data_SD6
# 
_chem_comp.id                                    SD6 
_chem_comp.name                                  "[(1~{R},2~{R})-2-(cyclohexylmethyl)cyclopropyl]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                               "C25 H44 N3 O8 S" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    1 
_chem_comp.pdbx_initial_date                     2022-06-29 
_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                        546.697 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     SD6 
_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        8DGY 
_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 
SD6 S1  S1  S 1 1 N Y N N N N -18.881 28.697 5.162  5.915   2.436  0.414  S1  SD6 1  
SD6 C14 C1  C 0 1 N N N N N N -20.306 24.040 7.591  3.331   -2.593 1.051  C14 SD6 2  
SD6 C16 C2  C 0 1 N N N N N N -22.602 23.519 7.699  5.013   -4.188 1.198  C16 SD6 3  
SD6 C17 C3  C 0 1 N N N N N N -22.444 24.696 6.731  5.423   -3.054 2.163  C17 SD6 4  
SD6 C19 C4  C 0 1 N N R N N N -20.643 28.637 5.487  5.129   1.139  -0.581 C19 SD6 5  
SD6 C13 C5  C 0 1 N N S N N N -20.930 24.875 6.494  4.507   -1.898 1.700  C13 SD6 6  
SD6 C12 C6  C 0 1 N N N N N N -20.439 26.317 6.501  5.233   -1.013 0.685  C12 SD6 7  
SD6 C11 C7  C 0 1 N N S N N N -21.087 27.167 5.384  4.355   0.191  0.337  C11 SD6 8  
SD6 C02 C8  C 0 1 N N N N N N -21.511 23.175 2.574  -1.602  -0.031 -0.171 C02 SD6 9  
SD6 C04 C9  C 0 1 N N S N N N -20.984 25.462 1.934  0.733   -0.076 -0.867 C04 SD6 10 
SD6 C05 C10 C 0 1 N N N N N N -21.235 26.423 0.780  0.729   0.184  -2.374 C05 SD6 11 
SD6 C06 C11 C 0 1 N N N N N N -20.619 25.951 -0.539 1.874   -0.591 -3.029 C06 SD6 12 
SD6 C07 C12 C 0 1 N N N N N N -19.104 25.805 -0.435 1.614   -2.093 -2.899 C07 SD6 13 
SD6 C08 C13 C 0 1 N N N N N N -20.912 26.900 -1.689 1.964   -0.214 -4.510 C08 SD6 14 
SD6 C09 C14 C 0 1 N N N N N N -21.543 26.024 3.239  2.010   0.456  -0.269 C09 SD6 15 
SD6 C23 C15 C 0 1 N N N N N N -22.312 21.042 3.120  -3.927  -0.116 0.357  C23 SD6 16 
SD6 C24 C16 C 0 1 N N R N N N -22.966 19.840 2.520  -5.030  0.786  0.914  C24 SD6 17 
SD6 C25 C17 C 0 1 N N S N N N -22.223 19.040 1.436  -6.453  0.226  0.945  C25 SD6 18 
SD6 C26 C18 C 0 1 N N N N N N -22.970 18.595 0.204  -7.603  1.203  0.691  C26 SD6 19 
SD6 C27 C19 C 0 1 N N N N N N -23.182 17.090 0.074  -8.925  0.434  0.640  C27 SD6 20 
SD6 C28 C20 C 0 1 N N N N N N -24.225 16.672 -0.961 -10.085 1.422  0.510  C28 SD6 21 
SD6 C29 C21 C 0 1 N N N N N N -24.414 15.179 -0.993 -11.407 0.653  0.459  C29 SD6 22 
SD6 C30 C22 C 0 1 N N N N N N -23.109 14.463 -1.303 -11.402 -0.289 -0.747 C30 SD6 23 
SD6 C31 C23 C 0 1 N N N N N N -22.033 14.868 -0.315 -10.241 -1.277 -0.618 C31 SD6 24 
SD6 C32 C24 C 0 1 N N N N N N -21.872 16.377 -0.255 -8.920  -0.508 -0.567 C32 SD6 25 
SD6 C33 C25 C 0 1 N N N N N N -22.487 18.433 2.807  -5.666  0.385  2.247  C33 SD6 26 
SD6 N03 N1  N 0 1 N N N N N N -21.686 24.200 1.680  -0.412  0.598  -0.251 N03 SD6 27 
