data_MJ0 # _chem_comp.id MJ0 _chem_comp.name "(2R,3S)-3-[[(2S)-3-cyclopropyl-2-[2-oxidanylidene-3-(3-phenylpropanoylamino)pyridin-1-yl]propanoyl]amino]-N-methyl-2-oxidanyl-4-[(3S)-2-oxidanylidenepyrrolidin-3-yl]butanamide" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C29 H37 N5 O6" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "(S)-3-((S)-3-cyclopropyl-2-(2-oxo-3-(3-phenylpropanamido)pyridin-1(2H)-yl)propanamido)-N-methyl-2-oxo-4-((S)-2-oxopyrrolidin-3-yl)butanamide; RK-90 inhibitor (covalently bound to protein)" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2022-07-27 _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 551.634 _chem_comp.one_letter_code ? _chem_comp.three_letter_code MJ0 _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 8AJ0 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBE _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 MJ0 N1 N1 N 0 1 N N N N N N -3.094 -0.401 12.738 0.234 2.233 -0.115 N1 MJ0 1 MJ0 N3 N2 N 0 1 N N N N N N -1.115 1.803 14.780 -2.892 0.375 0.516 N3 MJ0 2 MJ0 C4 C1 C 0 1 N N N N N N -2.589 -1.652 13.105 1.512 1.846 0.056 C4 MJ0 3 MJ0 C5 C2 C 0 1 N N N N N N -4.402 -0.225 12.374 -0.100 3.118 -1.092 C5 MJ0 4 MJ0 C6 C3 C 0 1 N N N N N N -3.709 -5.010 13.836 4.196 0.671 -0.709 C6 MJ0 5 MJ0 C7 C4 C 0 1 N N N N N N -2.953 -6.290 14.111 5.608 0.235 -0.416 C7 MJ0 6 MJ0 C8 C5 C 0 1 N N N N N N -2.521 -7.010 12.850 5.723 -1.280 -0.603 C8 MJ0 7 MJ0 C10 C6 C 0 1 N N N N N N -2.214 1.230 14.273 -1.832 0.960 -0.077 C10 MJ0 8 MJ0 C13 C7 C 0 1 N N N N N N -0.061 1.569 16.973 -4.487 -1.479 0.524 C13 MJ0 9 MJ0 C15 C8 C 0 1 N N N N N N -1.610 -0.429 17.470 -2.778 -3.123 -0.350 C15 MJ0 10 MJ0 C17 C9 C 0 1 N N N N N N 0.754 -0.797 17.517 -3.961 -3.625 1.694 C17 MJ0 11 MJ0 C20 C10 C 0 1 N N N N N N -2.523 1.872 11.807 -1.491 2.834 1.511 C20 MJ0 12 MJ0 C21 C11 C 0 1 N N N N N N -2.313 1.448 10.366 -0.482 3.496 2.451 C21 MJ0 13 MJ0 C22 C12 C 0 1 N N N N N N -2.539 2.399 9.225 -0.939 4.741 3.214 C22 MJ0 14 MJ0 C24 C13 C 0 1 Y N N N N N -3.658 -7.554 12.017 7.135 -1.716 -0.310 C24 MJ0 15 MJ0 C26 C14 C 0 1 Y N N N N N -5.373 -7.241 10.346 9.371 -2.142 -1.055 C26 MJ0 16 MJ0 C28 C15 C 0 1 Y N N N N N -5.125 -9.367 11.394 8.790 -2.480 1.243 C28 MJ0 17 MJ0 C1 C16 C 0 1 N N N N N N -5.258 -1.259 12.307 0.844 3.634 -1.912 C1 MJ0 18 MJ0 C2 C17 C 0 1 N N N N N N -4.801 -2.528 12.625 2.186 3.258 -1.760 C2 MJ0 19 MJ0 C3 C18 C 0 1 N N N N N N -3.477 -2.703 13.037 2.523 2.364 -0.781 C3 MJ0 20 MJ0 N2 N3 N 0 1 N N N N N N -2.976 -3.969 13.398 3.858 1.972 -0.608 N2 MJ0 21 MJ0 C9 C19 C 0 1 N N S N N N -2.196 0.763 12.820 -0.811 1.690 0.757 C9 MJ0 22 MJ0 C11 C20 C 0 1 N N S N N N -1.061 2.349 16.124 -3.885 -0.335 -0.294 C11 MJ0 23 MJ0 C12 C21 C 