data_SDO
# 
_chem_comp.id                                    SDO 
_chem_comp.name                                  "N~3~-{(2S)-4-[(dihydroxyphosphanyl)oxy]-2-hydroxy-3,3-dimethylbutanoyl}-N-{2-[(3,7-dioxooctyl)sulfanyl]ethyl}-beta-alaninamide" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C19 H35 N2 O8 P S" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2014-10-16 
_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                        482.529 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     SDO 
_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        2MVU 
_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 
SDO P24  P24  P 0 1 N N N N N N -11.348 9.561  -2.752 -8.152 2.740  0.938  P24  SDO 1  
SDO O26  O26  O 0 1 N N N N N N -12.261 10.314 -1.748 -6.695 3.351  1.244  O26  SDO 2  
SDO O23  O23  O 0 1 N N N N N N -12.026 8.855  -3.959 -8.861 3.945  0.141  O23  SDO 3  
SDO O27  O27  O 0 1 N N N N N N -10.316 10.571 -3.317 -7.836 1.696  -0.246 O27  SDO 4  
SDO C28  C28  C 0 1 N N N N N N -9.469  11.301 -2.372 -7.486 0.331  -0.008 C28  SDO 5  
SDO C29  C29  C 0 1 N N N N N N -8.385  12.106 -3.106 -7.253 -0.376 -1.345 C29  SDO 6  
SDO C30  C30  C 0 1 N N N N N N -7.596  12.857 -2.056 -8.530 -0.316 -2.184 C30  SDO 7  
SDO C31  C31  C 0 1 N N N N N N -7.455  11.138 -3.844 -6.115 0.318  -2.097 C31  SDO 8  
SDO C32  C32  C 0 1 N N S N N N -8.986  13.133 -4.166 -6.879 -1.838 -1.090 C32  SDO 9  
SDO O33  O33  O 0 1 N N N N N N -7.917  13.820 -4.817 -7.990 -2.519 -0.503 O33  SDO 10 
SDO C34  C34  C 0 1 N N N N N N -9.879  14.213 -3.521 -5.701 -1.899 -0.152 C34  SDO 11 
SDO O35  O35  O 0 1 N N N N N N -9.518  15.395 -3.549 -5.855 -2.268 0.993  O35  SDO 12 
SDO N36  N36  N 0 1 N N N N N N -10.996 13.837 -2.949 -4.475 -1.543 -0.586 N36  SDO 13 
SDO C37  C37  C 0 1 N N N N N N -11.937 14.753 -2.304 -3.312 -1.708 0.289  C37  SDO 14 
SDO C38  C38  C 0 1 N N N N N N -12.437 14.252 -0.941 -2.053 -1.232 -0.439 C38  SDO 15 
SDO C39  C39  C 0 1 N N N N N N -11.438 14.422 0.214  -0.857 -1.403 0.461  C39  SDO 16 
SDO O40  O40  O 0 1 N N N N N N -11.706 14.030 1.348  -0.997 -1.860 1.576  O40  SDO 17 
SDO N41  N41  N 0 1 N N N N N N -10.287 15.009 -0.092 0.369  -1.047 0.027  N41  SDO 18 
SDO C42  C42  C 0 1 N N N N N N -9.225  15.253 0.869  1.532  -1.212 0.902  C42  SDO 19 
SDO C43  C43  C 0 1 N N N N N N -8.105  16.086 0.291  2.790  -0.736 0.174  C43  SDO 20 
SDO S1   S1   S 0 1 N N N N N N -6.521  16.186 1.181  4.230  -0.941 1.257  S1   SDO 21 
SDO C1   C1   C 0 1 N N N N N N -6.401  15.248 2.737  5.600  -0.333 0.235  C1   SDO 22 
SDO C2   C2   C 0 1 N N N N N N -7.602  14.446 3.207  6.909  -0.441 1.019  C2   SDO 23 
