 C10  Y1T 1  
Y1T C15  C2  C  0 1 N N S -26.674 -1.454 -75.339 1.032  -1.430 0.799  C15  Y1T 2  
Y1T C17  C3  C  0 1 Y N N -28.706 -2.053 -74.280 -1.062 -0.355 0.852  C17  Y1T 3  
Y1T C21  C4  C  0 1 N N N -31.501 -0.481 -78.058 -4.418 -0.963 -1.723 C21  Y1T 4  
Y1T C22  C5  C  0 1 Y N N -32.126 -1.751 -78.633 -5.526 0.018  -1.439 C22  Y1T 5  
Y1T C02  C6  C  0 1 N N N -25.359 0.584  -75.750 3.330  -0.637 0.964  C02  Y1T 6  
Y1T C03  C7  C  0 1 N N N -25.162 2.083  -75.556 4.546  -0.009 0.367  C03  Y1T 7  
Y1T C05  C8  C  0 1 Y N N -23.771 4.098  -76.147 6.820  0.666  0.535  C05  Y1T 8  
Y1T C06  C9  C  0 1 Y N N -23.094 4.684  -77.213 8.060  0.212  0.967  C06  Y1T 9  
Y1T C07  C10 C  0 1 Y N N -22.867 6.050  -77.304 9.214  0.713  0.398  C07  Y1T 10 
Y1T C08  C11 C  0 1 Y N N -23.389 6.817  -76.297 9.137  1.653  -0.614 C08  Y1T 11 
Y1T C12  C12 C  0 1 Y N N -24.331 4.881  -75.182 6.743  1.614  -0.477 C12  Y1T 12 
Y1T C16  C13 C  0 1 Y N N -27.357 -1.892 -74.074 0.175  -0.383 1.475  C16  Y1T 13 
Y1T C19  C14 C  0 1 N N N -30.243 -1.361 -76.273 -2.213 -1.484 -0.974 C19  Y1T 14 
Y1T C23  C15 C  0 1 Y N N -33.366 -2.181 -78.200 -5.580 1.219  -2.125 C23  Y1T 15 
Y1T C25  C16 C  0 1 Y N N -33.900 -3.349 -78.724 -6.598 2.122  -1.864 C25  Y1T 16 
Y1T C27  C17 C  0 1 Y N N -33.200 -4.066 -79.664 -7.563 1.823  -0.916 C27  Y1T 17 
Y1T C29  C18 C  0 1 Y N N -31.982 -3.639 -80.088 -7.509 0.620  -0.229 C29  Y1T 18 
Y1T C31  C19 C  0 1 Y N N -31.432 -2.483 -79.581 -6.493 -0.284 -0.496 C31  Y1T 19 
Y1T C34  C20 C  0 1 N N R -27.706 -1.514 -76.416 0.132  -2.012 -0.304 C34  Y1T 20 
Y1T C35  C21 C  0 1 N N N -27.431 -2.605 -77.436 -0.091 -3.508 -0.073 C35  Y1T 21 
Y1T C37  C22 C  0 1 N N N -25.170 -2.756 -78.515 1.178  -5.606 -0.273 C37  Y1T 22 
Y1T C40  C23 C  0 1 Y N N -29.528 -2.443 -73.206 -2.030 0.541  1.308  C40  Y1T 23 
Y1T C41  C24 C  0 1 Y N N -28.943 -2.658 -71.958 -1.755 1.385  2.362  C41  Y1T 24 
Y1T C42  C25 C  0 1 N N N -29.730 -3.070 -70.725 -2.807 2.350  2.847  C42  Y1T 25 
Y1T C44  C26 C  0 1 N N N -31.891 -3.803 -70.165 -4.655 2.621  4.387  C44  Y1T 26 
Y1T C45  C27 C  0 1 Y N N -27.576 -2.473 -71.781 -0.517 1.349  2.978  C45  Y1T 27 
Y1T C46  C28 C  0 1 Y N N -26.770 -2.075 -72.826 0.447  0.464  2.533  C46  Y1T 28 
Y1T F11  F1  F  0 1 N N N -24.597 7.058  -74.335 7.829  3.026  -2.036 F11  Y1T 29 
Y1T F24  F2  F  0 1 N N N -34.054 -1.455 -77.255 -4.639 1.511  -3.049 F24  Y1T 30 
Y1T F26  F3  F  0 1 N N N -35.117 -3.800 -78.306 -6.649 3.295  -2.533 F26  Y1T 31 
Y1T F28  F4  F  0 1 N N N -33.696 -5.210 -80.202 -8.555 2.703  -0.660 F28  Y1T 32 
