data_BD3 # _chem_comp.id BD3 _chem_comp.name "Nalpha-[(3-tert-butyl-1-methyl-1H-pyrazol-5-yl)carbonyl]-N-[(2E)-2-iminoethyl]-3-{5-[(Z)-iminomethyl]-1,3,4-oxadiazol-2-yl}-L-phenylalaninamide" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C23 H28 N8 O3" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2009-06-19 _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 464.520 _chem_comp.one_letter_code ? _chem_comp.three_letter_code BD3 _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 3HWN _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB _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 BD3 C1 C1 C 0 1 Y N N N N N 31.345 -25.752 -13.764 -1.249 -2.445 -0.202 C1 BD3 1 BD3 C2 C2 C 0 1 Y N N N N N 31.181 -25.808 -15.149 -1.463 -3.281 -1.283 C2 BD3 2 BD3 C3 C3 C 0 1 Y N N N N N 30.337 -25.205 -12.966 0.033 -2.205 0.245 C3 BD3 3 BD3 C4 C4 C 0 1 Y N N N N N 30.029 -25.314 -15.747 -0.394 -3.887 -1.920 C4 BD3 4 BD3 C5 C5 C 0 1 Y N N N N N 29.181 -24.706 -13.568 1.117 -2.813 -0.392 C5 BD3 5 BD3 C6 C6 C 0 1 Y N N N N N 29.030 -24.761 -14.963 0.893 -3.661 -1.479 C6 BD3 6 BD3 C7 C7 C 0 1 Y N N N N N 28.068 -24.143 -12.797 2.493 -2.561 0.081 C7 BD3 7 BD3 C12 C12 C 0 1 N N N N N N 24.805 -23.211 -13.044 6.070 -2.865 0.098 C12 BD3 8 BD3 N13 N13 N 0 1 N N N N N N 24.237 -21.904 -12.679 6.950 -2.324 0.881 N13 BD3 9 BD3 C15 C15 C 0 1 N N S N N N 32.853 -27.791 -13.498 -2.713 -0.443 -0.182 C15 BD3 10 BD3 C17 C17 C 0 1 N N N N N N 31.035 -29.341 -14.177 -1.358 1.474 -0.831 C17 BD3 11 BD3 C18 C18 C 0 1 Y N N N N N 29.900 -30.210 -13.766 -0.160 2.317 -0.682 C18 BD3 12 BD3 N22 N22 N 0 1 N N N N N N 35.279 -28.069 -13.085 -5.128 -0.507 0.348 N22 BD3 13 BD3 C23 C23 C 0 1 N N N N N N 36.509 -28.536 -12.441 -6.338 0.075 0.935 C23 BD3 14 BD3 C24 C24 C 0 1 N N N N N N 37.302 -27.327 -11.913 -7.501 -0.857 0.716 C24 BD3 15 BD3 C30 C30 C 0 1 N N N N N N 28.637 -30.285 -15.937 -0.413 3.691 -2.771 C30 BD3 16 BD3 C31 C31 C 0 1 N N N N N N 27.858 -32.276 -11.476 2.924 3.603 0.859 C31 BD3 17 BD3 C32 C32 C 0 1 N N N N N N 28.475 -32.110 -10.077 2.539 3.687 2.337 C32 BD3 18 BD3 C33 C33 C 0 1 N N N N N N 27.906 -33.750 -11.876 3.480 4.952 0.399 C33 BD3 19 BD3 C34 C34 C 0 1 N N N N N N 26.381 -31.879 -11.405 3.991 2.522 0.671 C34 BD3 20 BD3 N25 N25 N 0 1 N N N N N N 38.599 -27.486 -11.765 -8.195 -1.259 1.713 N25 BD3 21 BD3 C20 C20 C 0 1 N N N N N N 33.992 -28.377 -12.700 -3.957 0.155 0.423 C20 BD3 22 BD3 O21 O21 O 0 1 N N N N N N 33.764 -29.109 -11.757 -3.904 1.233 0.976 O21 BD3 23 BD3 N16 N16 N 0 1 N N N N N N 31.714 -28.663 -13.211 -1.582 0.463 0.031 N16 BD3 24 BD3 O19 O19 O 0 1 N N N N N N 31.379 -29.202 -15.332 -2.145 1.691 -1.732 O19 BD3 25 BD3 C29 C29 C 0 1 Y N N N N N 29.708 -30.740 -12.510 0.765 2.270 0.347 C29 BD3 26 BD3 C28 C28 C 0 1 Y N N N N N 28.535 -31.452 -12.572 1.707 3.255 0.041 C28 BD3 27 BD3 N27 N27 N 0 1 Y N N N N N 28.065 -31.344 -13.841 1.346 3.822 -1.081 N27 BD3 28 BD3 N26 N26 N 0 1 Y N N N N N 28.849 -30.618 -14.519 0.264 3.297 -1.533 N26 BD3 29 BD3 C14 C14 C 0 1 N N N N N N 32.607 -26.313 -13.118 -2.420 -1.789 0.484 C14 BD3 30 BD3 O11 O11 O 0 1 Y N N N N N 27.024 -23.953 -13.357 3.622 -3.075 -0.442 O11 BD3 31 BD3 C10 C10 C 0 1 Y N N N N N 26.224 -23.514 -12.568 4.641 -2.583 0.294 C10 BD3 32 BD3 N9 N9 N 0 1 Y N N N N N 26.795 -23.389 -11.345 4.121 -1.805 1.219 N9 BD3 33 BD3 N8 N8 N 0 1 Y N N N N N 27.984 -23.811 -11.492 2.841 -1.787 1.089 N8 BD3 34 BD3 H2 H2 H 0 1 N N N N N N 31.958 -26.240 -15.762 -2.469 -3.463 -1.632 H2 BD3 35 BD3 H3 H3 H 0 1 N N N N N N 30.451 -25.169 -11.893 0.199 -1.548 1.087 H3 BD3 36 BD3 H4 H4 H 0 1 N N N N N N 29.912 -25.361 -16.820 -0.568 -4.539 -2.763 H4 BD3 37 BD3 H6 H6 H 0 1 N N N N N N 28.135 -24.372 -15.425 1.727 -4.135 -1.976 H6 BD3 38 BD3 H12 H12 H 0 1 N N N N N N 24.242 -23.927 -13.625 6.387 -3.522 -0.698 H12 BD3 39 BD3 HN13 HN13 H 0 0 N N N N N N 24.943 -21.432 -12.151 6.666 -1.733 1.596 HN13 BD3 40 BD3 H15 H15 H 0 1 N N N N N N 33.057 -27.760 -14.579 -2.864 -0.592 -1.251 H15 BD3 41 BD3 HN22 HN22 H 0 0 N N N N N N 35.383 -27.470 -13.879 -5.171 -1.369 -0.095 HN22 BD3 42 BD3 H23 H23 H 0 1 N N N N N N 36.254 -29.202 -11.603 -6.187 0.224 2.004 H23 BD3 43 BD3 H23A H23A H 0 0 N N N N N N 37.120 -29.085 -13.172 -6.547 1.034 0.461 H23A BD3 44 BD3 H24 H24 H 0 1 N N N N N N 36.816 -26.392 -11.675 -7.750 -1.186 -0.282 H24 BD3 45 BD3 H30 H30 H 0 1 N N N N N N 28.584 -29.192 -16.054 -1.082 4.528 -2.568 H30 BD3 46 BD3 H30A H30A H 0 0 N N N N N N 29.473 -30.677 -16.535 0.329 3.991 -3.511 H30A BD3 47 BD3 H30B H30B H 0 0 N N N N N N 27.695 -30.736 -16.283 -0.990 2.849 -3.154 H30B BD3 48 BD3 H32 H32 H 0 1 N N N N N N 29.571 -32.070 -10.161 3.419 3.938 2.929 H32 BD3 49 BD3 H32A H32A H 0 0 N N N N N N 28.108 -31.177 -9.623 1.779 4.457 2.471 H32A BD3 50 BD3 H32B H32B H 0 0 N N N N N N 28.187 -32.964 -9.446 2.143 2.726 2.665 H32B BD3 51 BD3 H33 H33 H 0 1 N N N N N N 27.918 -33.833 -12.973 3.755 4.892 -0.654 H33 BD3 52 BD3 H33A H33A H 0 0 N N N N N N 28.815 -34.212 -11.464 2.720 5.722 0.533 H33A BD3 53 BD3 H33B H33B H 0 0 N N N N N N 27.020 -34.266 -11.479 4.360 5.203 0.991 H33B BD3 54 BD3 H34 H34 H 0 1 N N N N N N 26.077 -31.784 -10.352 3.595 1.560 0.999 H34 BD3 55 BD3 H34A H34A H 0 0 N N N N N N 26.235 -30.916 -11.917 4.266 2.461 -0.382 H34A BD3 56 BD3 H34B H34B H 0 0 N N N N N N 25.770 -32.652 -11.895 4.871 2.773 1.263 H34B BD3 57 BD3 HN25 HN25 H 0 0 N N N N N N 38.974 -26.626 -11.419 -8.944 -1.859 1.572 HN25 BD3 58 BD3 HN16 HN16 H 0 0 N N N N N N 31.420 -28.766 -12.261 -0.994 0.335 0.792 HN16 BD3 59 BD3 H29 H29 H 0 1 N N N N N N 30.350 -30.620 -11.650 0.759 1.613 1.204 H29 BD3 60 BD3 H14 H14 H 0 1 N N N N N N 33.468 -25.717 -13.456 -3.296 -2.433 0.403 H14 BD3 61 BD3 H14A H14A H 0 0 N N N N N N 32.480 -26.261 -12.027 -2.182 -1.631 1.536 H14A BD3 62 # 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 BD3 C2 C1 DOUB Y N 1 BD3 C1 C14 SING N N 2 BD3 C1 C3 SING Y N 3 BD3 C4 C2 SING Y N 4 BD3 C2 H2 SING N N 5 BD3 C5 C3 DOUB Y N 6 BD3 C3 H3 SING N N 7 BD3 C4 C6 DOUB Y N 8 BD3 C4 H4 SING N N 9 BD3 C6 C5 SING Y N 10 BD3 C5 C7 SING Y N 11 BD3 C6 H6 SING N N 12 BD3 O11 C7 SING Y N 13 