data_A1MDH # _chem_comp.id A1MDH _chem_comp.name "~{N}-[3-[4-[[5-[4-[3-[[3,4-bis(oxidanyl)phenyl]carbonylamino]propylamino]butylamino]-5-oxidanyl-3-oxidanylidene-pent-4-enoyl]amino]butylamino]propyl]-3,4-bis(oxidanyl)benzamide" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C33 H48 N6 O9" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2026-01-09 _chem_comp.pdbx_modified_date 2026-04-17 _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 672.769 _chem_comp.one_letter_code ? _chem_comp.three_letter_code A1MDH _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 21ZF _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ _chem_comp.pdbx_pcm ? # 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_n_terminal_atom_flag _chem_comp_atom.pdbx_backbone_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 A1MDH CAD C1 C 0 1 Y N N N N N 13.836 -17.693 12.245 -18.390 0.271 0.244 CAD A1MDH 1 A1MDH CAE C2 C 0 1 Y N N N N N 13.950 -16.330 12.301 -19.498 -0.549 0.155 CAE A1MDH 2 A1MDH OAH O1 O 0 1 N N N N N N 14.480 -15.708 13.409 -20.746 -0.022 0.277 OAH A1MDH 3 A1MDH CAF C3 C 0 1 Y N N N N N 13.567 -15.537 11.271 -19.337 -1.917 -0.060 CAF A1MDH 4 A1MDH OAG O2 O 0 1 N N N N N N 13.727 -14.231 11.433 -20.427 -2.722 -0.148 OAG A1MDH 5 A1MDH CAA C4 C 0 1 Y N N N N N 13.022 -16.107 10.108 -18.065 -2.458 -0.186 CAA A1MDH 6 A1MDH CAB C5 C 0 1 Y N N N N N 12.911 -17.495 10.050 -16.955 -1.645 -0.097 CAB A1MDH 7 A1MDH CAC C6 C 0 1 Y N N N N N 13.303 -18.292 11.098 -17.110 -0.273 0.112 CAC A1MDH 8 A1MDH CAI C7 C 0 1 N N N N N N 13.147 -19.757 10.990 -15.922 0.599 0.206 CAI A1MDH 9 A1MDH OAK O3 O 0 1 N N N N N N 13.051 -20.317 9.878 -16.058 1.793 0.389 OAK A1MDH 10 A1MDH NAJ N1 N 0 1 N N N N N N 13.119 -20.497 12.187 -14.688 0.071 0.090 NAJ A1MDH 11 A1MDH CAL C8 C 0 1 N N N N N N 12.973 -21.965 12.156 -13.509 0.937 0.184 CAL A1MDH 12 A1MDH CAM C9 C 0 1 N N N N N N 14.057 -22.677 12.961 -12.243 0.093 0.020 CAM A1MDH 13 A1MDH CAN C10 C 0 1 N N N N N N 14.935 -21.734 13.788 -11.012 0.997 0.117 CAN A1MDH 14 A1MDH NAO N2 N 0 1 N N N N N N 16.387 -21.980 13.748 -9.797 0.188 -0.040 NAO A1MDH 15 A1MDH CAP C11 C 0 1 N N N N N N 17.136 -21.816 15.011 -8.592 1.024 0.048 CAP A1MDH 16 A1MDH CAQ C12 C 0 1 N N N N N N 18.627 -22.278 14.990 -7.350 0.147 -0.120 CAQ A1MDH 17 A1MDH CAR C13 C 0 1 N N N N N N 19.591 -21.087 15.105 -6.095 1.019 -0.028 CAR A1MDH 18 A1MDH CAS C14 C 0 1 N N N N N N 19.535 -20.319 16.446 -4.852 0.142 -0.196 CAS A1MDH 19 A1MDH NAT N3 N 0 1 N N N N N N 18.548 -19.185 16.485 -3.651 0.976 -0.108 NAT A1MDH 20 A1MDH CAU C15 C 0 1 N N N N N N 18.390 -18.271 17.552 -2.415 0.408 -0.230 CAU A1MDH 21 A1MDH OAX O4 O 0 1 N N N N N N 19.167 -18.344 18.729 -2.300 -0.920 -0.432 OAX A1MDH 22 A1MDH CAV C16 C 0 1 N N N N N N 17.525 -17.392 17.472 -1.284 1.193 -0.147 CAV A1MDH 23 A1MDH CAW C17 C 0 1 N N N N N N 18.143 -16.022 17.697 -0.026 0.599 -0.106 CAW A1MDH 24 A1MDH OAY O5 O 0 1 N N N N N N 17.925 -15.432 18.752 0.073 -0.611 -0.039 OAY A1MDH 25 A1MDH CAZ C18 C 0 1 N N N N N N 18.966 -15.427 16.582 1.213 1.456 -0.145 CAZ A1MDH 26 A1MDH CBA C19 C 0 1 N N N N N N 19.937 -14.295 16.900 2.435 0.575 -0.089 CBA A1MDH 27 A1MDH OBD O6 O 0 1 N N N N N N 20.440 -14.119 18.004 2.311 -0.630 -0.023 OBD A1MDH 28 A1MDH NBB N4 N 0 1 N N N N N N 20.227 -13.475 15.792 3.665 1.126 -0.111 NBB A1MDH 29 A1MDH CBC C20 C 0 1 N N N N N N 21.159 -12.324 15.873 4.852 0.270 -0.056 CBC A1MDH 30 A1MDH CBE C21 C 0 1 N N N N N N 22.358 -12.482 14.889 6.110 1.140 -0.096 CBE A1MDH 31 A1MDH CBF C22 C 0 1 N N N N N N 22.972 -11.155 14.444 7.350 0.245 -0.038 CBF A1MDH 32 A1MDH CBG C23 C 0 1 N N N N N N 21.976 -9.979 14.462 8.608 1.115 -0.078 CBG A1MDH 33 A1MDH NBH N5 N 0 1 N N N N N N 21.881 -9.162 13.240 9.799 0.257 -0.023 NBH A1MDH 34 A1MDH CBI C24 C 0 1 N N N N N N 21.142 -7.872 13.349 11.029 1.059 -0.059 CBI A1MDH 35 A1MDH CBJ C25 C 0 1 N N N N N N 21.231 -7.022 12.084 12.245 0.132 -0.000 CBJ A1MDH 36 A1MDH CBK C26 C 0 1 N N N N N N 20.563 -7.587 10.813 13.526 0.968 -0.038 CBK A1MDH 37 A1MDH NBL N6 N 0 1 N N N N N N 19.261 -8.245 11.177 14.690 0.080 0.019 NBL A1MDH 38 A1MDH CBM C27 C 0 1 N N N N N N 19.152 -9.660 11.440 15.934 0.598 -0.002 CBM A1MDH 39 A1MDH OBO O7 O 0 1 N N N N N N 20.131 -10.373 11.440 16.090 1.802 -0.067 OBO A1MDH 40 A1MDH CBN C28 C 0 1 Y N N N N N 17.828 -10.180 11.780 17.107 -0.296 0.056 CBN A1MDH 41 A1MDH CBT C29 C 0 1 Y N N N N N 17.689 -11.505 12.164 18.398 0.240 0.034 CBT A1MDH 42 A1MDH CBS C30 C 0 1 Y N N N N N 16.430 -11.974 12.466 19.492 -0.601 0.088 CBS A1MDH 43 A1MDH OBU O8 O 0 1 N N N N N N 16.214 -13.268 12.834 20.749 -0.083 0.068 OBU A1MDH 44 A1MDH CBR C31 C 0 1 Y N N N N N 15.321 -11.173 12.438 19.307 -1.981 0.164 CBR A1MDH 45 A1MDH OBV O9 O 0 1 N N N N N N 14.132 -11.771 12.788 20.384 -2.807 0.217 OBV A1MDH 46 A1MDH CBQ C32 C 0 1 Y N N N N N 15.435 -9.856 12.030 18.025 -2.513 0.185 CBQ A1MDH 47 A1MDH CBP C33 C 0 1 Y N N N N N 16.694 -9.343 11.699 16.929 -1.679 0.137 CBP A1MDH 48 A1MDH H1 H1 H 0 1 N N N N N N 14.155 -18.301 13.079 -18.513 1.331 0.411 H1 A1MDH 49 A1MDH H2 H2 H 0 1 N N N N N N 14.710 -16.361 14.060 -21.136 0.264 -0.560 H2 A1MDH 50 A1MDH H3 H3 H 0 1 N N N N N N 14.110 -14.062 