Y1T F30  F5  F  0 1 N N N -31.336 -4.387 -81.023 -8.449 0.327  0.695  F30  Y1T 33 
Y1T F32  F6  F  0 1 N N N -30.199 -2.064 -80.038 -6.440 -1.457 0.173  F32  Y1T 34 
Y1T N04  N1  N  0 1 N N N -23.999 2.669  -76.194 5.651  0.168  1.118  N04  Y1T 35 
Y1T N14  N2  N  0 1 N N N -26.499 -0.042 -75.149 2.225  -0.814 0.213  N14  Y1T 36 
Y1T N18  N3  N  0 1 N N N -28.965 -1.752 -75.715 -1.135 -1.285 -0.190 N18  Y1T 37 
Y1T N36  N4  N  0 1 N N N -26.472 -2.110 -78.411 1.159  -4.232 -0.319 N36  Y1T 38 
Y1T N38  N5  N  0 1 N N N -24.186 -2.260 -79.459 0.084  -6.264 -0.010 N38  Y1T 39 
Y1T N39  N6  N  0 1 N N N -24.877 -3.733 -77.774 2.351  -6.285 -0.504 N39  Y1T 40 
Y1T N43  N7  N  0 1 N N N -30.719 -4.088 -71.007 -3.617 1.708  3.891  N43  Y1T 41 
Y1T O01  O1  O  0 1 N N N -24.593 -0.067 -76.378 3.336  -0.989 2.125  O01  Y1T 42 
Y1T O13  O2  O  0 1 N N N -25.940 2.696  -74.891 4.539  0.343  -0.795 O13  Y1T 43 
Y1T O20  O3  O  0 1 N N N -30.242 -0.928 -77.602 -3.294 -0.691 -0.846 O20  Y1T 44 
Y1T O33  O4  O  0 1 N N N -31.251 -1.383 -75.629 -2.210 -2.380 -1.795 O33  Y1T 45 
Y1T CL09 CL1 CL 0 0 N N N -23.200 8.585  -76.237 10.590 2.269  -1.337 CL09 Y1T 46 
Y1T H1   H1  H  0 1 N N N -25.754 -2.013 -75.566 1.316  -2.206 1.509  H1   Y1T 47 
Y1T H2   H2  H  0 1 N N N -31.390 0.291  -78.833 -4.778 -1.977 -1.549 H2   Y1T 48 
Y1T H3   H3  H  0 1 N N N -32.104 -0.084 -77.228 -4.102 -0.863 -2.762 H3   Y1T 49 
Y1T H4   H4  H  0 1 N N N -22.729 4.047  -78.005 8.122  -0.525 1.754  H4   Y1T 50 
Y1T H5   H5  H  0 1 N N N -22.311 6.483  -78.122 10.178 0.360  0.734  H5   Y1T 51 
Y1T H6   H6  H  0 1 N N N -24.927 4.463  -74.384 5.780  1.968  -0.814 H6   Y1T 52 
Y1T H7   H7  H  0 1 N N N -27.747 -0.544 -76.933 0.578  -1.843 -1.284 H7   Y1T 53 
Y1T H8   H8  H  0 1 N N N -28.367 -2.878 -77.945 -0.410 -3.673 0.956  H8   Y1T 54 
Y1T H9   H9  H  0 1 N N N -27.018 -3.489 -76.928 -0.861 -3.870 -0.754 H9   Y1T 55 
Y1T H10  H10 H  0 1 N N N -30.591 -2.573 -73.345 -2.999 0.574  0.831  H10  Y1T 56 
Y1T H11  H11 H  0 1 N N N -29.028 -3.460 -69.974 -2.325 3.238  3.256  H11  Y1T 57 
Y1T H12  H12 H  0 1 N N N -30.242 -2.184 -70.322 -3.448 2.636  2.013  H12  Y1T 58 
Y1T H13  H13 H  0 1 N N N -32.669 -4.558 -70.351 -4.185 3.510  4.807  H13  Y1T 59 
Y1T H14  H14 H  0 1 N N N -31.597 -3.833 -69.105 -5.309 2.909  3.565  H14  Y1T 60 
Y1T H15  H15 H  0 1 N N N -32.283 -2.805 -70.409 -5.240 2.120  5.159  H15  Y1T 61 
Y1T H16  H16 H  0 1 N N N -27.139 -2.644 -70.808 -0.304 2.011  3.804  H16  Y1T 62 
Y1T H17  H17 H  0 1 N N N -25.713 -1.910 -72.680 1.414  0.434  3.012  H17  Y1T 63 
