data_VDJ
# 
_chem_comp.id                                    VDJ 
_chem_comp.name                                  "[4,4-bis(fluoranyl)cyclohexyl]methyl ~{N}-[(2~{S})-1-[[(1~{R},2~{S})-1-[bis(oxidanyl)-oxidanylidene-$l^{5}-sulfanyl]-1-oxidanyl-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]carbamate" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C21 H35 F2 N3 O8 S" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2020-07-30 
_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                        527.580 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     VDJ 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   Y 
_chem_comp.pdbx_ideal_coordinates_details        Corina 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        6W2A 
_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 
VDJ C11 C1  C 0 1 N N S N N N -12.014 -8.601  -24.486 -0.309 0.384  0.510  C11 VDJ 1  
VDJ C12 C2  C 0 1 N N N N N N -12.609 -10.020 -24.253 -0.721 1.500  1.472  C12 VDJ 2  
VDJ C13 C3  C 0 1 N N N N N N -14.134 -10.033 -24.019 -2.016 1.106  2.185  C13 VDJ 3  
VDJ C14 C4  C 0 1 N N N N N N -14.732 -11.447 -24.068 -1.753 -0.098 3.092  C14 VDJ 4  
VDJ C15 C5  C 0 1 N N N N N N -14.501 -9.427  -22.664 -2.511 2.282  3.030  C15 VDJ 5  
VDJ C16 C6  C 0 1 N N N N N N -10.465 -8.639  -24.437 -1.278 0.333  -0.643 C16 VDJ 6  
VDJ C18 C7  C 0 1 N N S N N N -8.347  -8.256  -23.188 -3.430 -0.302 -1.596 C18 VDJ 7  
VDJ C19 C8  C 0 1 N N N N N N -7.733  -6.810  -23.074 -4.479 -1.364 -1.264 C19 VDJ 8  
VDJ C20 C9  C 0 1 N N S N N N -7.815  -6.035  -24.401 -3.793 -2.720 -1.084 C20 VDJ 9  
VDJ C21 C10 C 0 1 N N N N N N -7.327  -4.596  -24.235 -2.903 -2.704 0.139  C21 VDJ 10 
VDJ C23 C11 C 0 1 N N N N N N -6.404  -5.339  -26.280 -4.828 -3.841 0.767  C23 VDJ 11 
VDJ C24 C12 C 0 1 N N N N N N -6.946  -6.571  -25.536 -4.838 -3.818 -0.778 C24 VDJ 12 
VDJ C26 C13 C 0 1 N N R N N N -7.938  -9.119  -21.961 -4.126 1.027  -1.898 C26 VDJ 13 
VDJ S   S1  S 0 1 N Y N N N N -8.769  -8.480  -20.492 -4.960 1.626  -0.403 S   VDJ 14 
VDJ C02 C14 C 0 1 N N N N N N -14.030 -3.295  -31.144 8.425  -0.112 -0.707 C02 VDJ 15 
VDJ C04 C15 C 0 1 N N N N N N -14.679 -3.970  -29.898 8.267  0.481  0.694  C04 VDJ 16 
VDJ C05 C16 C 0 1 N N N N N N -13.857 -5.148  -29.376 6.948  0.004  1.305  C05 VDJ 17 
VDJ C06 C17 C 0 1 N N N N N N -12.331 -4.916  -29.340 5.783  0.461  0.424  C06 VDJ 18 
VDJ C07 C18 C 0 1 N N N N N N -11.793 -5.354  -27.965 4.464  -0.016 1.034  C07 VDJ 19 
VDJ C09 C19 C 0 1 N N N N N N -12.097 -6.832  -26.190 2.114  0.188  0.673  C09 VDJ 20 
VDJ C30 C20 C 0 1 N N N N N N -12.037 -3.459  -29.593 5.941  -0.132 -0.978 C30 VDJ 21 
VDJ C31 C21 C 0 1 N N N N N N -12.535 -2.968  -30.924 7.260  0.345  -1.588 C31 VDJ 22 
VDJ F01 F1  F 0 1 N N N N N N -14.167 -4.094  -32.232 9.631  0.324  -1.266 F01 VDJ 23 
VDJ F03 F2  F 0 1 N N N N N N -14.720 -2.204  -31.522 8.427  -1.509 -0.625 F03 VDJ 24 
