data_A1AF4
# 
_chem_comp.id                                    A1AF4 
_chem_comp.name                                  "Golcadomide " 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C28 H30 F N5 O5" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2024-02-27 
_chem_comp.pdbx_modified_date                    2025-10-10 
_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                        535.567 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A1AF4 
_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        9ARM 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
_chem_comp.pdbx_pcm                              ? 
# 
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_n_terminal_atom_flag 
_chem_comp_atom.pdbx_backbone_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 
A1AF4 N1  N1  N 0 1 N N N N N N 111.206 103.629 54.477 -8.731  -0.789 -0.104 N1  A1AF4 1  
A1AF4 C7  C1  C 0 1 N N N N N N 109.934 103.014 54.069 -7.293  -0.917 0.166  C7  A1AF4 2  
A1AF4 C8  C2  C 0 1 N N N N N N 112.062 103.963 53.334 -8.969  -0.332 -1.481 C8  A1AF4 3  
A1AF4 N2  N2  N 0 1 N N N N N N 101.667 106.487 55.997 1.233   1.657  -0.096 N2  A1AF4 4  
A1AF4 C9  C3  C 0 1 N N N N N N 113.415 104.397 53.828 -10.474 -0.156 -1.701 C9  A1AF4 5  
A1AF4 O1  O1  O 0 1 N N N N N N 98.963  106.277 63.543 9.243   -3.748 -0.155 O1  A1AF4 6  
A1AF4 C1  C4  C 0 1 Y N N N N N 104.904 104.854 53.944 -2.590  0.433  1.704  C1  A1AF4 7  
A1AF4 C5  C5  C 0 1 N N N N N N 106.772 103.192 53.644 -4.613  -0.801 0.899  C5  A1AF4 8  
A1AF4 C6  C6  C 0 1 N N N N N N 109.104 103.885 53.107 -6.923  -0.742 1.650  C6  A1AF4 9  
A1AF4 N3  N3  N 0 1 N N N N N N 102.261 108.241 59.976 5.196   -0.228 -0.319 N3  A1AF4 10 
A1AF4 C4  C7  C 0 1 Y N N N N N 103.879 103.443 56.084 -1.990  1.264  -0.865 C4  A1AF4 11 
A1AF4 O4  O2  O 0 1 N N N N N N 103.416 110.239 60.222 7.060   1.031  -0.693 O4  A1AF4 12 
A1AF4 C3  C8  C 0 1 Y N N N N N 105.005 102.987 55.425 -3.101  0.475  -0.635 C3  A1AF4 13 
A1AF4 O3  O3  O 0 1 N N N N N N 101.228 106.395 59.038 3.033   -0.858 0.018  O3  A1AF4 14 
A1AF4 C2  C9  C 0 1 Y N N N N N 105.534 103.684 54.351 -3.401  0.059  0.649  C2  A1AF4 15 
A1AF4 N4  N4  N 0 1 N N N N N N 100.934 106.058 62.491 7.926   -2.306 0.870  N4  A1AF4 16 
A1AF4 N   N5  N 0 1 N N N N N N 107.986 103.884 54.089 -5.775  0.057  1.168  N   A1AF4 17 
A1AF4 C   C10 C 0 1 Y N N N N N 103.787 105.282 54.616 -1.477  1.224  1.474  C   A1AF4 18 
A1AF4 O   O4  O 0 1 N N N N N N 113.310 105.414 54.813 -11.140 -1.389 -1.417 O   A1AF4 19 
A1AF4 O2  O5  O 0 1 N N N N N N 102.950 105.791 61.530 6.618   -0.845 1.878  O2  A1AF4 20 
A1AF4 C10 C11 C 0 1 N N N N N N 111.978 105.901 54.858 -10.930 -1.863 -0.084 C10 A1AF4 21 
A1AF4 C11 C12 C 0 1 N N N N N N 111.012 104.832 55.293 -9.430  -2.057 0.152  C11 A1AF4 22 
A1AF4 C12 C13 C 0 1 N N N N N N 108.801 103.159 55.102 -6.498  0.377  -0.083 C12 A1AF4 23 
