data_3XI
# 
_chem_comp.id                                    3XI 
_chem_comp.name                                  "N-[(2S)-3-methyl-1-[[(2S)-4-methyl-1-oxidanylidene-1-[[(2S)-1-oxidanylidene-3-[(3S)-2-oxidanylidenepiperidin-3-yl]propan-2-yl]amino]pentan-2-yl]amino]-1-oxidanylidene-butan-2-yl]cyclohexanecarboxamide" 
_chem_comp.type                                  peptide-like 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C26 H44 N4 O5" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2022-02-01 
_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                        492.651 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     3XI 
_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        7WO1 
_chem_comp.pdbx_subcomponent_list                "RXK VAL LEU ELF" 
_chem_comp.pdbx_processing_site                  PDBJ 
_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 
3XI C22 C6  C 0 1 N N N N N N -18.538 12.498 -18.399 8.787  1.098  -1.161 C01  RXK 1  
3XI O25 O2  O 0 1 N N N N N N -21.159 14.261 -22.016 5.155  -0.361 1.684  O01  RXK 2  
3XI C21 C5  C 0 1 N N N N N N -18.126 12.006 -19.782 8.653  -0.315 -0.590 C02  RXK 3  
3XI C20 C4  C 0 1 N N N N N N -18.744 12.827 -20.917 7.452  -0.370 0.357  C03  RXK 4  
3XI C19 C20 C 0 1 N N N N N N -19.362 14.163 -20.493 6.179  -0.008 -0.412 C04  RXK 5  
3XI C24 C7  C 0 1 N N N N N N -20.303 14.071 -19.289 6.314  1.405  -0.984 C05  RXK 6  
3XI C23 C21 C 0 1 N N N N N N -20.016 12.877 -18.384 7.515  1.460  -1.930 C06  RXK 7  
3XI C18 C19 C 0 1 N N N N N N -20.148 14.764 -21.655 4.997  -0.062 0.520  C07  RXK 8  
3XI N17 N3  N 0 1 N N N N N N -19.652 15.965 -22.302 3.762  0.222  0.059  N    VAL 9  
3XI C13 C2  C 0 1 N N S N N N -20.378 16.576 -23.397 2.612  0.169  0.965  CA   VAL 10 
3XI C12 C16 C 0 1 N N N N N N -19.562 16.537 -24.681 1.358  -0.088 0.171  C    VAL 11 
3XI O26 O3  O 0 1 N N N N N N -18.441 16.918 -24.678 1.346  0.112  -1.026 O    VAL 12 
3XI C14 C17 C 0 1 N N N N N N -20.594 18.044 -23.052 2.484  1.503  1.704  CB   VAL 13 
3XI C15 C3  C 0 1 N N N N N N -20.812 18.218 -21.553 3.692  1.695  2.623  CG1  VAL 14 
3XI C16 C18 C 0 1 N N N N N N -21.726 18.654 -23.873 2.428  2.645  0.689  CG2  VAL 15 
3XI N11 N2  N 0 1 N N N N N N -20.163 16.054 -25.907 0.249  -0.539 0.789  N    LEU 16 
3XI C06 C12 C 0 1 N N S N N N -19.369 16.043 -27.118 -0.934 -0.898 0.003  CA   LEU 17 
3XI C05 C11 C 0 1 N N N N N N -19.393 17.461 -27.682 -2.165 -0.775 0.862  C    LEU 18 
3XI O27 O4  O 0 1 N N N N N N -20.419 18.047 -27.764 -2.065 -0.421 2.018  O    LEU 19 
3XI C07 C13 C 0 1 N N N N N N -19.952 15.053 -28.124 -0.800 -2.340 -0.491 CB   LEU 20 
3XI C08 C14 C 0 1 N N N N N N -19.620 13.606 -27.760 0.378  -2.439 -1.463 CG   LEU 21 
3XI C10 C1  C 0 1 N N N N N N -20.680 13.012 -26.835 0.590  -3.901 -1.860 CD1  LEU 22 
3XI C09 C15 C 0 1 N N N N N N -19.479 12.747 -29.013 0.078  -1.609 -2.713 CD2  LEU 23 
3XI C31 C24 C 0 1 N N N N N N -19.047 22.125 -25.616 -5.677 3.162  -0.056 C6   ELF 24 
3XI C03 C10 C 0 1 N N S N N N -18.212 19.457 -28.622 -4.576 -0.936 1.182  C11  ELF 25 
