data_6A8
# 
_chem_comp.id                                    6A8 
_chem_comp.name                                  "((R)-1-((S)-3-(4-(aminomethyl)phenyl)-2-benzamidopropaneamido)-4-guanidinobutyl)boronic acid, cyclic double ester with glycerol" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C25 H35 B N6 O5" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2016-02-25 
_chem_comp.pdbx_modified_date                    2024-09-27 
_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                        510.394 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     6A8 
_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        5IDK 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  EBI 
_chem_comp.pdbx_pcm                              Y 
# 
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.pdbx_backbone_atom_flag 
_chem_comp_atom.pdbx_n_terminal_atom_flag 
_chem_comp_atom.pdbx_c_terminal_atom_flag 
_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 
6A8 O24 O1  O 0 1 N N N N N N -1.086 10.724 24.909 2.020   -1.822 -0.581 O24 6A8 1  
6A8 C22 C1  C 0 1 N N N N N N -1.772 11.537 25.539 2.581   -1.556 0.464  C22 6A8 2  
6A8 C25 C2  C 0 1 Y N N N N N -2.897 12.295 24.881 3.526   -2.523 1.063  C25 6A8 3  
6A8 C30 C3  C 0 1 Y N N N N N -4.099 12.543 25.580 3.777   -3.741 0.430  C30 6A8 4  
6A8 C29 C4  C 0 1 Y N N N N N -5.130 13.300 24.979 4.661   -4.638 0.994  C29 6A8 5  
6A8 C28 C5  C 0 1 Y N N N N N -4.923 13.716 23.683 5.297   -4.333 2.184  C28 6A8 6  
6A8 C27 C6  C 0 1 Y N N N N N -3.792 13.385 22.971 5.052   -3.127 2.816  C27 6A8 7  
6A8 C26 C7  C 0 1 Y N N N N N -2.775 12.678 23.571 4.176   -2.218 2.260  C26 6A8 8  
6A8 N21 N1  N 0 1 N N N N N N -1.431 11.790 26.785 2.345   -0.378 1.075  N21 6A8 9  
6A8 C18 C8  C 0 1 N N S N N N -0.463 11.177 27.607 1.412   0.582  0.479  C18 6A8 10 
6A8 C20 C9  C 0 1 N N N N N N 0.438  12.217 28.286 1.910   0.979  -0.913 C20 6A8 11 
6A8 C31 C10 C 0 1 Y N N N N N 1.448  12.922 27.429 3.217   1.719  -0.786 C31 6A8 12 
6A8 C36 C11 C 0 1 Y N N N N N 1.655  12.704 26.070 3.222   3.093  -0.639 C36 6A8 13 
6A8 C35 C12 C 0 1 Y N N N N N 2.616  13.360 25.314 4.420   3.771  -0.518 C35 6A8 14 
6A8 C34 C13 C 0 1 Y N N N N N 3.496  14.284 25.977 5.614   3.075  -0.544 C34 6A8 15 
6A8 C37 C14 C 0 1 N N N N N N 4.638  14.919 25.148 6.921   3.813  -0.412 C37 6A8 16 
6A8 N38 N2  N 0 1 N N N N N N 4.457  16.410 25.063 7.289   3.907  1.007  N38 6A8 17 
6A8 C33 C15 C 0 1 Y N N N N N 3.249  14.540 27.341 5.609   1.700  -0.690 C33 6A8 18 
6A8 C32 C16 C 0 1 Y N N N N N 2.290  13.857 28.032 4.410   1.022  -0.812 C32 6A8 19 
6A8 C17 C17 C 0 1 N N N N N N -1.148 10.370 28.699 0.048   -0.048 0.363  C17 6A8 20 
6A8 O19 O2  O 0 1 N N N N N N -2.190 10.733 29.270 -0.066  -1.255 0.389  O19 6A8 21 
6A8 N2  N3  N 0 1 N N N N N N -0.500 9.267  29.100 -1.044  0.730  0.232  N2  6A8 22 
6A8 C1  C18 C 0 1 N N R N N N -0.712 8.598  30.409 -2.371  0.117  0.119  C1  6A8 23 
6A8 B4  B1  B 0 1 N N N N N N 0.730  8.628  31.132 -2.862  0.203  -1.369 B4  6A8 24 
6A8 O1  O3  O 0 1 N N N N N N 1.475  9.915  31.146 -2.224  -0.362 -2.515 O1  6A8 25 
