data_D5R
# 
_chem_comp.id                                    D5R 
_chem_comp.name                                  "~{O}3-~{tert}-butyl ~{O}1-methyl (1~{S},3~{R})-1-methyl-4-oxidanylidene-cyclohexane-1,3-dicarboxylate" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C14 H22 O5" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-07-17 
_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                        270.321 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     D5R 
_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        8PT5 
_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 
D5R C1  C1  C 0 1 N N N N N N -24.756 -30.654 21.853 -0.149 1.236  0.835  C1  D5R 1  
D5R C2  C2  C 0 1 N N R N N N -23.745 -30.579 20.748 0.044  -0.013 0.004  C2  D5R 2  
D5R C3  C3  C 0 1 N N N N N N -22.728 -31.714 20.878 -0.795 0.115  -1.271 C3  D5R 3  
D5R C4  C4  C 0 1 N N S N N N -23.266 -33.057 21.377 -2.250 0.403  -0.895 C4  D5R 4  
D5R C5  C5  C 0 1 N N N N N N -24.315 -32.950 22.477 -2.344 1.751  -0.180 C5  D5R 5  
D5R C6  C6  C 0 1 N N N N N N -25.424 -31.970 22.145 -1.562 1.685  1.136  C6  D5R 6  
D5R C20 C7  C 0 1 N N N N N N -23.915 -27.607 17.142 4.216  0.817  -0.621 C20 D5R 7  
D5R C7  C8  C 0 1 N N N N N N -23.800 -33.898 20.222 -3.105 0.441  -2.164 C7  D5R 8  
D5R C14 C9  C 0 1 N N N N N N -22.089 -33.770 21.983 -2.756 -0.685 0.017  C14 D5R 9  
D5R C16 C10 C 0 1 N N N N N N -24.398 -30.589 19.391 1.499  -0.157 -0.361 C16 D5R 10 
D5R C18 C11 C 0 1 N N N N N N -25.509 -27.971 19.011 4.706  -0.554 1.410  C18 D5R 11 
D5R C15 C12 C 0 1 N N N N N N -21.991 -36.264 22.208 -4.434 -1.723 1.353  C15 D5R 12 
D5R O3  O1  O 0 1 N N N N N N -23.940 -29.663 18.365 2.424  -0.285 0.604  O3  D5R 13 
D5R C17 C13 C 0 1 N N N N N N -24.785 -28.634 17.852 3.806  -0.420 0.180  C17 D5R 14 
D5R C19 C14 C 0 1 N N N N N N -25.792 -29.210 16.866 3.951  -1.666 -0.696 C19 D5R 15 
D5R O4  O2  O 0 1 N N N N N N -25.026 -29.667 22.510 0.799  1.857  1.251  O4  D5R 16 
D5R O1  O3  O 0 1 N N N N N N -21.480 -33.246 22.903 -2.027 -1.595 0.334  O1  D5R 17 
D5R O2  O4  O 0 1 N N N N N N -25.302 -31.366 19.129 1.834  -0.158 -1.522 O2  D5R 18 
D5R O   O5  O 0 1 N N N N N N -21.661 -35.072 21.492 -4.015 -0.642 0.479  O   D5R 19 
D5R H1  H1  H 0 1 N N N N N N -23.199 -29.630 20.852 -0.282 -0.884 0.571  H1  D5R 20 
D5R H2  H2  H 0 1 N N N N N N -22.283 -31.880 19.886 -0.409 0.933  -1.881 H2  D5R 21 
D5R H3  H3  H 0 1 N N N N N N -21.947 -31.385 21.580 -0.743 -0.816 -1.836 H3  D5R 22 
D5R H4  H4  H 0 1 N N N N N N -24.761 -33.943 22.634 -1.921 2.530  -0.815 H4  D5R 23 
D5R H5  H5  H 0 1 N N N N N N -23.820 -32.619 23.402 -3.389 1.980  0.029  H5  D5R 24 
D5R H6  H6  H 0 1 N N N N N N -26.109 -31.867 22.999 -2.039 0.968  1.805  H6  D5R 25 
D5R H7  H7  H 0 1 N N N N N N -25.985 -32.315 21.264 -1.542 2.669  1.605  H7  D5R 26 
D5R H8  H8  H 0 1 N N N N N N -23.186 -27.189 17.852 4.113  1.704  0.002  H8  D5R 27 
D5R H9  H9  H 0 1 N N N N N N -23.381 -28.091 16.311 5.254  0.715  -0.940 H9  D5R 28 
D5R H10 H10 H 0 1 N N N N N N -24.549 -26.798 16.749 3.575  0.912  -1.497 H10 D5R 29 
D5R H11 H11 H 0 1 N N N N N N -24.179 -34.855 20.609 -3.044 -0.521 -2.672 H11 D5R 30 
D5R H12 H12 H 0 1 N N N N N N -24.616 -33.356 19.721 -4.142 0.646  -1.896 H12 D5R 31 
D5R H13 H13 H 0 1 N N N N N N -22.990 -34.089 19.502 -2.739 1.225  -2.825 H13 D5R 32 
D5R H14 H14 H 0 1 N N N N N N -24.773 -27.559 19.716 4.603  0.334  2.033  H14 D5R 33 
D5R H15 H15 H 0 1 N N N N N N -26.145 -27.159 18.629 4.414  -1.435 1.980  H15 D5R 34 