3XI C30 C23 C 0 1 N N N N N N -18.959 20.765 -26.107 -5.577 1.810  0.660  C13  ELF 26 
3XI C34 C26 C 0 1 N N N N N N -16.466 21.027 -25.452 -6.755 0.932  -1.341 C15  ELF 27 
3XI C28 C8  C 0 1 N N N N N N -17.265 20.325 -27.796 -5.790 -0.653 0.296  C17  ELF 28 
3XI C02 C9  C 0 1 N N N N N N -17.806 19.479 -30.094 -4.793 -2.222 1.936  C24  ELF 29 
3XI C29 C22 C 0 1 N N S N N N -17.620 20.277 -26.258 -5.612 0.701  -0.395 C25  ELF 30 
3XI C32 C25 C 0 1 N N N N N N -18.382 22.245 -24.298 -7.068 3.286  -0.677 C27  ELF 31 
3XI N04 N1  N 0 1 N N N N N N -18.163 18.103 -28.104 -3.378 -1.056 0.347  N3   ELF 32 
3XI N33 N4  N 0 1 N N N N N N -16.877 22.069 -24.411 -7.381 2.103  -1.468 N4   ELF 33 
3XI O01 O1  O 0 1 N N N N N N -17.800 20.503 -30.693 -4.028 -3.145 1.791  O3   ELF 34 
3XI O35 O5  O 0 1 N N N N N N -15.325 20.779 -25.649 -7.130 0.004  -2.027 O4   ELF 35 
3XI H12 H12 H 0 1 N N N N N N -18.362 11.699 -17.663 8.934  1.807  -0.346 H1   RXK 36 
3XI H13 H13 H 0 1 N N N N N N -17.936 13.380 -18.134 9.643  1.137  -1.835 H2   RXK 37 
3XI H10 H10 H 0 1 N N N N N N -18.446 10.959 -19.892 8.506  -1.024 -1.404 H3   RXK 38 
3XI H8  H8  H 0 1 N N N N N N -19.533 12.220 -21.385 7.356  -1.377 0.764  H5   RXK 39 
3XI H31 H31 H 0 1 N N N N N N -18.544 14.853 -20.237 6.033  -0.717 -1.227 H6   RXK 40 
3XI H14 H14 H 0 1 N N N N N N -20.200 14.991 -18.695 5.408  1.663  -1.531 H7   RXK 41 
3XI H15 H15 H 0 1 N N N N N N -21.335 13.987 -19.659 6.461  2.114  -0.169 H8   RXK 42 
3XI H32 H32 H 0 1 N N N N N N -20.308 13.132 -17.355 7.611  2.467  -2.337 H9   RXK 43 
3XI H33 H33 H 0 1 N N N N N N -20.608 12.017 -18.731 7.368  0.751  -2.745 H10  RXK 44 
3XI H11 H11 H 0 1 N N N N N N -17.031 12.065 -19.863 9.559  -0.573 -0.042 H11  RXK 45 
3XI H9  H9  H 0 1 N N N N N N -17.955 13.036 -21.655 7.598  0.339  1.171  H12  RXK 46 
3XI H43 H43 H 0 1 N N N N N N -18.797 16.377 -21.987 3.635  0.461  -0.872 H    VAL 47 
3XI H4  H4  H 0 1 N N N N N N -21.348 16.080 -23.553 2.755  -0.634 1.688  HA   VAL 48 
3XI H27 H27 H 0 1 N N N N N N -19.671 18.582 -23.314 1.571  1.501  2.300  HB   VAL 49 
3XI H5  H5  H 0 1 N N N N N N -19.973 17.764 -21.005 4.590  1.822  2.020  HG11 VAL 50 
3XI H6  H6  H 0 1 N N N N N N -20.869 19.290 -21.313 3.541  2.580  3.241  HG12 VAL 51 
3XI H7  H7  H 0 1 N N N N N N -21.751 17.726 -21.260 3.805  0.820  3.263  HG13 VAL 52 
3XI H28 H28 H 0 1 N N N N N N -21.852 19.711 -23.597 1.567  2.508  0.034  HG21 VAL 53 
3XI H29 H29 H 0 1 N N N N N N -21.483 18.581 -24.943 2.336  3.595  1.215  HG22 VAL 54 
3XI H30 H30 H 0 1 N N N N N N -22.660 18.109 -23.671 3.341  2.647  0.093  HG23 VAL 55 
3XI H42 H42 H 0 1 N N N N N N -21.110 15.734 -25.917 0.234  -0.627 1.755  H2   LEU 56 
3XI H20 H20 H 0 1 N N N N N N -18.330 15.760 -26.892 -1.019 -0.228 -0.853 HA   LEU 57 
3XI H21 H21 H 0 1 N N N N N N -19.539 15.273 -29.119 -0.626 -3.001 0.358  HB2  LEU 58 
3XI H22 H22 H 0 1 N N N N N N -21.045 15.172 -28.147 -1.717 -2.637 -1.000 HB3  LEU 59 
3XI H23 H23 H 0 1 N N N N N N -18.657 13.598 -27.228 1.279  -2.059 -0.982 HG   LEU 60 
