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 ? #