12.286 -20.772 -2.821 -1.046 H3 A1MDH 51 A1MDH H4 H4 H 0 1 N N N N N N 12.699 -15.488 9.284 -17.944 -3.518 -0.352 H4 A1MDH 52 A1MDH H5 H5 H 0 1 N N N N N N 12.507 -17.955 9.160 -15.967 -2.069 -0.195 H5 A1MDH 53 A1MDH H6 H6 H 0 1 N N N N N N 13.199 -20.024 13.065 -14.580 -0.882 -0.055 H6 A1MDH 54 A1MDH H7 H7 H 0 1 N N N N N N 11.991 -22.231 12.574 -13.549 1.690 -0.603 H7 A1MDH 55 A1MDH H8 H8 H 0 1 N N N N N N 13.030 -22.303 11.111 -13.495 1.427 1.157 H8 A1MDH 56 A1MDH H9 H9 H 0 1 N N N N N N 13.570 -23.387 13.646 -12.204 -0.660 0.806 H9 A1MDH 57 A1MDH H10 H10 H 0 1 N N N N N N 14.703 -23.227 12.261 -12.257 -0.398 -0.953 H10 A1MDH 58 A1MDH H11 H11 H 0 1 N N N N N N 14.760 -20.711 13.425 -11.052 1.751 -0.669 H11 A1MDH 59 A1MDH H12 H12 H 0 1 N N N N N N 14.612 -21.811 14.837 -10.998 1.488 1.090 H12 A1MDH 60 A1MDH H13 H13 H 0 1 N N N N N N 17.119 -20.749 15.276 -8.615 1.778 -0.739 H13 A1MDH 61 A1MDH H14 H14 H 0 1 N N N N N N 18.801 -22.961 15.835 -7.327 -0.606 0.667 H14 A1MDH 62 A1MDH H15 H15 H 0 1 N N N N N N 18.824 -22.806 14.045 -7.380 -0.344 -1.093 H15 A1MDH 63 A1MDH H16 H16 H 0 1 N N N N N N 20.615 -21.465 14.972 -6.117 1.772 -0.815 H16 A1MDH 64 A1MDH H17 H17 H 0 1 N N N N N N 19.354 -20.379 14.297 -6.064 1.510 0.945 H17 A1MDH 65 A1MDH H18 H18 H 0 1 N N N N N N 19.266 -21.033 17.238 -4.830 -0.612 0.591 H18 A1MDH 66 A1MDH H19 H19 H 0 1 N N N N N N 20.536 -19.908 16.647 -4.883 -0.349 -1.169 H19 A1MDH 67 A1MDH H20 H20 H 0 1 N N N N N N 18.759 -18.623 15.685 -3.734 1.932 0.037 H20 A1MDH 68 A1MDH H21 H21 H 0 1 N N N N N N 16.479 -17.572 17.271 -1.375 2.269 -0.114 H21 A1MDH 69 A1MDH H23 H23 H 0 1 N N N N N N 18.260 -15.044 15.830 1.225 2.035 -1.069 H23 A1MDH 70 A1MDH H24 H24 H 0 1 N N N N N N 19.558 -16.246 16.146 1.214 2.133 0.709 H24 A1MDH 71 A1MDH H25 H25 H 0 1 N N N N N N 19.787 -13.677 14.917 3.763 2.090 -0.164 H25 A1MDH 72 A1MDH H26 H26 H 0 1 N N N N N N 21.548 -12.252 16.900 4.840 -0.309 0.867 H26 A1MDH 73 A1MDH H27 H27 H 0 1 N N N N N N 20.611 -11.404 15.622 4.851 -0.407 -0.910 H27 A1MDH 74 A1MDH H28 H28 H 0 1 N N N N N N 22.005 -13.017 13.995 6.122 1.719 -1.019 H28 A1MDH 75 A1MDH H29 H29 H 0 1 N N N N N N 23.139 -13.075 15.387 6.111 1.817 0.758 H29 A1MDH 76 A1MDH H30 H30 H 0 1 N N N N N N 23.352 -11.274 13.418 7.338 -0.334 0.885 H30 A1MDH 77 A1MDH H31 H31 H 0 1 N N N N N N 23.807 -10.914 15.119 7.350 -0.432 -0.892 H31 A1MDH 78 A1MDH H32 H32 H 0 1 N N N N N N 22.267 -9.311 15.286 8.621 1.694 -1.001 H32 A1MDH 79 A1MDH H33 H33 H 0 1 N N N N N N 21.563 -7.297 14.187 11.058 1.638 -0.982 H33 A1MDH 80 A1MDH H34 H34 H 0 1 N N N N N N 20.083 -8.091 