3XI H1  H1  H 0 1 N N N N N N -20.774 13.638 -25.935 -0.311 -4.281 -2.342 HD11 LEU 61 
3XI H2  H2  H 0 1 N N N N N N -21.646 12.977 -27.360 1.429  -3.971 -2.553 HD12 LEU 62 
3XI H3  H3  H 0 1 N N N N N N -20.383 11.994 -26.544 0.804  -4.492 -0.970 HD13 LEU 63 
3XI H24 H24 H 0 1 N N N N N N -19.241 11.713 -28.724 -0.823 -1.989 -3.194 HD21 LEU 64 
3XI H25 H25 H 0 1 N N N N N N -20.424 12.762 -29.576 -0.073 -0.567 -2.430 HD22 LEU 65 
3XI H26 H26 H 0 1 N N N N N N -18.671 13.147 -29.643 0.917  -1.679 -3.405 HD23 LEU 66 
3XI H37 H37 H 0 1 N N N N N N -18.556 22.801 -26.332 -5.524 3.968  0.662  H1   ELF 67 
3XI H38 H38 H 0 1 N N N N N N -20.106 22.405 -25.514 -4.920 3.221  -0.838 H2   ELF 68 
3XI H19 H19 H 0 1 N N N N N N -19.233 19.857 -28.529 -4.444 -0.118 1.890  H3   ELF 69 
3XI H35 H35 H 0 1 N N N N N N -19.454 20.720 -27.088 -4.641 1.757  1.216  H4   ELF 70 
3XI H36 H36 H 0 1 N N N N N N -19.487 20.109 -25.400 -6.418 1.693  1.343  H5   ELF 71 
3XI H16 H16 H 0 1 N N N N N N -16.236 19.962 -27.936 -5.881 -1.436 -0.457 H6   ELF 72 
3XI H17 H17 H 0 1 N N N N N N -17.338 21.365 -28.146 -6.691 -0.632 0.909  H7   ELF 73 
3XI H18 H18 H 0 1 N N N N N N -17.524 18.562 -30.590 -5.634 -2.320 2.607  H8   ELF 74 
3XI H34 H34 H 0 1 N N N N N N -17.589 19.221 -25.952 -4.676 0.702  -0.953 H9   ELF 75 
3XI H39 H39 H 0 1 N N N N N N -18.594 23.240 -23.881 -7.808 3.397  0.115  H10  ELF 76 
3XI H40 H40 H 0 1 N N N N N N -18.782 21.472 -23.625 -7.097 4.165  -1.322 H11  ELF 77 
3XI H41 H41 H 0 1 N N N N N N -17.291 17.618 -28.039 -3.459 -1.339 -0.578 H14  ELF 78 
3XI H44 H44 H 0 1 N N N N N N -16.220 22.583 -23.859 -8.089 2.171  -2.128 H15  ELF 79 
# 
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 
3XI O01 C02 DOUB N N 1  
3XI C02 C03 SING N N 2  
3XI C09 C08 SING N N 3  
3XI C03 N04 SING N N 4  
3XI C03 C28 SING N N 5  
3XI C07 C08 SING N N 6  
3XI C07 C06 SING N N 7  
3XI N04 C05 SING N N 8  
3XI C28 C29 SING N N 9  
3XI O27 C05 DOUB N N 10 
3XI C08 C10 SING N N 11 
3XI C05 C06 SING N N 12 
3XI C06 N11 SING N N 13 
3XI C29 C30 SING N N 14 
3XI C29 C34 SING N N 15 
3XI C30 C31 SING N N 16 
3XI N11 C12 SING N N 17 
3XI O35 C34 DOUB N N 18 
3XI C31 C32 SING N N 19 
3XI C34 N33 SING N N 20 
3XI C12 O26 DOUB N N 21 
3XI C12 C13 SING N N 22 
3XI N33 C32 SING N N 23 
3XI C16 C14 SING N N 24 
3XI C13 C14 SING N N 25 
3XI C13 N17 SING N N 26 
3XI C14 C15 SING N N 27 
3XI N17 C18 SING N N 28 
3XI O25 C18 DOUB N N 29 
3XI C18 C19 SING N N 30 
3XI C20 C19 SING N N 31 
3XI C20 C21 SING N N 32 
3XI C19 C24 SING N N 33 
3XI C21 C22 SING N N 34 
3XI C24 C23 SING N N 35 
3XI C22 C23 SING N N 36 
3XI C10 H1  SING N N 37 
3XI C10 H2  SING N N 38 
3XI C10 H3  SING N N 39 
3XI C13 H4  SING N N 40 
3XI C15 H5  SING N N 41 
3XI C15 H6  SING N N 42 
3XI C15 H7  SING N N 43 
3XI C20 H8  SING N N 44 
3XI C20 H9  SING N N 45 
3XI C21 H10 SING N N 46 
3XI C21 H11 SING N N 47 
3XI C22 H12 SING N N 48 
3XI C22 H13 SING N N 49 
3XI C24 H14 SING N N 50 
3XI C24 H15 SING N N 51 
3XI C28 H16 SING N N 52 