6A8 C4  C19 C 0 1 N N S N N N 1.937  10.308 32.405 -3.243  -0.575 -3.508 C4  6A8 26 
6A8 C2  C20 C 0 1 N N N N N N 1.754  9.091  33.337 -4.541  -0.038 -2.864 C2  6A8 27 
6A8 O3  O4  O 0 1 N N N N N N 0.872  8.171  32.516 -4.045  0.859  -1.846 O3  6A8 28 
6A8 C3  C21 C 0 1 N N N N N N -1.258 7.181  30.010 -3.354  0.861  1.025  C3  6A8 29 
6A8 C11 C22 C 0 1 N N N N N N -2.577 7.171  29.128 -4.739  0.221  0.908  C11 6A8 30 
6A8 C12 C23 C 0 1 N N N N N N -3.714 7.722  29.990 -5.723  0.965  1.814  C12 6A8 31 
6A8 N13 N4  N 0 1 N N N N N N -4.996 7.636  29.189 -7.049  0.352  1.702  N13 6A8 32 
6A8 C14 C24 C 0 1 N N N N N N -5.606 8.575  28.477 -8.102  0.855  2.429  C14 6A8 33 
6A8 N15 N5  N 0 1 N N N N N N -5.019 9.813  28.461 -9.346  0.280  2.324  N15 6A8 34 
6A8 N16 N6  N 0 1 N N N N N N -6.773 8.413  27.997 -7.920  1.876  3.218  N16 6A8 35 
6A8 C6  C25 C 0 1 N N N N N N 0.878  11.383 32.707 -3.381  -2.067 -3.819 C6  6A8 36 
6A8 O2  O5  O 0 1 N N N N N N 1.170  12.513 31.854 -2.188  -2.533 -4.452 O2  6A8 37 
6A8 H1  H1  H 0 1 N N N N N N -4.231 12.152 26.578 3.281   -3.981 -0.499 H1  6A8 38 
6A8 H2  H2  H 0 1 N N N N N N -6.038 13.541 25.512 4.856   -5.582 0.505  H2  6A8 39 
6A8 H3  H3  H 0 1 N N N N N N -5.677 14.325 23.207 5.988   -5.039 2.621  H3  6A8 40 
6A8 H4  H4  H 0 1 N N N N N N -3.702 13.682 21.936 5.556   -2.892 3.743  H4  6A8 41 
6A8 H5  H5  H 0 1 N N N N N N -1.886 12.426 23.012 3.986   -1.277 2.754  H5  6A8 42 
6A8 H6  H6  H 0 1 N N N N N N -1.939 12.535 27.217 2.792   -0.166 1.909  H6  6A8 43 
6A8 H7  H7  H 0 1 N N N N N N 0.169  10.501 27.012 1.351   1.468  1.110  H7  6A8 44 
6A8 H8  H8  H 0 1 N N N N N N 0.988  11.703 29.089 2.056   0.084  -1.516 H8  6A8 45 
6A8 H9  H9  H 0 1 N N N N N N -0.217 12.985 28.723 1.173   1.624  -1.391 H9  6A8 46 
6A8 H10 H10 H 0 1 N N N N N N 1.028  11.979 25.573 2.289   3.638  -0.619 H10 6A8 47 
6A8 H11 H11 H 0 1 N N N N N N 2.701  13.181 24.252 4.424   4.845  -0.403 H11 6A8 48 
6A8 H12 H12 H 0 1 N N N N N N 4.629  14.494 24.133 7.698   3.276  -0.954 H12 6A8 49 
6A8 H13 H13 H 0 1 N N N N N N 5.602  14.698 25.630 6.815   4.816  -0.826 H13 6A8 50 
6A8 H14 H14 H 0 1 N N N N N N 5.201  16.806 24.525 8.163   4.398  1.122  H14 6A8 51 
6A8 H15 H15 H 0 1 N N N N N N 3.582  16.615 24.624 6.555   4.344  1.544  H15 6A8 52 
6A8 H17 H17 H 0 1 N N N N N N 3.831  15.293 27.851 6.542   1.156  -0.709 H17 6A8 53 
6A8 H18 H18 H 0 1 N N N N N N 2.178  14.048 29.089 4.406   -0.052 -0.923 H18 6A8 54 
6A8 H19 H19 H 0 1 N N N N N N 0.171  8.868  28.476 -0.953  1.695  0.212  H19 6A8 55 
6A8 H20 H20 H 0 1 N N N N N N -1.450 9.134  31.024 -2.315  -0.928 0.424  H20 6A8 56 
6A8 H21 H21 H 0 1 N N N N N N 2.963  10.705 32.424 -3.010  -0.019 -4.416 H21 6A8 57 
6A8 H22 H22 H 0 1 N N N N N N 2.720  8.616  33.563 -5.142  0.501  -3.598 H22 6A8 58 
6A8 H23 H23 H 0 1 N N N N N N 1.259  9.381  34.276 -5.115  -0.849 -2.418 H23 6A8 59 
6A8 H24 H24 H 0 1 N N N N N N -1.468 6.627  30.937 -3.013  0.801  2.059  H24 6A8 60 
6A8 H25 H25 H 0 1 N N N N N N -0.470 6.663  29.444 -3.410  1.906  0.721  H25 6A8 61 