13.550 11.046 1.736 0.795 H34 A1MDH 81 A1MDH H35 H35 H 0 1 N N N N N N 22.297 -6.871 11.860 12.216 -0.447 0.923 H35 A1MDH 82 A1MDH H36 H36 H 0 1 N N N N N N 20.761 -6.052 12.302 12.227 -0.545 -0.854 H36 A1MDH 83 A1MDH H37 H37 H 0 1 N N N N N N 21.230 -8.328 10.347 13.555 1.547 -0.961 H37 A1MDH 84 A1MDH H38 H38 H 0 1 N N N N N N 20.373 -6.768 10.104 13.543 1.645 0.816 H38 A1MDH 85 A1MDH H39 H39 H 0 1 N N N N N N 18.438 -7.680 11.239 14.565 -0.880 0.071 H39 A1MDH 86 A1MDH H40 H40 H 0 1 N N N N N N 18.549 -12.155 12.225 18.539 1.309 -0.025 H40 A1MDH 87 A1MDH H41 H41 H 0 1 N N N N N N 15.288 -13.400 13.001 21.107 0.116 0.945 H41 A1MDH 88 A1MDH H42 H42 H 0 1 N N N N N N 14.292 -12.675 13.033 20.690 -2.997 1.115 H42 A1MDH 89 A1MDH H43 H43 H 0 1 N N N N N N 14.558 -9.228 11.967 17.887 -3.582 0.244 H43 A1MDH 90 A1MDH H44 H44 H 0 1 N N N N N N 16.797 -8.315 11.384 15.933 -2.095 0.157 H44 A1MDH 91 A1MDH H45 H45 H 0 1 N N N N N N 16.524 -22.921 13.437 -9.769 -0.559 0.638 H45 A1MDH 92 A1MDH H46 H46 H 0 1 N N N N N N 16.616 -22.395 15.788 -8.562 1.515 1.021 H46 A1MDH 93 A1MDH H47 H47 H 0 1 N N N N N N 18.912 -17.646 19.321 -1.413 -1.262 -0.609 H47 A1MDH 94 A1MDH H22 H22 H 0 1 N N N N N N 20.977 -10.394 14.662 8.609 1.793 0.776 H22 A1MDH 95 A1MDH H48 H48 H 0 1 N N N N N N 21.425 -9.714 12.542 9.789 -0.424 -0.768 H48 A1MDH 96 # 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 A1MDH OAK CAI DOUB N N 1 A1MDH CAB CAA DOUB Y N 2 A1MDH CAB CAC SING Y N 3 A1MDH CAA CAF SING Y N 4 A1MDH CBK NBL SING N N 5 A1MDH CBK CBJ SING N N 6 A1MDH CAI CAC SING N N 7 A1MDH CAI NAJ SING N N 8 A1MDH CAC CAD DOUB Y N 9 A1MDH NBL CBM SING N N 10 A1MDH CAF OAG SING N N 11 A1MDH CAF CAE DOUB Y N 12 A1MDH OBO CBM DOUB N N 13 A1MDH CBM CBN SING N N 14 A1MDH CBP CBN DOUB Y N 15 A1MDH CBP CBQ SING Y N 16 A1MDH CBN CBT SING Y N 17 A1MDH CBQ CBR DOUB Y N 18 A1MDH CBJ CBI SING N N 19 A1MDH CAL NAJ SING N N 20 A1MDH CAL CAM SING N N 21 A1MDH CBT CBS DOUB Y N 22 A1MDH CAD CAE SING Y N 23 A1MDH CAE OAH SING N N 24 A1MDH CBR CBS SING Y N 25 A1MDH CBR OBV SING N N 26 A1MDH CBS OBU SING N N 27 A1MDH CAM CAN SING N N 28 A1MDH NBH CBI SING N N 29 A1MDH NBH CBG SING N N 30 A1MDH NAO CAN SING N N 31 A1MDH NAO CAP SING N N 32 A1MDH CBF CBG SING N N 33 A1MDH CBF CBE SING N N 34 A1MDH CBE CBC SING N N 35 A1MDH CAQ CAP SING N N 36 A1MDH CAQ CAR SING N N 37 A1MDH CAR CAS SING N N 38 A1MDH NBB CBC SING N N 39 A1MDH NBB CBA SING N N 40 A1MDH CAS NAT SING N N 41 A1MDH NAT CAU SING N N 42 A1MDH CAZ CBA SING N N 43 A1MDH CAZ CAW SING N N 44 A1MDH CBA OBD DOUB N N 45 A1MDH CAV CAU DOUB N Z 46 A1MDH CAV