SDO C3   C3   C 0 1 N N N N N N -7.524  13.618 4.558  8.047  0.063  0.170  C3   SDO 24 
SDO O3   O3   O 0 1 N N N N N N -8.535  12.983 4.863  7.833  0.468  -0.948 O3   SDO 25 
SDO C4   C4   C 0 1 N N N N N N -6.285  13.502 5.546  9.452  0.064  0.715  C4   SDO 26 
SDO C5   C5   C 0 1 N N N N N N -4.982  14.245 5.226  10.408 0.622  -0.340 C5   SDO 27 
SDO C6   C6   C 0 1 N N N N N N -3.816  13.836 6.150  11.835 0.622  0.213  C6   SDO 28 
SDO C7   C7   C 0 1 N N N N N N -3.867  14.339 7.612  12.777 1.171  -0.827 C7   SDO 29 
SDO O7   O7   O 0 1 N N N N N N -2.965  14.035 8.395  12.352 1.526  -1.900 O7   SDO 30 
SDO C8   C8   C 0 1 N N N N N N -5.027  15.203 8.089  14.250 1.278  -0.527 C8   SDO 31 
SDO H1   H1   H 0 1 N N N N N N -11.728 10.699 -1.062 -6.111 2.753  1.730  H1   SDO 32 
SDO H2   H2   H 0 1 N N N N N N -11.363 8.434  -4.494 -9.129 4.685  0.704  H2   SDO 33 
SDO H28A H28A H 0 0 N N N N N N -10.095 11.991 -1.788 -6.576 0.288  0.590  H28A SDO 34 
SDO H28B H28B H 0 0 N N N N N N -8.985  10.582 -1.694 -8.297 -0.163 0.527  H28B SDO 35 
SDO H30A H30A H 0 0 N N N N N N -6.807  13.448 -2.543 -8.826 0.725  -2.322 H30A SDO 36 
SDO H30B H30B H 0 0 N N N N N N -8.269  13.529 -1.503 -8.348 -0.773 -3.157 H30B SDO 37 
SDO H30C H30C H 0 0 N N N N N N -7.139  12.140 -1.358 -9.327 -0.855 -1.672 H30C SDO 38 
SDO H31A H31A H 0 0 N N N N N N -6.676  11.708 -4.372 -5.241 0.388  -1.449 H31A SDO 39 
SDO H31B H31B H 0 0 N N N N N N -6.984  10.458 -3.119 -5.863 -0.259 -2.986 H31B SDO 40 
SDO H31C H31C H 0 0 N N N N N N -8.037  10.553 -4.571 -6.431 1.319  -2.390 H31C SDO 41 
SDO H32A H32A H 0 0 N N N N N N -9.582  12.566 -4.897 -6.617 -2.316 -2.034 H32A SDO 42 
SDO H33A H33A H 0 0 N N N N N N -7.996  14.753 -4.658 -8.278 -2.146 0.341  H33A SDO 43 
SDO H36A H36A H 0 0 N N N N N N -11.220 12.862 -2.954 -4.363 -1.178 -1.477 H36A SDO 44 
SDO H37A H37A H 0 0 N N N N N N -11.436 15.721 -2.157 -3.452 -1.119 1.195  H37A SDO 45 
SDO H37B H37B H 0 0 N N N N N N -12.805 14.885 -2.967 -3.203 -2.760 0.554  H37B SDO 46 
SDO H38A H38A H 0 0 N N N N N N -13.352 14.808 -0.687 -1.913 -1.822 -1.345 H38A SDO 47 
SDO H38B H38B H 0 0 N N N N N N -12.672 13.182 -1.035 -2.163 -0.181 -0.704 H38B SDO 48 
SDO H41A H41A H 0 0 N N N N N N -10.143 15.300 -1.038 0.480  -0.682 -0.864 H41A SDO 49 
SDO H42A H42A H 0 0 N N N N N N -9.648  15.782 1.736  1.392  -0.623 1.808  H42A SDO 50 
SDO H42B H42B H 0 0 N N N N N N -8.814  14.286 1.195  1.641  -2.264 1.167  H42B SDO 51 
SDO H43A H43A H 0 0 N N N N N N -7.887  15.682 -0.708 2.930  -1.326 -0.732 H43A SDO 52 
SDO H43B H43B H 0 0 N N N N N N -8.485  17.114 0.196  2.681  0.315  -0.091 H43B SDO 53 
SDO H1A  H1A  H 0 1 N N N N N N -5.566  14.541 2.624  5.670  -0.933 -0.673 H1A  SDO 54 