SD6 N10 N2  N 0 1 N N N N N N -20.691 26.626 4.117  3.144   -0.269 -0.346 N10 SD6 28 
SD6 N15 N3  N 0 1 N N N N N N -21.266 23.305 8.243  3.638   -3.875 0.789  N15 SD6 29 
SD6 O01 O1  O 0 1 N N N N N N -20.736 23.126 3.514  -1.701  -1.190 -0.524 O01 SD6 30 
SD6 O18 O2  O 0 1 N N N N N N -19.120 23.981 7.921  2.263   -2.071 0.808  O18 SD6 31 
SD6 O20 O3  O 0 1 N N N N N N -21.292 29.351 4.467  6.133   0.405  -1.285 O20 SD6 32 
SD6 O21 O4  O 0 1 N N N N N N -22.766 25.913 3.526  2.018   1.536  0.282  O21 SD6 33 
SD6 O22 O5  O 0 1 N N N N N N -22.343 22.183 2.281  -2.680  0.624  0.299  O22 SD6 34 
SD6 H2  H2  H 0 1 N N N N N N -23.312 23.769 8.501  5.670   -4.203 0.329  H2  SD6 35 
SD6 H3  H3  H 0 1 N N N N N N -22.952 22.623 7.166  5.044   -5.149 1.711  H3  SD6 36 
SD6 H4  H4  H 0 1 N N N N N N -22.869 25.609 7.172  5.214   -3.328 3.197  H4  SD6 37 
SD6 H5  H5  H 0 1 N N N N N N -22.953 24.476 5.781  6.474   -2.795 2.035  H5  SD6 38 
SD6 H6  H6  H 0 1 N N N N N N -20.823 29.043 6.493  4.443   1.594  -1.295 H6  SD6 39 
SD6 H7  H7  H 0 1 N N N N N N -20.677 24.425 5.523  4.177   -1.305 2.554  H7  SD6 40 
SD6 H8  H8  H 0 1 N N N N N N -19.348 26.319 6.359  6.174   -0.665 1.112  H8  SD6 41 
SD6 H9  H9  H 0 1 N N N N N N -20.683 26.768 7.474  5.436   -1.588 -0.219 H9  SD6 42 
SD6 H10 H10 H 0 1 N N N N N N -22.180 27.119 5.493  4.080   0.715  1.252  H10 SD6 43 
SD6 H11 H11 H 0 1 N N N N N N -19.903 25.286 2.041  0.665   -1.149 -0.683 H11 SD6 44 
SD6 H12 H12 H 0 1 N N N N N N -20.802 27.401 1.038  -0.221  -0.145 -2.797 H12 SD6 45 
SD6 H13 H13 H 0 1 N N N N N N -22.321 26.528 0.641  0.859   1.250  -2.559 H13 SD6 46 
SD6 H14 H14 H 0 1 N N N N N N -21.045 24.967 -0.785 2.812   -0.340 -2.533 H14 SD6 47 
SD6 H15 H15 H 0 1 N N N N N N -18.857 25.122 0.391  0.709   -2.353 -3.449 H15 SD6 48 
SD6 H16 H16 H 0 1 N N N N N N -18.709 25.398 -1.378 2.460   -2.645 -3.309 H16 SD6 49 
SD6 H17 H17 H 0 1 N N N N N N -18.653 26.790 -0.244 1.487   -2.350 -1.848 H17 SD6 50 
SD6 H18 H18 H 0 1 N N N N N N -22.000 27.028 -1.792 1.026   -0.465 -5.005 H18 SD6 51 
SD6 H19 H19 H 0 1 N N N N N N -20.446 27.876 -1.487 2.149   0.856  -4.602 H19 SD6 52 
SD6 H20 H20 H 0 1 N N N N N N -20.502 26.484 -2.621 2.780   -0.766 -4.976 H20 SD6 53 
SD6 H21 H21 H 0 1 N N N N N N -21.261 20.796 3.334  -3.806  -0.984 1.006  H21 SD6 54 
SD6 H22 H22 H 0 1 N N N N N N -22.829 21.287 4.059  -4.200  -0.447 -0.645 H22 SD6 55 
SD6 H23 H23 H 0 1 N N N N N N -24.049 19.933 2.352  -4.912  1.851  0.714  H23 SD6 56 
SD6 H24 H24 H 0 1 N N N N N N -21.184 19.358 1.263  -6.604  -0.786 0.568  H24 SD6 57 
SD6 H25 H25 H 0 1 N N N N N N -22.405 18.935 -0.676 -7.641  1.937  1.496  H25 SD6 58 
SD6 H26 H26 H 0 1 N N N N N N -23.959 19.077 0.214  -7.443  1.714  -0.259 H26 SD6 59 
SD6 H27 H27 H 0 1 N N N N N N -23.522 16.719 1.052  -9.042  -0.148 1.554  H27 SD6 60 
SD6 H28 H28 H 0 1 N N N N N N -23.896 17.011 -1.955 -10.089 2.093  1.370  H28 SD6 61 
SD6 H29 H29 H 0 1 N N N N N N -25.185 17.147 -0.711 -9.968  2.003  -0.404 H29 SD6 62 