6A8 H26 H26 H 0 1 N N N N N N -2.810 6.143  28.813 -5.081  0.281  -0.125 H26 6A8 62 
6A8 H27 H27 H 0 1 N N N N N N -2.439 7.805  28.240 -4.684  -0.824 1.213  H27 6A8 63 
6A8 H28 H28 H 0 1 N N N N N N -3.808 7.125  30.909 -5.381  0.905  2.847  H28 6A8 64 
6A8 H29 H29 H 0 1 N N N N N N -3.508 8.770  30.253 -5.778  2.010  1.509  H29 6A8 65 
6A8 H30 H30 H 0 1 N N N N N N -5.448 6.744  29.198 -7.184  -0.408 1.114  H30 6A8 66 
6A8 H31 H31 H 0 1 N N N N N N -4.173 9.972  28.970 -9.481  -0.480 1.736  H31 6A8 67 
6A8 H32 H32 H 0 1 N N N N N N -5.437 10.558 27.940 -10.089 0.634  2.837  H32 6A8 68 
6A8 H33 H33 H 0 1 N N N N N N -7.150 7.515  28.223 -7.042  2.282  3.293  H33 6A8 69 
6A8 H34 H34 H 0 1 N N N N N N 0.934  11.683 33.764 -3.539  -2.618 -2.891 H34 6A8 70 
6A8 H35 H35 H 0 1 N N N N N N -0.128 10.995 32.489 -4.230  -2.223 -4.484 H35 6A8 71 
6A8 H36 H36 H 0 1 N N N N N N 0.535  13.202 32.011 -2.205  -3.473 -4.678 H36 6A8 72 
# 
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 
6A8 C27 C26 DOUB Y N 1  
6A8 C27 C28 SING Y N 2  
6A8 C26 C25 SING Y N 3  
6A8 C28 C29 DOUB Y N 4  
6A8 C25 C22 SING N N 5  
6A8 C25 C30 DOUB Y N 6  
6A8 O24 C22 DOUB N N 7  
6A8 C29 C30 SING Y N 8  
6A8 N38 C37 SING N N 9  
6A8 C37 C34 SING N N 10 
6A8 C35 C34 DOUB Y N 11 
6A8 C35 C36 SING Y N 12 
6A8 C22 N21 SING N N 13 
6A8 C34 C33 SING Y N 14 
6A8 C36 C31 DOUB Y N 15 
6A8 N21 C18 SING N N 16 
6A8 C33 C32 DOUB Y N 17 
6A8 C31 C32 SING Y N 18 
6A8 C31 C20 SING N N 19 
6A8 C18 C20 SING N N 20 
6A8 C18 C17 SING N N 21 
6A8 N16 C14 DOUB N N 22 
6A8 N15 C14 SING N N 23 
6A8 C14 N13 SING N N 24 
6A8 C17 N2  SING N N 25 
6A8 C17 O19 DOUB N N 26 
6A8 N2  C1  SING N N 27 
6A8 C11 C12 SING N N 28 
6A8 C11 C3  SING N N 29 
6A8 N13 C12 SING N N 30 
6A8 C3  C1  SING N N 31 
6A8 C1  B4  SING N N 32 
6A8 B4  O1  SING N N 33 
6A8 B4  O3  SING N N 34 
6A8 O1  C4  SING N N 35 
6A8 O2  C6  SING N N 36 
6A8 C4  C6  SING N N 37 
6A8 C4  C2  SING N N 38 
6A8 O3  C2  SING N N 39 
6A8 C30 H1  SING N N 40 
6A8 C29 H2  SING N N 41 
6A8 C28 H3  SING N N 42 
6A8 C27 H4  SING N N 43 
6A8 C26 H5  SING N N 44 
6A8 N21 H6  SING N N 45 
6A8 C18 H7  SING N N 46 
6A8 C20 H8  SING N N 47 
6A8 C20 H9  SING N N 48 
6A8 C36 H10 SING N N 49 
6A8 C35 H11 SING N N 50 
6A8 C37 H12 SING N N 51 
6A8 C37 H13 SING N N 52 
6A8 N38 H14 SING N N 53 
6A8 N38 H15 SING N N 54 
6A8 C33 H17 SING N N 55 
6A8 C32 H18 SING N N 56 
6A8 N2  H19 SING N N 57 
6A8 C1  H20 SING N N 58 
6A8 C4  H21 SING N N 59 
6A8 C2  H22 SING N N 60 
6A8 C2  H23 SING N N 61 
6A8 C3  H24 SING N N 62 
6A8 C3  H25 SING N N 63 
6A8 C11 H26 SING N N 64 
6A8 C11 H27 SING N N 65 
6A8 C12 H28 SING N N 66 
6A8 C12 H29 SING N N 67 
6A8 N13 H30 SING N N 68 
6A8 N15 H31 SING N N 69 
6A8 N15 H32 SING N N 70 
6A8 N16 H33 SING N N 71 
6A8 C6  H34 SING N N 72 
6A8 C6  H35 SING N N 73 
6A8 O2  H36 SING N N 74 
# 
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 
6A8 SMILES           ACDLabs              12.01 "O=C(NC(Cc1ccc(cc1)CN)C(NC(B2OC(CO)CO2)CCCN/C(N)=N)=O)c3ccccc3"                                                                                                                                                                  