SDO H1B  H1B  H 0 1 N N N N N N -6.165  15.971 3.532  5.420  0.708  -0.031 H1B  SDO 55 
SDO H2A  H2A  H 0 1 N N N N N N -8.435  15.156 3.318  6.839  0.158  1.927  H2A  SDO 56 
SDO H2B  H2B  H 0 1 N N N N N N -7.837  13.728 2.408  7.089  -1.483 1.285  H2B  SDO 57 
SDO H4A  H4A  H 0 1 N N N N N N -6.625  13.864 6.527  9.494  0.686  1.609  H4A  SDO 58 
SDO H4B  H4B  H 0 1 N N N N N N -6.033  12.434 5.617  9.744  -0.956 0.968  H4B  SDO 59 
SDO H5A  H5A  H 0 1 N N N N N N -4.699  14.026 4.186  10.366 -0.001 -1.235 H5A  SDO 60 
SDO H5B  H5B  H 0 1 N N N N N N -5.157  15.325 5.339  10.116 1.641  -0.593 H5B  SDO 61 
SDO H6A  H6A  H 0 1 N N N N N N -3.785  12.737 6.178  11.877 1.244  1.107  H6A  SDO 62 
SDO H6B  H6B  H 0 1 N N N N N N -2.887  14.217 5.700  12.127 -0.398 0.465  H6B  SDO 63 
SDO H8A  H8A  H 0 1 N N N N N N -4.885  15.454 9.150  14.749 0.356  -0.826 H8A  SDO 64 
SDO H8B  H8B  H 0 1 N N N N N N -5.064  16.128 7.495  14.674 2.116  -1.081 H8B  SDO 65 
SDO H8C  H8C  H 0 1 N N N N N N -5.970  14.651 7.966  14.393 1.439  0.541  H8C  SDO 66 
# 
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 
SDO P24 O26  SING N N 1  
SDO P24 O23  SING N N 2  
SDO P24 O27  SING N N 3  
SDO O27 C28  SING N N 4  
SDO C28 C29  SING N N 5  
SDO C29 C30  SING N N 6  
SDO C29 C31  SING N N 7  
SDO C29 C32  SING N N 8  
SDO C32 O33  SING N N 9  
SDO C32 C34  SING N N 10 
SDO C34 O35  DOUB N N 11 
SDO C34 N36  SING N N 12 
SDO N36 C37  SING N N 13 
SDO C37 C38  SING N N 14 
SDO C38 C39  SING N N 15 
SDO C39 O40  DOUB N N 16 
SDO C39 N41  SING N N 17 
SDO N41 C42  SING N N 18 
SDO C42 C43  SING N N 19 
SDO C43 S1   SING N N 20 
SDO S1  C1   SING N N 21 
SDO C1  C2   SING N N 22 
SDO C2  C3   SING N N 23 
SDO C3  O3   DOUB N N 24 
SDO C3  C4   SING N N 25 
SDO C4  C5   SING N N 26 
SDO C5  C6   SING N N 27 
SDO C6  C7   SING N N 28 
SDO C7  O7   DOUB N N 29 
SDO C7  C8   SING N N 30 
SDO O26 H1   SING N N 31 
SDO O23 H2   SING N N 32 
SDO C28 H28A SING N N 33 
SDO C28 H28B SING N N 34 
SDO C30 H30A SING N N 35 
SDO C30 H30B SING N N 36 
SDO C30 H30C SING N N 37 
SDO C31 H31A SING N N 38 
SDO C31 H31B SING N N 39 
SDO C31 H31C SING N N 40 
SDO C32 H32A SING N N 41 
SDO O33 H33A SING N N 42 
SDO N36 H36A SING N N 43 
SDO C37 H37A SING N N 44 
SDO C37 H37B SING N N 45 
SDO C38 H38A SING N N 46 
SDO C38 H38B SING N N 47 
SDO N41 H41A SING N N 48 
SDO C42 H42A SING N N 49 
SDO C42 H42B SING N N 50 
SDO C43 H43A SING N N 51 
SDO C43 H43B SING N N 52 
SDO C1  H1A  SING N N 53 
SDO C1  H1B  SING N N 54 
SDO C2  H2A  SING N N 55 
SDO C2  H2B  SING N N 56 
SDO C4  H4A  SING N N 57 
SDO C4  H4B  SING N N 58 
SDO C5  H5A  SING N N 59 
SDO C5  H5B  SING N N 60 
SDO C6  H6A  SING N N 61 
SDO C6  H6B  SING N N 62 