SD6 H30 H30 H 0 1 N N N N N N -25.153 14.928 -1.768 -11.525 0.071  1.373  H30 SD6 63 
SD6 H31 H31 H 0 1 N N N N N N -24.783 14.843 -0.012 -12.234 1.357  0.367  H31 SD6 64 
SD6 H32 H32 H 0 1 N N N N N N -23.268 13.376 -1.239 -12.344 -0.837 -0.784 H32 SD6 65 
SD6 H33 H33 H 0 1 N N N N N N -22.784 14.727 -2.320 -11.284 0.292  -1.661 H33 SD6 66 
SD6 H34 H34 H 0 1 N N N N N N -22.307 14.498 0.684  -10.359 -1.859 0.296  H34 SD6 67 
SD6 H35 H35 H 0 1 N N N N N N -21.077 14.419 -0.623 -10.238 -1.948 -1.477 H35 SD6 68 
SD6 H36 H36 H 0 1 N N N N N N -21.132 16.623 0.521  -8.802  0.074  -1.481 H36 SD6 69 
SD6 H37 H37 H 0 1 N N N N N N -21.512 16.733 -1.232 -8.093  -1.212 -0.475 H37 SD6 70 
SD6 H38 H38 H 0 1 N N N N N N -23.217 17.617 2.913  -5.298  -0.522 2.727  H38 SD6 71 
SD6 H39 H39 H 0 1 N N N N N N -21.652 18.271 3.504  -5.967  1.186  2.923  H39 SD6 72 
SD6 H40 H40 H 0 1 N N N N N N -22.275 24.090 0.879  -0.315  1.497  0.099  H40 SD6 73 
SD6 H41 H41 H 0 1 N N N N N N -19.727 26.695 3.860  3.157   -1.096 -0.853 H41 SD6 74 
SD6 H42 H42 H 0 1 N N N N N N -21.070 22.690 9.007  3.030   -4.511 0.382  H42 SD6 75 
SD6 H43 H43 H 0 1 N N N N N N -22.230 29.335 4.616  5.784   -0.307 -1.839 H43 SD6 76 
SD6 O1  O6  O 0 1 N Y N N N N ?       ?      ?      6.764   3.311  -0.317 O1  SD6 77 
SD6 O2  O7  O 0 1 N Y N N N N ?       ?      ?      4.820   3.267  1.068  O2  SD6 78 
SD6 O3  O8  O 0 1 N Y N N N N ?       ?      ?      6.740   1.770  1.505  O3  SD6 79 
SD6 H1  H1  H 0 1 N Y N N N N ?       ?      ?      5.151   3.988  1.621  H1  SD6 80 
SD6 H44 H44 H 0 1 N Y N N N N ?       ?      ?      6.239   1.151  2.055  H44 SD6 81 
# 
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 
SD6 C08 C06 SING N N 1  
SD6 C30 C29 SING N N 2  
SD6 C30 C31 SING N N 3  
SD6 C29 C28 SING N N 4  
SD6 C28 C27 SING N N 5  
SD6 C06 C07 SING N N 6  
SD6 C06 C05 SING N N 7  
SD6 C31 C32 SING N N 8  
SD6 C32 C27 SING N N 9  
SD6 C27 C26 SING N N 10 
SD6 C26 C25 SING N N 11 
SD6 C05 C04 SING N N 12 
SD6 C25 C24 SING N N 13 
SD6 C25 C33 SING N N 14 
SD6 N03 C04 SING N N 15 
SD6 N03 C02 SING N N 16 
SD6 C04 C09 SING N N 17 
SD6 O22 C02 SING N N 18 
SD6 O22 C23 SING N N 19 
SD6 C24 C33 SING N N 20 
SD6 C24 C23 SING N N 21 
SD6 C02 O01 DOUB N N 22 
SD6 C09 O21 DOUB N N 23 
SD6 C09 N10 SING N N 24 
SD6 N10 C11 SING N N 25 
SD6 O20 C19 SING N N 26 
SD6 S1  C19 SING N N 27 
SD6 C11 C19 SING N N 28 
SD6 C11 C12 SING N N 29 
SD6 C13 C12 SING N N 30 
SD6 C13 C17 SING N N 31 
SD6 C13 C14 SING N N 32 
SD6 C17 C16 SING N N 33 
SD6 C14 O18 DOUB N N 34 
SD6 C14 N15 SING N N 35 
SD6 C16 N15 SING N N 36 
SD6 C16 H2  SING N N 37 
SD6 C16 H3  SING N N 38 
SD6 C17 H4  SING N N 39 
SD6 C17 H5  SING N N 40 
SD6 C19 H6  SING N N 41 
SD6 C13 H7  SING N N 42 
SD6 C12 H8  SING N N 43 
SD6 C12 H9  SING N N 44 
SD6 C11 H10 SING N N 45 
SD6 C04 H11 SING N N 46 
SD6 C05 H12 SING N N 47 
SD6 C05 H13 SING N N 48 
SD6 C06 H14 SING N N 49 
SD6 C07 H15 SING N N 50 
SD6 C07 H16 SING N N 51 
SD6 C07 H17 SING N N 52 
SD6 C08 H18 SING N N 53 