Y1T H18  H18 H  0 1 N N N -23.347 2.080  -76.672 5.635  -0.050 2.063  H18  Y1T 64 
Y1T H19  H19 H  0 1 N N N -27.154 0.490  -74.612 2.219  -0.533 -0.716 H19  Y1T 65 
Y1T H20  H20 H  0 1 N N N -26.703 -1.337 -79.002 1.973  -3.742 -0.514 H20  Y1T 66 
Y1T H21  H21 H  0 1 N N N -23.332 -2.778 -79.416 0.097  -7.234 0.022  H21  Y1T 67 
Y1T H22  H22 H  0 1 N N N -25.541 -4.071 -77.107 3.165  -5.795 -0.699 H22  Y1T 68 
Y1T H23  H23 H  0 1 N N N -23.981 -4.169 -77.853 2.364  -7.254 -0.471 H23  Y1T 69 
Y1T H24  H24 H  0 1 N N N -30.976 -4.058 -71.973 -4.023 0.847  3.555  H24  Y1T 70 
# 
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 
Y1T F30 C29  SING N N 1  
Y1T F28 C27  SING N N 2  
Y1T C29 C27  DOUB Y N 3  
Y1T C29 C31  SING Y N 4  
Y1T F32 C31  SING N N 5  
Y1T C27 C25  SING Y N 6  
Y1T C31 C22  DOUB Y N 7  
Y1T N38 C37  DOUB N N 8  
Y1T C25 F26  SING N N 9  
Y1T C25 C23  DOUB Y N 10 
Y1T C22 C23  SING Y N 11 
Y1T C22 C21  SING N N 12 
Y1T C37 N36  SING N N 13 
Y1T C37 N39  SING N N 14 
Y1T N36 C35  SING N N 15 
Y1T C23 F24  SING N N 16 
Y1T C21 O20  SING N N 17 
Y1T O20 C19  SING N N 18 
Y1T C35 C34  SING N N 19 
Y1T C07 C06  DOUB Y N 20 
Y1T C07 C08  SING Y N 21 
Y1T C06 C05  SING Y N 22 
Y1T C34 N18  SING N N 23 
Y1T C34 C15  SING N N 24 
Y1T O01 C02  DOUB N N 25 
Y1T C08 CL09 SING N N 26 
Y1T C08 C10  DOUB Y N 27 
Y1T C19 N18  SING N N 28 
Y1T C19 O33  DOUB N N 29 
Y1T N04 C05  SING N N 30 
Y1T N04 C03  SING N N 31 
Y1T C05 C12  DOUB Y N 32 
Y1T C02 C03  SING N N 33 
Y1T C02 N14  SING N N 34 
Y1T N18 C17  SING N N 35 
Y1T C03 O13  DOUB N N 36 
Y1T C15 N14  SING N N 37 
Y1T C15 C16  SING N N 38 
Y1T C10 C12  SING Y N 39 
Y1T C10 F11  SING N N 40 
Y1T C17 C16  DOUB Y N 41 
Y1T C17 C40  SING Y N 42 
Y1T C16 C46  SING Y N 43 
Y1T C40 C41  DOUB Y N 44 
Y1T C46 C45  DOUB Y N 45 
Y1T C41 C45  SING Y N 46 
Y1T C41 C42  SING N N 47 
Y1T N43 C42  SING N N 48 
Y1T N43 C44  SING N N 49 
Y1T C15 H1   SING N N 50 
Y1T C21 H2   SING N N 51 
Y1T C21 H3   SING N N 52 
Y1T C06 H4   SING N N 53 
Y1T C07 H5   SING N N 54 
Y1T C12 H6   SING N N 55 
Y1T C34 H7   SING N N 56 
Y1T C35 H8   SING N N 57 
Y1T C35 H9   SING N N 58 
Y1T C40 H10  SING N N 59 
Y1T C42 H11  SING N N 60 
Y1T C42 H12  SING N N 61 
Y1T C44 H13  SING N N 62 
Y1T C44 H14  SING N N 63 
Y1T C44 H15  SING N N 64 
Y1T C45 H16  SING N N 65 
Y1T C46 H17  SING N N 66 
Y1T N04 H18  SING N N 67 
Y1T N14 H19  SING N N 68 
Y1T N36 H20  SING N N 69 
Y1T N38 H21  SING N N 70 
Y1T N39 H22  SING N N 71 
Y1T N39 H23  SING N N 72 
Y1T N43 H24  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 