VDJ N10 N1  N 0 1 N N N N N N -12.467 -8.071  -25.778 1.039  0.649  0.003  N10 VDJ 25 
VDJ N17 N2  N 0 1 N N N N N N -9.800  -8.245  -23.303 -2.529 -0.132 -0.453 N17 VDJ 26 
VDJ N22 N3  N 0 1 N N N N N N -6.538  -4.248  -25.306 -3.504 -3.343 1.157  N22 VDJ 27 
VDJ O08 O1  O 0 1 N N N N N N -12.427 -6.511  -27.464 3.354  0.516  0.265  O08 VDJ 28 
VDJ O25 O2  O 0 1 N N N N N N -7.558  -3.826  -23.317 -1.805 -2.191 0.192  O25 VDJ 29 
VDJ O27 O3  O 0 1 N N N N N N -8.478  -10.395 -22.251 -3.157 1.988  -2.320 O27 VDJ 30 
VDJ O28 O4  O 0 1 N N N N N N -9.847  -9.008  -25.430 -0.932 0.709  -1.743 O28 VDJ 31 
VDJ O29 O5  O 0 1 N N N N N N -11.493 -6.034  -25.477 1.963  -0.524 1.646  O29 VDJ 32 
VDJ H1  H1  H 0 1 N N N N N N -12.368 -7.943  -23.679 -0.319 -0.571 1.035  H1  VDJ 33 
VDJ H2  H2  H 0 1 N N N N N N -12.390 -10.636 -25.138 0.067  1.653  2.209  H2  VDJ 34 
VDJ H3  H3  H 0 1 N N N N N N -12.120 -10.459 -23.371 -0.880 2.422  0.913  H3  VDJ 35 
VDJ H4  H4  H 0 1 N N N N N N -14.608 -9.430  -24.808 -2.773 0.846  1.446  H4  VDJ 36 
VDJ H5  H5  H 0 1 N N N N N N -15.817 -11.393 -23.895 -2.690 -0.424 3.543  H5  VDJ 37 
VDJ H6  H6  H 0 1 N N N N N N -14.540 -11.892 -25.055 -1.332 -0.912 2.501  H6  VDJ 38 
VDJ H7  H7  H 0 1 N N N N N N -14.267 -12.069 -23.289 -1.051 0.183  3.876  H7  VDJ 39 
VDJ H8  H8  H 0 1 N N N N N N -15.593 -9.454  -22.533 -2.698 3.140  2.385  H8  VDJ 40 
VDJ H9  H9  H 0 1 N N N N N N -14.022 -10.007 -21.861 -3.434 2.001  3.538  H9  VDJ 41 
VDJ H10 H10 H 0 1 N N N N N N -14.152 -8.385  -22.622 -1.753 2.542  3.770  H10 VDJ 42 
VDJ H11 H11 H 0 1 N N N N N N -7.921  -8.727  -24.086 -2.855 -0.617 -2.467 H11 VDJ 43 
VDJ H12 H12 H 0 1 N N N N N N -6.677  -6.896  -22.779 -4.994 -1.092 -0.342 H12 VDJ 44 
VDJ H13 H13 H 0 1 N N N N N N -8.284  -6.251  -22.303 -5.202 -1.428 -2.078 H13 VDJ 45 
VDJ H14 H14 H 0 1 N N N N N N -8.863  -6.018  -24.734 -3.217 -2.976 -1.973 H14 VDJ 46 
VDJ H15 H15 H 0 1 N N N N N N -5.351  -5.484  -26.562 -5.608 -3.187 1.158  H15 VDJ 47 
VDJ H16 H16 H 0 1 N N N N N N -7.000  -5.133  -27.182 -4.971 -4.858 1.130  H16 VDJ 48 
VDJ H17 H17 H 0 1 N N N N N N -7.547  -7.193  -26.216 -5.821 -3.539 -1.158 H17 VDJ 49 
VDJ H18 H18 H 0 1 N N N N N N -6.115  -7.168  -25.131 -4.523 -4.780 -1.184 H18 VDJ 50 
VDJ H19 H19 H 0 1 N N N N N N -6.851  -9.111  -21.790 -4.861 0.880  -2.690 H19 VDJ 51 
VDJ H21 H21 H 0 1 N N N N N N -14.769 -3.221  -29.098 9.097  0.156  1.322  H21 VDJ 52 
VDJ H22 H22 H 0 1 N N N N N N -15.680 -4.333  -30.175 8.265  1.569  0.630  H22 VDJ 53 
VDJ H23 H23 H 0 1 N N N N N N -14.192 -5.371  -28.352 6.950  -1.084 1.369  H23 VDJ 54 
VDJ H24 H24 H 0 1 N N N N N N -14.055 -6.015  -30.023 6.836  0.427  2.303  H24 VDJ 55 
VDJ H25 H25 H 0 1 N N N N N N -11.857 -5.527  -30.122 5.781  1.549  0.359  H25 VDJ 56 
VDJ H26 H26 H 0 1 N N N N N N -10.716 -5.558  -28.060 4.429  -1.105 1.017  H26 VDJ 57 