A1AF4 C13 C14 C 0 1 Y N N N N N 103.243 104.615 55.689 -1.177  1.639  0.188  C13 A1AF4 24 
A1AF4 C14 C15 C 0 1 N N N N N N 102.027 105.141 56.404 0.034   2.499  -0.064 C14 A1AF4 25 
A1AF4 C15 C16 C 0 1 Y N N N N N 102.361 107.612 56.357 2.477   2.230  -0.315 C15 A1AF4 26 
A1AF4 C16 C17 C 0 1 Y N N N N N 102.427 108.042 57.692 3.621   1.434  -0.346 C16 A1AF4 27 
A1AF4 C17 C18 C 0 1 Y N N N N N 103.071 109.193 58.047 4.881   2.029  -0.570 C17 A1AF4 28 
A1AF4 C18 C19 C 0 1 N N N N N N 102.976 109.352 59.517 5.859   0.921  -0.541 C18 A1AF4 29 
A1AF4 C19 C20 C 0 1 N N S N N N 102.007 107.969 61.381 5.831   -1.545 -0.223 C19 A1AF4 30 
A1AF4 C20 C21 C 0 1 N N N N N N 102.012 106.520 61.806 6.822   -1.546 0.910  C20 A1AF4 31 
A1AF4 C21 C22 C 0 1 N N N N N N 99.789  106.739 62.764 8.221   -3.096 -0.173 C21 A1AF4 32 
A1AF4 C22 C23 C 0 1 N N N N N N 99.639  108.084 62.131 7.307   -3.190 -1.366 C22 A1AF4 33 
A1AF4 C23 C24 C 0 1 N N N N N N 100.972 108.810 62.071 6.555   -1.865 -1.529 C23 A1AF4 34 
A1AF4 C24 C25 C 0 1 N N N N N N 101.885 107.408 58.921 3.876   -0.008 -0.190 C24 A1AF4 35 
A1AF4 C25 C26 C 0 1 Y N N N N N 103.691 109.985 57.089 4.974   3.396  -0.757 C25 A1AF4 36 
A1AF4 C26 C27 C 0 1 Y N N N N N 103.646 109.577 55.765 3.828   4.180  -0.724 C26 A1AF4 37 
A1AF4 C27 C28 C 0 1 Y N N N N N 102.992 108.409 55.401 2.593   3.609  -0.506 C27 A1AF4 38 
A1AF4 F   F1  F 0 1 N N N N N N 103.180 106.419 54.210 -0.683  1.590  2.505  F   A1AF4 39 
A1AF4 H2  H2  H 0 1 N N N N N N 110.043 101.980 53.709 -6.850  -1.799 -0.297 H2  A1AF4 40 
A1AF4 H3  H3  H 0 1 N N N N N N 111.603 104.780 52.759 -8.464  0.620  -1.641 H3  A1AF4 41 
A1AF4 H4  H4  H 0 1 N N N N N N 112.174 103.079 52.689 -8.583  -1.072 -2.182 H4  A1AF4 42 
A1AF4 H5  H5  H 0 1 N N N N N N 100.734 106.628 56.327 1.156   0.699  0.036  H5  A1AF4 43 
A1AF4 H6  H6  H 0 1 N N N N N N 113.931 103.529 54.265 -10.850 0.623  -1.036 H6  A1AF4 44 
A1AF4 H7  H7  H 0 1 N N N N N N 113.999 104.782 52.979 -10.660 0.128  -2.737 H7  A1AF4 45 
A1AF4 H8  H8  H 0 1 N N N N N N 105.289 105.420 53.109 -2.827  0.112  2.708  H8  A1AF4 46 
A1AF4 H9  H9  H 0 1 N N N N N N 106.649 103.355 52.563 -4.810  -1.415 0.020  H9  A1AF4 47 
A1AF4 H10 H10 H 0 1 N N N N N N 106.887 102.116 53.842 -4.430  -1.445 1.759  H10 A1AF4 48 
A1AF4 H11 H11 H 0 1 N N N N N N 109.534 104.879 52.914 -7.652  -0.164 2.219  H11 A1AF4 49 
A1AF4 H12 H12 H 0 1 N N N N N N 108.864 103.397 52.151 -6.636  -1.670 2.144  H12 A1AF4 50 
A1AF4 H13 H13 H 0 1 N N N N N N 103.487 102.881 56.919 -1.757  1.588  -1.869 H13 A1AF4 51 
A1AF4 H14 H14 H 0 1 N N N N N N 105.480 102.074 55.752 -3.735  0.182  -1.459 H14 A1AF4 52 
A1AF4 H15 H15 H 0 1 N N N N N N 100.988 105.119 62.830 8.538   -2.280 1.622  H15 A1AF4 53 
A1AF4 H17 H17 H 0 1 N N N N N N 111.928 106.738 55.569 -11.319 -1.135 0.627  H17 A1AF4 54 
A1AF4 H18 H18 H 0 1 N N N N N N 111.693 106.254 53.856 -11.445 -2.814 0.049  H18 A1AF4 55 