CAW SING N N 47 A1MDH CAU OAX SING N N 48 A1MDH CAW OAY DOUB N N 49 A1MDH CAD H1 SING N N 50 A1MDH OAH H2 SING N N 51 A1MDH OAG H3 SING N N 52 A1MDH CAA H4 SING N N 53 A1MDH CAB H5 SING N N 54 A1MDH NAJ H6 SING N N 55 A1MDH CAL H7 SING N N 56 A1MDH CAL H8 SING N N 57 A1MDH CAM H9 SING N N 58 A1MDH CAM H10 SING N N 59 A1MDH CAN H11 SING N N 60 A1MDH CAN H12 SING N N 61 A1MDH CAP H13 SING N N 62 A1MDH CAQ H14 SING N N 63 A1MDH CAQ H15 SING N N 64 A1MDH CAR H16 SING N N 65 A1MDH CAR H17 SING N N 66 A1MDH CAS H18 SING N N 67 A1MDH CAS H19 SING N N 68 A1MDH NAT H20 SING N N 69 A1MDH CAV H21 SING N N 70 A1MDH CAZ H23 SING N N 71 A1MDH CAZ H24 SING N N 72 A1MDH NBB H25 SING N N 73 A1MDH CBC H26 SING N N 74 A1MDH CBC H27 SING N N 75 A1MDH CBE H28 SING N N 76 A1MDH CBE H29 SING N N 77 A1MDH CBF H30 SING N N 78 A1MDH CBF H31 SING N N 79 A1MDH CBG H32 SING N N 80 A1MDH CBI H33 SING N N 81 A1MDH CBI H34 SING N N 82 A1MDH CBJ H35 SING N N 83 A1MDH CBJ H36 SING N N 84 A1MDH CBK H37 SING N N 85 A1MDH CBK H38 SING N N 86 A1MDH NBL H39 SING N N 87 A1MDH CBT H40 SING N N 88 A1MDH OBU H41 SING N N 89 A1MDH OBV H42 SING N N 90 A1MDH CBQ H43 SING N N 91 A1MDH CBP H44 SING N N 92 A1MDH NAO H45 SING N N 93 A1MDH CAP H46 SING N N 94 A1MDH OAX H47 SING N N 95 A1MDH CBG H22 SING N N 96 A1MDH NBH H48 SING N N 97 # 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 A1MDH InChI InChI 1.06 "InChI=1S/C33H48N6O9/c40-25(21-30(45)36-15-3-1-11-34-13-5-17-38-32(47)23-7-9-26(41)28(43)19-23)22-31(46)37-16-4-2-12-35-14-6-18-39-33(48)24-8-10-27(42)29(44)20-24/h7-10,19-21,34-36,41-45H,1-6,11-18,22H2,(H,37,46)(H,38,47)(H,39,48)" A1MDH InChIKey InChI 1.06 WFAHMCMMJYQJDB-UHFFFAOYSA-N A1MDH SMILES_CANONICAL CACTVS 3.385 "OC(\NCCCCNCCCNC(=O)c1ccc(O)c(O)c1)=C/C(=O)CC(=O)NCCCCNCCCNC(=O)c2ccc(O)c(O)c2" A1MDH SMILES CACTVS 3.385 "OC(NCCCCNCCCNC(=O)c1ccc(O)c(O)c1)=CC(=O)CC(=O)NCCCCNCCCNC(=O)c2ccc(O)c(O)c2" A1MDH SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1cc(c(cc1C(=O)NCCCNCCCCNC(=O)CC(=O)C=C(NCCCCNCCCNC(=O)c2ccc(c(c2)O)O)O)O)O" A1MDH SMILES "OpenEye OEToolkits" 2.0.7 "c1cc(c(cc1C(=O)NCCCNCCCCNC(=O)CC(=O)C=C(NCCCCNCCCNC(=O)c2ccc(c(c2)O)O)O)O)O" # _pdbx_chem_comp_identifier.comp_id A1MDH _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.7 _pdbx_chem_comp_identifier.identifier "~{N}-[3-[4-[[5-[4-[3-[[3,4-bis(oxidanyl)phenyl]carbonylamino]propylamino]butylamino]-5-oxidanyl-3-oxidanylidene-pent-4-enoyl]amino]butylamino]propyl]-3,4-bis(oxidanyl)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 A1MDH "Create component" 2026-01-09 PDBJ A1MDH "Initial release" 2026-04-22 RCSB #