VDJ H27 H27 H 0 1 N N N N N N -11.949 -4.532  -27.250 4.393  0.334  2.064  H27 VDJ 58 
VDJ H28 H28 H 0 1 N N N N N N -10.948 -3.312  -29.553 5.943  -1.221 -0.913 H28 VDJ 59 
VDJ H29 H29 H 0 1 N N N N N N -12.516 -2.865  -28.801 5.111  0.193  -1.605 H29 VDJ 60 
VDJ H30 H30 H 0 1 N N N N N N -11.947 -3.446  -31.721 7.258  1.433  -1.653 H30 VDJ 61 
VDJ H31 H31 H 0 1 N N N N N N -12.400 -1.877  -30.973 7.372  -0.078 -2.587 H31 VDJ 62 
VDJ H32 H32 H 0 1 N N N N N N -13.056 -8.630  -26.362 1.159  1.157  -0.815 H32 VDJ 63 
VDJ H33 H33 H 0 1 N N N N N N -10.338 -7.936  -22.519 -2.833 -0.353 0.442  H33 VDJ 64 
VDJ H34 H34 H 0 1 N N N N N N -6.104  -3.353  -25.410 -3.113 -3.459 2.037  H34 VDJ 65 
VDJ H35 H35 H 0 1 N N N N N N -8.273  -10.995 -21.543 -2.470 2.168  -1.664 H35 VDJ 66 
VDJ O1  O6  O 0 1 N Y N N N N -8.030  -9.498  -19.188 -5.607 2.937  -0.829 O1  VDJ 67 
VDJ O2  O7  O 0 1 N Y N N N N ?       ?       ?       -6.057 0.785  -0.073 O2  VDJ 68 
VDJ O3  O8  O 0 1 N Y N N N N ?       ?       ?       -4.008 2.009  0.580  O3  VDJ 69 
VDJ H20 H20 H 0 1 N N N N N N -8.396  -9.250  -18.347 -6.097 3.381  -0.123 H20 VDJ 70 
# 
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 
VDJ F01 C02 SING N N 1  
VDJ F03 C02 SING N N 2  
VDJ C02 C31 SING N N 3  
VDJ C02 C04 SING N N 4  
VDJ C31 C30 SING N N 5  
VDJ C04 C05 SING N N 6  
VDJ C30 C06 SING N N 7  
VDJ C05 C06 SING N N 8  
VDJ C06 C07 SING N N 9  
VDJ C07 O08 SING N N 10 
VDJ O08 C09 SING N N 11 
VDJ C23 C24 SING N N 12 
VDJ C23 N22 SING N N 13 
VDJ C09 N10 SING N N 14 
VDJ C09 O29 DOUB N N 15 
VDJ N10 C11 SING N N 16 
VDJ C24 C20 SING N N 17 
VDJ O28 C16 DOUB N N 18 
VDJ N22 C21 SING N N 19 
VDJ C11 C16 SING N N 20 
VDJ C11 C12 SING N N 21 
VDJ C16 N17 SING N N 22 
VDJ C20 C21 SING N N 23 
VDJ C20 C19 SING N N 24 
VDJ C12 C13 SING N N 25 
VDJ C21 O25 DOUB N N 26 
VDJ C14 C13 SING N N 27 
VDJ C13 C15 SING N N 28 
VDJ N17 C18 SING N N 29 
VDJ C18 C19 SING N N 30 
VDJ C18 C26 SING N N 31 
VDJ O27 C26 SING N N 32 
VDJ C26 S   SING N N 33 
VDJ C11 H1  SING N N 34 
VDJ C12 H2  SING N N 35 
VDJ C12 H3  SING N N 36 
VDJ C13 H4  SING N N 37 
VDJ C14 H5  SING N N 38 
VDJ C14 H6  SING N N 39 
VDJ C14 H7  SING N N 40 
VDJ C15 H8  SING N N 41 
VDJ C15 H9  SING N N 42 
VDJ C15 H10 SING N N 43 
VDJ C18 H11 SING N N 44 
VDJ C19 H12 SING N N 45 
VDJ C19 H13 SING N N 46 
VDJ C20 H14 SING N N 47 
VDJ C23 H15 SING N N 48 
VDJ C23 H16 SING N N 49 
VDJ C24 H17 SING N N 50 
VDJ C24 H18 SING N N 51 
VDJ C26 H19 SING N N 52 
VDJ C04 H21 SING N N 53 
VDJ C04 H22 SING N N 54 
VDJ C05 H23 SING N N 55 
VDJ C05 H24 SING N N 56 
VDJ C06 H25 SING N N 57 
VDJ C07 H26 SING N N 58 
VDJ C07 H27 SING N N 59 
VDJ C30 H28 SING N N 60 
VDJ C30 H29 SING N N 61 
VDJ C31 H30 SING N N 62 
VDJ C31 H31 SING N N 63 
VDJ N10 H32 SING N N 64 
VDJ N17 H33 SING N N 65 
VDJ N22 H34 SING N N 66 
VDJ O27 H35 SING N N 67 
VDJ S   O1  SING N N 68 
VDJ S   O2  DOUB N N 69 