0 1 N N R N N N -0.787 3.864 16.052 -4.993 0.635 -0.708 C12 MJ0 24 MJ0 C14 C22 C 0 1 N N S N N N -0.313 0.076 16.886 -3.384 -2.465 0.911 C14 MJ0 25 MJ0 C16 C23 C 0 1 N N N N N N -1.216 -1.331 18.625 -2.506 -4.561 0.144 C16 MJ0 26 MJ0 N4 N4 N 0 1 N N N N N N 0.221 -1.514 18.466 -3.456 -4.785 1.240 N4 MJ0 27 MJ0 O1 O1 O 0 1 N N N N N N -1.540 4.547 15.055 -4.434 1.689 -1.495 O1 MJ0 28 MJ0 C18 C24 C 0 1 N N N N N N -0.958 4.503 17.413 -6.029 -0.101 -1.517 C18 MJ0 29 MJ0 N5 N5 N 0 1 N N N N N N -1.865 5.451 17.580 -6.861 -0.973 -0.914 N5 MJ0 30 MJ0 C19 C25 C 0 1 N N N N N N -3.103 5.561 16.826 -7.803 -1.760 -1.714 C19 MJ0 31 MJ0 C23 C26 C 0 1 N N N N N N -1.155 1.973 9.569 -0.757 3.414 3.954 C23 MJ0 32 MJ0 O2 O2 O 0 1 N N N N N N -4.917 -4.937 13.949 3.363 -0.149 -1.035 O2 MJ0 33 MJ0 O3 O3 O 0 1 N N N N N N -1.415 -1.744 13.431 1.796 1.047 0.935 O3 MJ0 34 MJ0 O4 O4 O 0 1 N N N N N N -3.211 1.018 14.958 -1.701 0.900 -1.281 O4 MJ0 35 MJ0 O5 O5 O 0 1 N N N N N N 1.949 -0.841 17.170 -4.761 -3.522 2.599 O5 MJ0 36 MJ0 O6 O6 O 0 1 N N N N N N -0.170 4.157 18.292 -6.115 0.091 -2.712 O6 MJ0 37 MJ0 C25 C27 C 0 1 Y N N N N N -4.321 -6.748 11.101 8.074 -1.747 -1.325 C25 MJ0 38 MJ0 C27 C28 C 0 1 Y N N N N N -5.774 -8.546 10.495 9.730 -2.505 0.229 C27 MJ0 39 MJ0 C29 C29 C 0 1 Y N N N N N -4.069 -8.876 12.147 7.494 -2.080 0.974 C29 MJ0 40 MJ0 H1 H1 H 0 1 N N N N N N -0.296 1.857 14.208 -2.997 0.423 1.479 H1 MJ0 41 MJ0 H2 H2 H 0 1 N N N N N N -4.754 0.768 12.135 -1.132 3.412 -1.215 H2 MJ0 42 MJ0 H3 H3 H 0 1 N N N N N N -3.602 -6.962 14.692 6.293 0.738 -1.098 H3 MJ0 43 MJ0 H4 H4 H 0 1 N N N N N N -2.056 -6.047 14.700 5.863 0.494 0.612 H4 MJ0 44 MJ0 H5 H5 H 0 1 N N N N N N -1.874 -7.851 13.139 5.038 -1.783 0.080 H5 MJ0 45 MJ0 H6 H6 H 0 1 N N N N N N -1.949 -6.304 12.230 5.468 -1.539 -1.630 H6 MJ0 46 MJ0 H7 H7 H 0 1 N N N N N N 0.957 1.782 16.615 -4.949 -1.077 1.426 H7 MJ0 47 MJ0 H8 H8 H 0 1 N N N N N N -0.155 1.888 18.022 -5.242 -1.993 -0.072 H8 MJ0 48 MJ0 H9 H9 H 0 1 N N N N N N -2.221 0.411 17.831 -3.494 -3.122 -1.172 H9 MJ0 49 MJ0 H10 H10 H 0 1 N N N N N N -2.175 -0.996 16.716 -1.852 -2.628 -0.642 H10 MJ0 50 MJ0 H11 H11 H 0 1 N N N N N N -1.876 2.737 12.015 -2.326 2.441 2.092 H11 MJ0 51 MJ0 H12 H12 H 0 1 N N N N N N -3.576 2.163 11.936 -1.861 3.571 0.798 H12 MJ0 52 MJ0 H13 H13 H 0 1 N N N N N N -2.582 0.403 10.154 0.558 3.458 2.128 H13 MJ0 53 MJ0 H14 H14 H 0 1 N N N N N N -2.862 3.431 9.426 -0.200 5.522 3.392 H14 MJ0 54 MJ0 H15 H15 H 0 1 N N N N N N -3.009 2.042 8.297 -1.959 5.089 3.047 H15 MJ0 55 MJ0 H16 H16 H 0 1 N N N N N N -5.878 -6.599 9.640 10.105 -2.161 -1.847 H16 MJ0 56 MJ0 H17 H17 H 0 1 N N N N N N -5.440 -10.393 11.511 9.070 -2.765 2.246 H17 MJ0 57 MJ0 H18 H18 H 0 1 N N N N N N -6.285 -1.103 12.010 0.564 4.336 -2.683 H18 MJ0 58 MJ0 H19 H19 H 0 1 N N N N N N -5.464 -3.377 12.555 2.944 3.666 -2.412 H19 MJ0 59 MJ0 H20 H20 H 0 1 N N N N N N -1.988 -4.107 13.322 4.538 2.636 -0.416 H20 MJ0 60 MJ0 H21 H21 H 0 1 N N N N N N -1.175 0.417 12.602 -0.364 0.999 1.472 H21 MJ0 61 MJ0 H22 H22 H 0 1 N N N N N N -2.051 2.221 16.586 -3.405 -0.739 -1.186 H22 MJ0 62 MJ0 H23 H23 H 0 1 N N N N N N 0.277 3.969 15.791 -5.459 1.055 0.184 H23 MJ0 63 MJ0 H24 H24 H 0 1 N N N N N N -0.331 -0.176 15.815 -2.608 -1.961 1.488 H24 MJ0 64 MJ0 H25 H25 H 0 1 N N N N N N -1.443 -0.852 19.589 -2.681 -5.276 -0.660 H25 MJ0 65 MJ0 H26 H26 H 0 1 N N N N N N -1.741 -2.296 18.562 -1.482 -4.647 0.507 H26 MJ0 66 MJ0 H27 H27 H 0 1 N N N N N N 0.754 -2.138 19.038 -3.690 -5.658 1.591 H27 MJ0 67 MJ0 H28 H28 H 0 1 N N N N N N -1.320 5.471 15.069 -3.759 2.207 -1.036 H28 MJ0 68 MJ0 H29 H29 H 0 1 N N N N N N -1.686 6.145 18.278 -6.835 -1.080 0.050 H29 MJ0 69 MJ0 H30 H30 H 0 1 N N N N N N -3.666 6.441 17.171 -8.471 -1.088 -2.253 H30 MJ0 70 MJ0 H31 H31 H 0 1 N N N N N N -2.872 5.670 15.756 -7.251 -2.372 -2.427 H31 MJ0 71 MJ0 H32 H32 H 0 1 N N N N N N -3.708 4.655 16.980 -8.387 -2.404 -1.057 H32 MJ0 72 MJ0 H33 H33 H 0 1 N N N N N N -0.604 1.302 8.894 -1.657 2.888 4.273 H33 MJ0 73 MJ0 H34 H34 H 0 1 N N N N N N -0.456 2.691 10.023 0.101 3.322 4.619 H34 MJ0 74 MJ0 H35 H35 H 0 1 N N N N N N -4.012 -5.721 10.975 7.793 -1.463 -2.328 H35 MJ0 75 MJ0 H36 H36 H 0 1 N N N N N N -6.596 -8.929 9.909 10.743 -2.814 0.440 H36 MJ0 76 MJ0 H37 H37 H 0 1 N N N N N N -3.560 -9.528 12.842 6.762 -2.052 1.768 H37 MJ0 77 # 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 MJ0 C22 C23 SING N N 1 MJ0 C22 C21 SING N N 2 MJ0 C23 C21 SING N N 3 MJ0 C26 C27 DOUB Y N 4 MJ0 C26 C25 SING Y N 5 MJ0 C21 C20 SING N N 6 MJ0 C27 C28 SING Y N 7 MJ0 C25 C24 DOUB Y N 8 MJ0 C28 C29 DOUB Y N 9 MJ0 C20 C9 SING N N 10 MJ0 C24 C29 SING Y N 11 MJ0 C24 C8 SING N N 12 MJ0 C1 C5 DOUB N N 13 MJ0 C1 C2 SING N N 14 MJ0 C5 N1 SING N N 15 MJ0 C2 C3 DOUB N N 16 MJ0 N1 C9 SING N N 17 MJ0 N1 C4 SING N N 18 MJ0 C9 C10 SING N N 19 MJ0 C8 C7 SING N N 20 MJ0 C3 C4 SING N N 21 MJ0 C3 N2 SING N N 22 MJ0 C4 O3 DOUB N N 23 MJ0 N2 C6 SING N N 24 MJ0 C6 O2 DOUB N N 25 MJ0 C6 C7 SING N N 26 MJ0 C10 N3 SING N N 27 MJ0 C10 O4 DOUB N N 28 MJ0 N3 C11 SING N N 29 MJ0 O1 C12 SING N N 30 MJ0 C12 C11 SING N N 31 MJ0 C12 C18 SING N N 32 MJ0 C11 C13 SING N N 33 MJ0 C19 N5 SING N N 34 MJ0 C14 C13 SING N N 35 MJ0 C14 C15 SING N N 36 MJ0 C14 C17 SING N N 37 MJ0 O5 C17 DOUB N N 38 MJ0 C18 N5 SING N N 39 MJ0 C18 O6 DOUB N N 40 MJ0 C15 C16 SING N N 41 MJ0 C17 N4 SING N N 42 MJ0 N4 C16 SING N N 43 MJ0 N3 H1 SING N N 44 MJ0 C5 H2 SING N N 45 MJ0 C7 H3 SING N N 46 MJ0 C7 H4 SING N N 47 MJ0 C8 H5 