Y1T SMILES           ACDLabs              12.01 "Clc1ccc(cc1F)NC(=O)C(=O)NC1c2ccc(cc2N(C1CNC(=N)N)C(=O)OCc1c(F)c(F)c(F)c(F)c1F)CNC"                                                                                                                                                              
Y1T InChI            InChI                1.06  "InChI=1S/C28H24ClF6N7O4/c1-38-8-11-2-4-13-17(6-11)42(28(45)46-10-14-19(31)21(33)23(35)22(34)20(14)32)18(9-39-27(36)37)24(13)41-26(44)25(43)40-12-3-5-15(29)16(30)7-12/h2-7,18,24,38H,8-10H2,1H3,(H,40,43)(H,41,44)(H4,36,37,39)/t18-,24+/m1/s1" 
Y1T InChIKey         InChI                1.06  ZLEHMUPVIABTKG-KOSHJBKYSA-N                                                                                                                                                                                                                      
Y1T SMILES_CANONICAL CACTVS               3.385 "CNCc1ccc2[C@H](NC(=O)C(=O)Nc3ccc(Cl)c(F)c3)[C@@H](CNC(N)=N)N(C(=O)OCc4c(F)c(F)c(F)c(F)c4F)c2c1"                                                                                                                                                 
Y1T SMILES           CACTVS               3.385 "CNCc1ccc2[CH](NC(=O)C(=O)Nc3ccc(Cl)c(F)c3)[CH](CNC(N)=N)N(C(=O)OCc4c(F)c(F)c(F)c(F)c4F)c2c1"                                                                                                                                                    
Y1T SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "[H]/N=C(/N)\NC[C@@H]1[C@H](c2ccc(cc2N1C(=O)OCc3c(c(c(c(c3F)F)F)F)F)CNC)NC(=O)C(=O)Nc4ccc(c(c4)F)Cl"                                                                                                                                             
Y1T SMILES           "OpenEye OEToolkits" 2.0.7 "CNCc1ccc2c(c1)N(C(C2NC(=O)C(=O)Nc3ccc(c(c3)F)Cl)CNC(=N)N)C(=O)OCc4c(c(c(c(c4F)F)F)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 
Y1T "SYSTEMATIC NAME" ACDLabs              12.01 "(pentafluorophenyl)methyl (2R,3S)-2-(carbamimidamidomethyl)-3-[2-(4-chloro-3-fluoroanilino)(oxo)acetamido]-6-[(methylamino)methyl]-2,3-dihydro-1H-indole-1-carboxylate"                                                  
Y1T "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[2,3,4,5,6-pentakis(fluoranyl)phenyl]methyl (2~{R},3~{S})-2-(carbamimidamidomethyl)-3-[[2-[(4-chloranyl-3-fluoranyl-phenyl)amino]-2-oxidanylidene-ethanoyl]amino]-6-(methylaminomethyl)-2,3-dihydroindole-1-carboxylate" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
Y1T "Create component" 2022-12-27 RCSB 
Y1T "Initial release"  2023-04-05 RCSB 
# 