VDJ S   O3  DOUB N N 70 
VDJ O1  H20 SING N N 71 
# 
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 
VDJ SMILES           ACDLabs              12.01 "C(C(NC(CC1C(=O)NCC1)C(S(O)(=O)=O)O)=O)(CC(C)C)NC(=O)OCC2CCC(CC2)(F)F"                                                                                                                                                    
VDJ InChI            InChI                1.03  "InChI=1S/C21H35F2N3O8S/c1-12(2)9-15(26-20(30)34-11-13-3-6-21(22,23)7-4-13)18(28)25-16(19(29)35(31,32)33)10-14-5-8-24-17(14)27/h12-16,19,29H,3-11H2,1-2H3,(H,24,27)(H,25,28)(H,26,30)(H,31,32,33)/t14-,15-,16-,19+/m0/s1" 
VDJ InChIKey         InChI                1.03  BHZBRFONZANPNK-IUVQAAGXSA-N                                                                                                                                                                                               
VDJ SMILES_CANONICAL CACTVS               3.385 "CC(C)C[C@H](NC(=O)OCC1CCC(F)(F)CC1)C(=O)N[C@@H](C[C@@H]2CCNC2=O)[C@H](O)[S](O)(=O)=O"                                                                                                                                    
VDJ SMILES           CACTVS               3.385 "CC(C)C[CH](NC(=O)OCC1CCC(F)(F)CC1)C(=O)N[CH](C[CH]2CCNC2=O)[CH](O)[S](O)(=O)=O"                                                                                                                                          
VDJ SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC(C)C[C@@H](C(=O)N[C@@H](C[C@@H]1CCNC1=O)[C@H](O)S(=O)(=O)O)NC(=O)OCC2CCC(CC2)(F)F"                                                                                                                                     
VDJ SMILES           "OpenEye OEToolkits" 2.0.7 "CC(C)CC(C(=O)NC(CC1CCNC1=O)C(O)S(=O)(=O)O)NC(=O)OCC2CCC(CC2)(F)F"                                                                                                                                                        
# 
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 
VDJ "SYSTEMATIC NAME" ACDLabs              12.01 "(1R,2S)-2-[(N-{[(4,4-difluorocyclohexyl)methoxy]carbonyl}-L-leucyl)amino]-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid"                                                
VDJ "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(1~{R},2~{S})-2-[[(2~{S})-2-[[4,4-bis(fluoranyl)cyclohexyl]methoxycarbonylamino]-4-methyl-pentanoyl]amino]-1-oxidanyl-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propane-1-sulfonic acid" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
VDJ "Create component" 2020-07-30 RCSB 
VDJ "Initial release"  2020-08-12 RCSB 
VDJ "Modify PCM"       2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            VDJ 
_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               C26 
_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      ? 
# 