BD3 C7 N8 DOUB Y N 14 BD3 C12 N13 DOUB N N 15 BD3 C12 C10 SING N N 16 BD3 C12 H12 SING N N 17 BD3 N13 HN13 SING N N 18 BD3 C15 N16 SING N N 19 BD3 C15 C14 SING N N 20 BD3 C15 C20 SING N N 21 BD3 C15 H15 SING N N 22 BD3 O19 C17 DOUB N N 23 BD3 C17 C18 SING N N 24 BD3 C17 N16 SING N N 25 BD3 N26 C18 SING Y N 26 BD3 C18 C29 DOUB Y N 27 BD3 N22 C20 SING N N 28 BD3 N22 C23 SING N N 29 BD3 N22 HN22 SING N N 30 BD3 C23 C24 SING N N 31 BD3 C23 H23 SING N N 32 BD3 C23 H23A SING N N 33 BD3 C24 N25 DOUB N N 34 BD3 C24 H24 SING N N 35 BD3 C30 N26 SING N N 36 BD3 C30 H30 SING N N 37 BD3 C30 H30A SING N N 38 BD3 C30 H30B SING N N 39 BD3 C28 C31 SING N N 40 BD3 C33 C31 SING N N 41 BD3 C31 C34 SING N N 42 BD3 C31 C32 SING N N 43 BD3 C32 H32 SING N N 44 BD3 C32 H32A SING N N 45 BD3 C32 H32B SING N N 46 BD3 C33 H33 SING N N 47 BD3 C33 H33A SING N N 48 BD3 C33 H33B SING N N 49 BD3 C34 H34 SING N N 50 BD3 C34 H34A SING N N 51 BD3 C34 H34B SING N N 52 BD3 N25 HN25 SING N N 53 BD3 C20 O21 DOUB N N 54 BD3 N16 HN16 SING N N 55 BD3 C28 C29 SING Y N 56 BD3 C29 H29 SING N N 57 BD3 N27 C28 DOUB Y N 58 BD3 N26 N27 SING Y N 59 BD3 C14 H14 SING N N 60 BD3 C14 H14A SING N N 61 BD3 O11 C10 SING Y N 62 BD3 C10 N9 DOUB Y N 63 BD3 N8 N9 SING Y N 64 # 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 BD3 SMILES ACDLabs 10.04 "O=C(NCC=[N@H])C(NC(=O)c1cc(nn1C)C(C)(C)C)Cc3cc(c2nnc(o2)C=[N@H])ccc3" BD3 SMILES_CANONICAL CACTVS 3.341 "Cn1nc(cc1C(=O)N[C@@H](Cc2cccc(c2)c3oc(C=N)nn3)C(=O)NCC=N)C(C)(C)C" BD3 SMILES CACTVS 3.341 "Cn1nc(cc1C(=O)N[CH](Cc2cccc(c2)c3oc(C=N)nn3)C(=O)NCC=N)C(C)(C)C" BD3 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "[H]/N=C/CNC(=O)[C@H](Cc1cccc(c1)c2nnc(o2)\C=N/[H])NC(=O)c3cc(nn3C)C(C)(C)C" BD3 SMILES "OpenEye OEToolkits" 1.5.0 "[H]N=CCNC(=O)C(Cc1cccc(c1)c2nnc(o2)C=N[H])NC(=O)c3cc(nn3C)C(C)(C)C" BD3 InChI InChI 1.03 "InChI=1S/C23H28N8O3/c1-23(2,3)18-12-17(31(4)30-18)21(33)27-16(20(32)26-9-8-24)11-14-6-5-7-15(10-14)22-29-28-19(13-25)34-22/h5-8,10,12-13,16,24-25H,9,11H2,1-4H3,(H,26,32)(H,27,33)/b24-8+,25-13-/t16-/m0/s1" BD3 InChIKey InChI 1.03 TVWDSIGUOHNHHP-TTWIPJPDSA-N # 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 BD3 "SYSTEMATIC NAME" ACDLabs 10.04 "Nalpha-[(3-tert-butyl-1-methyl-1H-pyrazol-5-yl)carbonyl]-N-[(2E)-2-iminoethyl]-3-{5-[(Z)-iminomethyl]-1,3,4-oxadiazol-2-yl}-L-phenylalaninamide" BD3 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "5-tert-butyl-N-[(2S)-1-(2-iminoethylamino)-3-[3-[5-(iminomethyl)-1,3,4-oxadiazol-2-yl]phenyl]-1-oxo-propan-2-yl]-2-methyl-pyrazole-3-carboxamide" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site BD3 "Create component" 2009-06-19 RCSB BD3 "Modify aromatic_flag" 2011-06-04 RCSB BD3 "Modify descriptor" 2011-06-04 RCSB BD3 "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id BD3 _pdbx_chem_comp_pcm.modified_residue_id CYS _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 C24 _pdbx_chem_comp_pcm.modified_residue_id_linking_atom SG _pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ? _pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ? #