SD6 C08 H19 SING N N 54 
SD6 C08 H20 SING N N 55 
SD6 C23 H21 SING N N 56 
SD6 C23 H22 SING N N 57 
SD6 C24 H23 SING N N 58 
SD6 C25 H24 SING N N 59 
SD6 C26 H25 SING N N 60 
SD6 C26 H26 SING N N 61 
SD6 C27 H27 SING N N 62 
SD6 C28 H28 SING N N 63 
SD6 C28 H29 SING N N 64 
SD6 C29 H30 SING N N 65 
SD6 C29 H31 SING N N 66 
SD6 C30 H32 SING N N 67 
SD6 C30 H33 SING N N 68 
SD6 C31 H34 SING N N 69 
SD6 C31 H35 SING N N 70 
SD6 C32 H36 SING N N 71 
SD6 C32 H37 SING N N 72 
SD6 C33 H38 SING N N 73 
SD6 C33 H39 SING N N 74 
SD6 N03 H40 SING N N 75 
SD6 N10 H41 SING N N 76 
SD6 N15 H42 SING N N 77 
SD6 O20 H43 SING N N 78 
SD6 S1  O1  DOUB N N 79 
SD6 S1  O2  SING N N 80 
SD6 S1  O3  SING N N 81 
SD6 O2  H1  SING N N 82 
SD6 O3  H44 SING N N 83 
# 
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 
SD6 InChI            InChI                1.06  "InChI=1S/C25H43N3O8S/c1-15(2)10-20(28-25(32)36-14-19-12-18(19)11-16-6-4-3-5-7-16)23(30)27-21(24(31)37(33,34)35)13-17-8-9-26-22(17)29/h15-21,24,31H,3-14H2,1-2H3,(H4-,26,27,28,29,30,32,33,34,35)/p+1/t17-,18+,19-,20-,21-,24+/m0/s1" 
SD6 InChIKey         InChI                1.06  PBWNADCYPGWHEB-UEYTUVLBSA-O                                                                                                                                                                                                           
SD6 SMILES_CANONICAL CACTVS               3.385 "CC(C)C[C@H](NC(=O)OC[C@@H]1C[C@H]1CC2CCCCC2)C(=O)N[C@@H](C[C@@H]3CCNC3=O)[C@H](O)[S+](O)(O)=O"                                                                                                                                       
SD6 SMILES           CACTVS               3.385 "CC(C)C[CH](NC(=O)OC[CH]1C[CH]1CC2CCCCC2)C(=O)N[CH](C[CH]3CCNC3=O)[CH](O)[S+](O)(O)=O"                                                                                                                                                
SD6 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)OC[C@@H]2C[C@H]2CC3CCCCC3"                                                                                                                                      
SD6 SMILES           "OpenEye OEToolkits" 2.0.7 "CC(C)CC(C(=O)NC(CC1CCNC1=O)C(O)[S+](=O)(O)O)NC(=O)OCC2CC2CC3CCCCC3"                                                                                                                                                                  
# 
_pdbx_chem_comp_identifier.comp_id           SD6 
_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        "[(1~{R},2~{R})-2-(cyclohexylmethyl)cyclopropyl]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" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
SD6 "Create component" 2022-06-29 RCSB 
SD6 "Initial release"  2022-07-06 RCSB 
SD6 "Modify PCM"       2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            SD6 
_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               C19 
_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      ? 
# 