6A8 InChI            InChI                1.03  "InChI=1S/C25H35BN6O5/c27-14-18-10-8-17(9-11-18)13-21(31-23(34)19-5-2-1-3-6-19)24(35)32-22(7-4-12-30-25(28)29)26-36-16-20(15-33)37-26/h1-3,5-6,8-11,20-22,33H,4,7,12-16,27H2,(H,31,34)(H,32,35)(H4,28,29,30)/t20-,21-,22-/m0/s1" 
6A8 InChIKey         InChI                1.03  UBPZINWFQYNJIA-FKBYEOEOSA-N                                                                                                                                                                                                      
6A8 SMILES_CANONICAL CACTVS               3.385 "NCc1ccc(C[C@H](NC(=O)c2ccccc2)C(=O)N[C@@H](CCCNC(N)=N)B3OC[C@H](CO)O3)cc1"                                                                                                                                                      
6A8 SMILES           CACTVS               3.385 "NCc1ccc(C[CH](NC(=O)c2ccccc2)C(=O)N[CH](CCCNC(N)=N)B3OC[CH](CO)O3)cc1"                                                                                                                                                          
6A8 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.4 "[H]/N=C(\N)/NCCC[C@@H](B1OC[C@@H](O1)CO)NC(=O)[C@H](Cc2ccc(cc2)CN)NC(=O)c3ccccc3"                                                                                                                                               
6A8 SMILES           "OpenEye OEToolkits" 2.0.4 "B1(OCC(O1)CO)C(CCCNC(=N)N)NC(=O)C(Cc2ccc(cc2)CN)NC(=O)c3ccccc3"                                                                                                                                                                 
# 
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 
6A8 "SYSTEMATIC NAME" ACDLabs              12.01 "4-(aminomethyl)-Nalpha-(benzenecarbonyl)-N-{(1R)-4-carbamimidamido-1-[(4S)-4-(hydroxymethyl)-1,3,2-dioxaborolan-2-yl]butyl}-L-phenylalaninamide"                               
6A8 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.4 "~{N}-[(2~{S})-3-[4-(aminomethyl)phenyl]-1-[[(1~{R})-4-carbamimidamido-1-[(4~{S})-4-(hydroxymethyl)-1,3,2-dioxaborolan-2-yl]butyl]amino]-1-oxidanylidene-propan-2-yl]benzamide" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
6A8 "Create component" 2016-02-25 EBI  
6A8 "Initial release"  2016-12-14 RCSB 
6A8 "Modify PCM"       2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            6A8 
_pdbx_chem_comp_pcm.modified_residue_id                SER 
_pdbx_chem_comp_pcm.type                               None 
_pdbx_chem_comp_pcm.category                           "Covalent chemical modification" 
_pdbx_chem_comp_pcm.position                           "Amino-acid side chain" 
_pdbx_chem_comp_pcm.polypeptide_position               "Any position" 
_pdbx_chem_comp_pcm.comp_id_linking_atom               B4 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom   OG 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession     ? 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession      ? 
# 