A1AF4 H19 H19 H 0 1 N N N N N N 109.982 105.197 55.167 -9.051  -2.824 -0.523 H19 A1AF4 56 
A1AF4 H20 H20 H 0 1 N N N N N N 111.188 104.588 56.351 -9.260  -2.364 1.184  H20 A1AF4 57 
A1AF4 H21 H21 H 0 1 N N N N N N 108.366 102.204 55.431 -5.871  0.343  -0.974 H21 A1AF4 58 
A1AF4 H22 H22 H 0 1 N N N N N N 109.068 103.763 55.982 -7.102  1.283  -0.021 H22 A1AF4 59 
A1AF4 H23 H23 H 0 1 N N N N N N 101.180 104.472 56.192 0.129   3.236  0.734  H23 A1AF4 60 
A1AF4 H24 H24 H 0 1 N N N N N N 102.230 105.144 57.485 -0.076  3.011  -1.020 H24 A1AF4 61 
A1AF4 H25 H25 H 0 1 N N N N N N 102.932 108.335 61.851 5.069   -2.304 -0.041 H25 A1AF4 62 
A1AF4 H26 H26 H 0 1 N N N N N N 98.930  108.682 62.722 7.897   -3.386 -2.262 H26 A1AF4 63 
A1AF4 H27 H27 H 0 1 N N N N N N 99.251  107.959 61.109 6.593   -4.000 -1.216 H27 A1AF4 64 
A1AF4 H28 H28 H 0 1 N N N N N N 101.310 109.029 63.095 5.830   -1.947 -2.339 H28 A1AF4 65 
A1AF4 H29 H29 H 0 1 N N N N N N 100.845 109.752 61.517 7.270   -1.074 -1.754 H29 A1AF4 66 
A1AF4 H30 H30 H 0 1 N N N N N N 104.196 110.897 57.369 5.937   3.854  -0.927 H30 A1AF4 67 
A1AF4 H31 H31 H 0 1 N N N N N N 104.127 110.177 55.006 3.905   5.247  -0.870 H31 A1AF4 68 
A1AF4 H32 H32 H 0 1 N N N N N N 102.971 108.112 54.363 1.710   4.230  -0.483 H32 A1AF4 69 
# 
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 
A1AF4 C6  C7  SING N N 1  
A1AF4 C6  N   SING N N 2  
A1AF4 C8  C9  SING N N 3  
A1AF4 C8  N1  SING N N 4  
A1AF4 C5  N   SING N N 5  
A1AF4 C5  C2  SING N N 6  
A1AF4 C9  O   SING N N 7  
A1AF4 C1  C2  DOUB Y N 8  
A1AF4 C1  C   SING Y N 9  
A1AF4 C7  N1  SING N N 10 
A1AF4 C7  C12 SING N N 11 
A1AF4 N   C12 SING N N 12 
A1AF4 F   C   SING N N 13 
A1AF4 C2  C3  SING Y N 14 
A1AF4 N1  C11 SING N N 15 
A1AF4 C   C13 DOUB Y N 16 
A1AF4 O   C10 SING N N 17 
A1AF4 C10 C11 SING N N 18 
A1AF4 C27 C26 DOUB Y N 19 
A1AF4 C27 C15 SING Y N 20 
A1AF4 C3  C4  DOUB Y N 21 
A1AF4 C13 C4  SING Y N 22 
A1AF4 C13 C14 SING N N 23 
A1AF4 C26 C25 SING Y N 24 
A1AF4 N2  C15 SING N N 25 
A1AF4 N2  C14 SING N N 26 
A1AF4 C15 C16 DOUB Y N 27 
A1AF4 C25 C17 DOUB Y N 28 
A1AF4 C16 C17 SING Y N 29 
A1AF4 C16 C24 SING N N 30 
A1AF4 C17 C18 SING N N 31 
A1AF4 C24 O3  DOUB N N 32 
A1AF4 C24 N3  SING N N 33 
A1AF4 C18 N3  SING N N 34 
A1AF4 C18 O4  DOUB N N 35 
A1AF4 N3  C19 SING N N 36 
A1AF4 C19 C20 SING N N 37 
A1AF4 C19 C23 SING N N 38 
A1AF4 O2  C20 DOUB N N 39 
A1AF4 C20 N4  SING N N 40 
A1AF4 C23 C22 SING N N 41 
A1AF4 C22 C21 SING N N 42 
A1AF4 N4  C21 SING N N 43 
A1AF4 C21 O1  DOUB N N 44 
A1AF4 C7  H2  SING N N 45 
A1AF4 C8  H3  SING N N 46 
A1AF4 C8  H4  SING N N 47 
A1AF4 N2  H5  SING N N 48 
A1AF4 C9  H6  SING N N 49 
A1AF4 C9  H7  SING N N 50 
A1AF4 C1  H8  SING N N 51 
A1AF4 C5  H9  SING N N 52 
A1AF4 C5  H10 SING N N 53 
A1AF4 C6  H11 SING N N 54 
A1AF4 C6  H12 SING N N 55 
A1AF4 C4  H13 SING N N 56 
A1AF4 C3  H14 SING N N 57 
A1AF4 N4  H15 SING N N 58 