D5R H16 H16 H 0 1 N N N N N N -26.134 -28.715 19.527 5.744  -0.655 1.091  H16 D5R 35 
D5R H17 H17 H 0 1 N N N N N N -21.580 -37.136 21.678 -4.348 -2.672 0.824  H17 D5R 36 
D5R H18 H18 H 0 1 N N N N N N -21.563 -36.214 23.220 -3.799 -1.741 2.238  H18 D5R 37 
D5R H19 H19 H 0 1 N N N N N N -23.085 -36.359 22.277 -5.470 -1.566 1.653  H19 D5R 38 
D5R H20 H20 H 0 1 N N N N N N -26.422 -29.953 17.377 4.988  -1.768 -1.015 H20 D5R 39 
D5R H21 H21 H 0 1 N N N N N N -26.425 -28.400 16.473 3.658  -2.548 -0.125 H21 D5R 40 
D5R H22 H22 H 0 1 N N N N N N -25.257 -29.693 16.035 3.309  -1.572 -1.572 H22 D5R 41 
# 
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 
D5R C19 C17 SING N N 1  
D5R C20 C17 SING N N 2  
D5R C17 O3  SING N N 3  
D5R C17 C18 SING N N 4  
D5R O3  C16 SING N N 5  
D5R O2  C16 DOUB N N 6  
D5R C16 C2  SING N N 7  
D5R C7  C4  SING N N 8  
D5R C2  C3  SING N N 9  
D5R C2  C1  SING N N 10 
D5R C3  C4  SING N N 11 
D5R C4  C14 SING N N 12 
D5R C4  C5  SING N N 13 
D5R O   C14 SING N N 14 
D5R O   C15 SING N N 15 
D5R C1  C6  SING N N 16 
D5R C1  O4  DOUB N N 17 
D5R C14 O1  DOUB N N 18 
D5R C6  C5  SING N N 19 
D5R C2  H1  SING N N 20 
D5R C3  H2  SING N N 21 
D5R C3  H3  SING N N 22 
D5R C5  H4  SING N N 23 
D5R C5  H5  SING N N 24 
D5R C6  H6  SING N N 25 
D5R C6  H7  SING N N 26 
D5R C20 H8  SING N N 27 
D5R C20 H9  SING N N 28 
D5R C20 H10 SING N N 29 
D5R C7  H11 SING N N 30 
D5R C7  H12 SING N N 31 
D5R C7  H13 SING N N 32 
D5R C18 H14 SING N N 33 
D5R C18 H15 SING N N 34 
D5R C18 H16 SING N N 35 
D5R C15 H17 SING N N 36 
D5R C15 H18 SING N N 37 
D5R C15 H19 SING N N 38 
D5R C19 H20 SING N N 39 
D5R C19 H21 SING N N 40 
D5R C19 H22 SING N N 41 
# 
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 
D5R InChI            InChI                1.06  "InChI=1S/C14H22O5/c1-13(2,3)19-11(16)9-8-14(4,12(17)18-5)7-6-10(9)15/h9H,6-8H2,1-5H3/t9-,14+/m1/s1" 
D5R InChIKey         InChI                1.06  KLZBEQAKBDGOQP-OTYXRUKQSA-N                                                                          
D5R SMILES_CANONICAL CACTVS               3.385 "COC(=O)[C@@]1(C)CCC(=O)[C@@H](C1)C(=O)OC(C)(C)C"                                                    
D5R SMILES           CACTVS               3.385 "COC(=O)[C]1(C)CCC(=O)[CH](C1)C(=O)OC(C)(C)C"                                                        
D5R SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C[C@@]1(CCC(=O)[C@@H](C1)C(=O)OC(C)(C)C)C(=O)OC"                                                    
D5R SMILES           "OpenEye OEToolkits" 2.0.7 "CC1(CCC(=O)C(C1)C(=O)OC(C)(C)C)C(=O)OC"                                                             
# 
_pdbx_chem_comp_identifier.comp_id           D5R 
_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        "~{O}3-~{tert}-butyl ~{O}1-methyl (1~{S},3~{R})-1-methyl-4-oxidanylidene-cyclohexane-1,3-dicarboxylate" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
D5R "Create component" 2023-07-17 PDBE 
D5R "Initial release"  2024-07-24 RCSB 
D5R "Modify PCM"       2024-09-27 PDBE 
# 
loop_
_pdbx_chem_comp_pcm.pcm_id 
_pdbx_chem_comp_pcm.comp_id 
_pdbx_chem_comp_pcm.modified_residue_id 
_pdbx_chem_comp_pcm.type 
_pdbx_chem_comp_pcm.category 
_pdbx_chem_comp_pcm.position 
_pdbx_chem_comp_pcm.polypeptide_position 
_pdbx_chem_comp_pcm.comp_id_linking_atom 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession 
1 D5R HIS None "Covalent chemical modification" "Amino-acid side chain" "Any position" C3 NE2 ? ? 
2 D5R CYS None "Covalent chemical modification" "Amino-acid side chain" "Any position" C3 SG  ? ? 
# 