SING N N 48 MJ0 C8 H6 SING N N 49 MJ0 C13 H7 SING N N 50 MJ0 C13 H8 SING N N 51 MJ0 C15 H9 SING N N 52 MJ0 C15 H10 SING N N 53 MJ0 C20 H11 SING N N 54 MJ0 C20 H12 SING N N 55 MJ0 C21 H13 SING N N 56 MJ0 C22 H14 SING N N 57 MJ0 C22 H15 SING N N 58 MJ0 C26 H16 SING N N 59 MJ0 C28 H17 SING N N 60 MJ0 C1 H18 SING N N 61 MJ0 C2 H19 SING N N 62 MJ0 N2 H20 SING N N 63 MJ0 C9 H21 SING N N 64 MJ0 C11 H22 SING N N 65 MJ0 C12 H23 SING N N 66 MJ0 C14 H24 SING N N 67 MJ0 C16 H25 SING N N 68 MJ0 C16 H26 SING N N 69 MJ0 N4 H27 SING N N 70 MJ0 O1 H28 SING N N 71 MJ0 N5 H29 SING N N 72 MJ0 C19 H30 SING N N 73 MJ0 C19 H31 SING N N 74 MJ0 C19 H32 SING N N 75 MJ0 C23 H33 SING N N 76 MJ0 C23 H34 SING N N 77 MJ0 C25 H35 SING N N 78 MJ0 C27 H36 SING N N 79 MJ0 C29 H37 SING N N 80 # 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 MJ0 InChI InChI 1.06 "InChI=1S/C29H37N5O6/c1-30-28(39)25(36)22(17-20-13-14-31-26(20)37)33-27(38)23(16-19-9-10-19)34-15-5-8-21(29(34)40)32-24(35)12-11-18-6-3-2-4-7-18/h2-8,15,19-20,22-23,25,36H,9-14,16-17H2,1H3,(H,30,39)(H,31,37)(H,32,35)(H,33,38)/t20-,22-,23-,25+/m0/s1" MJ0 InChIKey InChI 1.06 ZZWBXRBGXJAYNA-ALJFMCDRSA-N MJ0 SMILES_CANONICAL CACTVS 3.385 "CNC(=O)[C@H](O)[C@H](C[C@@H]1CCNC1=O)NC(=O)[C@H](CC2CC2)N3C=CC=C(NC(=O)CCc4ccccc4)C3=O" MJ0 SMILES CACTVS 3.385 "CNC(=O)[CH](O)[CH](C[CH]1CCNC1=O)NC(=O)[CH](CC2CC2)N3C=CC=C(NC(=O)CCc4ccccc4)C3=O" MJ0 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CNC(=O)[C@@H]([C@H](C[C@@H]1CCNC1=O)NC(=O)[C@H](CC2CC2)N3C=CC=C(C3=O)NC(=O)CCc4ccccc4)O" MJ0 SMILES "OpenEye OEToolkits" 2.0.7 "CNC(=O)C(C(CC1CCNC1=O)NC(=O)C(CC2CC2)N3C=CC=C(C3=O)NC(=O)CCc4ccccc4)O" # _pdbx_chem_comp_identifier.comp_id MJ0 _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 "(2~{R},3~{S})-3-[[(2~{S})-3-cyclopropyl-2-[2-oxidanylidene-3-(3-phenylpropanoylamino)pyridin-1-yl]propanoyl]amino]-~{N}-methyl-2-oxidanyl-4-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]butanamide" # loop_ _pdbx_chem_comp_synonyms.ordinal _pdbx_chem_comp_synonyms.comp_id _pdbx_chem_comp_synonyms.name _pdbx_chem_comp_synonyms.provenance _pdbx_chem_comp_synonyms.type 1 MJ0 "(S)-3-((S)-3-cyclopropyl-2-(2-oxo-3-(3-phenylpropanamido)pyridin-1(2H)-yl)propanamido)-N-methyl-2-oxo-4-((S)-2-oxopyrrolidin-3-yl)butanamide" AUTHOR ? 2 MJ0 "RK-90 inhibitor (covalently bound to protein)" AUTHOR ? # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site MJ0 "Create component" 2022-07-27 PDBE MJ0 "Modify synonyms" 2022-08-14 PDBE MJ0 "Initial release" 2023-08-16 RCSB MJ0 "Modify descriptor" 2023-09-23 RCSB MJ0 "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id MJ0 _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 C12 _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 ? #