A1AF4 C10 H17 SING N N 59 
A1AF4 C10 H18 SING N N 60 
A1AF4 C11 H19 SING N N 61 
A1AF4 C11 H20 SING N N 62 
A1AF4 C12 H21 SING N N 63 
A1AF4 C12 H22 SING N N 64 
A1AF4 C14 H23 SING N N 65 
A1AF4 C14 H24 SING N N 66 
A1AF4 C19 H25 SING N N 67 
A1AF4 C22 H26 SING N N 68 
A1AF4 C22 H27 SING N N 69 
A1AF4 C23 H28 SING N N 70 
A1AF4 C23 H29 SING N N 71 
A1AF4 C25 H30 SING N N 72 
A1AF4 C26 H31 SING N N 73 
A1AF4 C27 H32 SING N N 74 
# 
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 
A1AF4 SMILES           ACDLabs              12.01 "O=C1NC(=O)CCC1N1C(=O)c2cccc(NCc3ccc(cc3F)CN3CC(C3)N3CCOCC3)c2C1=O"                                                                                                                                          
A1AF4 InChI            InChI                1.06  "InChI=1S/C28H30FN5O5/c29-21-12-17(14-32-15-19(16-32)33-8-10-39-11-9-33)4-5-18(21)13-30-22-3-1-2-20-25(22)28(38)34(27(20)37)23-6-7-24(35)31-26(23)36/h1-5,12,19,23,30H,6-11,13-16H2,(H,31,35,36)/t23-/m0/s1" 
A1AF4 InChIKey         InChI                1.06  NZYDBVQXOGPDDU-QHCPKHFHSA-N                                                                                                                                                                                  
A1AF4 SMILES_CANONICAL CACTVS               3.385 "Fc1cc(CN2CC(C2)N3CCOCC3)ccc1CNc4cccc5C(=O)N([C@H]6CCC(=O)NC6=O)C(=O)c45"                                                                                                                                    
A1AF4 SMILES           CACTVS               3.385 "Fc1cc(CN2CC(C2)N3CCOCC3)ccc1CNc4cccc5C(=O)N([CH]6CCC(=O)NC6=O)C(=O)c45"                                                                                                                                     
A1AF4 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1cc2c(c(c1)NCc3ccc(cc3F)CN4CC(C4)N5CCOCC5)C(=O)N(C2=O)[C@H]6CCC(=O)NC6=O"                                                                                                                                  
A1AF4 SMILES           "OpenEye OEToolkits" 2.0.7 "c1cc2c(c(c1)NCc3ccc(cc3F)CN4CC(C4)N5CCOCC5)C(=O)N(C2=O)C6CCC(=O)NC6=O"                                                                                                                                      
# 
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 
A1AF4 "SYSTEMATIC NAME" ACDLabs              12.01 "2-[(3S)-2,6-dioxopiperidin-3-yl]-4-{[(2-fluoro-4-{[3-(morpholin-4-yl)azetidin-1-yl]methyl}phenyl)methyl]amino}-1H-isoindole-1,3(2H)-dione"        
A1AF4 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "2-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-4-[[2-fluoranyl-4-[(3-morpholin-4-ylazetidin-1-yl)methyl]phenyl]methylamino]isoindole-1,3-dione" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
A1AF4 "Create component" 2024-02-27 RCSB 
A1AF4 "Initial release"  2025-10-15 RCSB 
# 