SDO C8  H8A  SING N N 63 
SDO C8  H8B  SING N N 64 
SDO C8  H8C  SING N N 65 
# 
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 
SDO SMILES           ACDLabs              12.01 "O=C(NCCSCCC(=O)CCCC(=O)C)CCNC(=O)C(O)C(C)(C)COP(O)O"                                                                                                                 
SDO InChI            InChI                1.03  "InChI=1S/C19H35N2O8PS/c1-14(22)5-4-6-15(23)8-11-31-12-10-20-16(24)7-9-21-18(26)17(25)19(2,3)13-29-30(27)28/h17,25,27-28H,4-13H2,1-3H3,(H,20,24)(H,21,26)/t17-/m1/s1" 
SDO InChIKey         InChI                1.03  TUVOCCHXVSLSRA-QGZVFWFLSA-N                                                                                                                                           
SDO SMILES_CANONICAL CACTVS               3.385 "CC(=O)CCCC(=O)CCSCCNC(=O)CCNC(=O)[C@@H](O)C(C)(C)COP(O)O"                                                                                                            
SDO SMILES           CACTVS               3.385 "CC(=O)CCCC(=O)CCSCCNC(=O)CCNC(=O)[CH](O)C(C)(C)COP(O)O"                                                                                                              
SDO SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "CC(=O)CCCC(=O)CCSCCNC(=O)CCNC(=O)[C@H](C(C)(C)COP(O)O)O"                                                                                                             
SDO SMILES           "OpenEye OEToolkits" 1.7.6 "CC(=O)CCCC(=O)CCSCCNC(=O)CCNC(=O)C(C(C)(C)COP(O)O)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 
SDO "SYSTEMATIC NAME" ACDLabs              12.01 "N~3~-{(2S)-4-[(dihydroxyphosphanyl)oxy]-2-hydroxy-3,3-dimethylbutanoyl}-N-{2-[(3,7-dioxooctyl)sulfanyl]ethyl}-beta-alaninamide"                                    
SDO "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(3S)-4-[[3-[2-[3,7-bis(oxidanylidene)octylsulfanyl]ethylamino]-3-oxidanylidene-propyl]amino]-2,2-dimethyl-3-oxidanyl-4-oxidanylidene-butyl] dihydrogen phosphite" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
SDO "Create component" 2014-10-16 RCSB 
SDO "Initial release"  2015-10-21 RCSB 
SDO "Modify PCM"       2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            SDO 
_pdbx_chem_comp_pcm.modified_residue_id                SER 
_pdbx_chem_comp_pcm.type                               None 
_pdbx_chem_comp_pcm.category                           Lipid/lipid-like 
_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               P24 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom   OG 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession     ? 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession      ? 
# 