3XI C28 H17 SING N N 53 
3XI C02 H18 SING N N 54 
3XI C03 H19 SING N N 55 
3XI C06 H20 SING N N 56 
3XI C07 H21 SING N N 57 
3XI C07 H22 SING N N 58 
3XI C08 H23 SING N N 59 
3XI C09 H24 SING N N 60 
3XI C09 H25 SING N N 61 
3XI C09 H26 SING N N 62 
3XI C14 H27 SING N N 63 
3XI C16 H28 SING N N 64 
3XI C16 H29 SING N N 65 
3XI C16 H30 SING N N 66 
3XI C19 H31 SING N N 67 
3XI C23 H32 SING N N 68 
3XI C23 H33 SING N N 69 
3XI C29 H34 SING N N 70 
3XI C30 H35 SING N N 71 
3XI C30 H36 SING N N 72 
3XI C31 H37 SING N N 73 
3XI C31 H38 SING N N 74 
3XI C32 H39 SING N N 75 
3XI C32 H40 SING N N 76 
3XI N04 H41 SING N N 77 
3XI N11 H42 SING N N 78 
3XI N17 H43 SING N N 79 
3XI N33 H44 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 
3XI InChI            InChI                1.03  "InChI=1S/C26H44N4O5/c1-16(2)13-21(25(34)28-20(15-31)14-19-11-8-12-27-23(19)32)29-26(35)22(17(3)4)30-24(33)18-9-6-5-7-10-18/h15-22H,5-14H2,1-4H3,(H,27,32)(H,28,34)(H,29,35)(H,30,33)/t19-,20-,21-,22-/m0/s1" 
3XI InChIKey         InChI                1.03  LOOFBLJETYWAIL-CMOCDZPBSA-N                                                                                                                                                                                   
3XI SMILES_CANONICAL CACTVS               3.385 "CC(C)C[C@H](NC(=O)[C@@H](NC(=O)C1CCCCC1)C(C)C)C(=O)N[C@@H](C[C@@H]2CCCNC2=O)C=O"                                                                                                                             
3XI SMILES           CACTVS               3.385 "CC(C)C[CH](NC(=O)[CH](NC(=O)C1CCCCC1)C(C)C)C(=O)N[CH](C[CH]2CCCNC2=O)C=O"                                                                                                                                    
3XI SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC(C)C[C@@H](C(=O)N[C@@H](C[C@@H]1CCCNC1=O)C=O)NC(=O)[C@H](C(C)C)NC(=O)C2CCCCC2"                                                                                                                             
3XI SMILES           "OpenEye OEToolkits" 2.0.7 "CC(C)CC(C(=O)NC(CC1CCCNC1=O)C=O)NC(=O)C(C(C)C)NC(=O)C2CCCCC2"                                                                                                                                                
# 
_pdbx_chem_comp_identifier.comp_id           3XI 
_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}-[(2~{S})-3-methyl-1-[[(2~{S})-4-methyl-1-oxidanylidene-1-[[(2~{S})-1-oxidanylidene-3-[(3~{S})-2-oxidanylidenepiperidin-3-yl]propan-2-yl]amino]pentan-2-yl]amino]-1-oxidanylidene-butan-2-yl]cyclohexanecarboxamide" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
3XI "Create component"         2022-02-01 PDBJ 
3XI "Modify component comp_id" 2022-02-02 PDBJ 
3XI "Initial release"          2022-04-13 RCSB 
3XI "Modify PCM"               2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            3XI 
_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               C02 
_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      ? 
# 
