data_SXD
# 
_chem_comp.id                                    SXD 
_chem_comp.name                                  "N-{2-[(3,5-dioxohexyl)sulfanyl]ethyl}-N~3~-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alaninamide" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C17 H31 N2 O9 P S" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2009-04-02 
_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                        470.475 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     SXD 
_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        2KGE 
_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 
SXD O25  O25  O 0 1 N N N N N N 4.689  -11.325 0.195  8.365   2.175  -1.265 O25  SXD 1  
SXD P24  P24  P 0 1 N N N N N N 5.088  -12.529 -0.649 7.059   2.557  -0.405 P24  SXD 2  
SXD O26  O26  O 0 1 N N N N N N 5.991  -13.405 0.214  7.350   3.889  0.451  O26  SXD 3  
SXD O23  O23  O 0 1 N N N N N N 5.616  -12.035 -2.016 5.919   2.797  -1.318 O23  SXD 4  
SXD O27  O27  O 0 1 N N N N N N 3.777  -13.314 -0.856 6.700   1.345  0.593  O27  SXD 5  
SXD C28  C28  C 0 1 N N N N N N 3.054  -13.701 0.360  6.291   0.055  0.135  C28  SXD 6  
SXD C29  C29  C 0 1 N N N N N N 1.924  -14.694 0.066  6.030   -0.854 1.338  C29  SXD 7  
SXD C30  C30  C 0 1 N N N N N N 1.391  -15.147 1.399  7.312   -0.989 2.163  C30  SXD 8  
SXD C31  C31  C 0 1 N N N N N N 0.815  -14.006 -0.742 4.926   -0.247 2.206  C31  SXD 9  
SXD C32  C32  C 0 1 N N S N N N 2.435  -15.962 -0.732 5.591   -2.235 0.848  C32  SXD 10 
SXD O33  O33  O 0 1 N N N N N N 1.344  -16.826 -1.049 6.670   -2.856 0.145  O33  SXD 11 
SXD C34  C34  C 0 1 N N N N N N 3.421  -16.833 0.063  4.409   -2.089 -0.075 C34  SXD 12 
SXD O35  O35  O 0 1 N N N N N N 3.191  -18.042 0.133  4.544   -2.268 -1.267 O35  SXD 13 
SXD N36  N36  N 0 1 N N N N N N 4.470  -16.272 0.637  3.201   -1.758 0.424  N36  SXD 14 
SXD C37  C37  C 0 1 N N N N N N 5.474  -17.015 1.415  2.030   -1.726 -0.454 C37  SXD 15 
SXD C38  C38  C 0 1 N N N N N N 6.836  -16.293 1.514  0.795   -1.324 0.357  C38  SXD 16 
SXD C39  C39  C 0 1 N N N N N N 7.544  -16.036 0.167  -0.410  -1.291 -0.547 C39  SXD 17 
SXD O40  O40  O 0 1 N N N N N N 8.760  -15.778 0.117  -0.294  -1.561 -1.723 O40  SXD 18 
SXD N41  N41  N 0 1 N N N N N N 6.770  -16.112 -0.907 -1.617  -0.960 -0.048 N41  SXD 19 
SXD C42  C42  C 0 1 N N N N N N 7.217  -15.910 -2.274 -2.789  -0.928 -0.926 C42  SXD 20 
SXD C43  C43  C 0 1 N N N N N N 6.080  -15.473 -3.186 -4.023  -0.526 -0.115 C43  SXD 21 
SXD S1   S1   S 0 1 N N N N N N 6.528  -15.499 -4.934 -5.475  -0.486 -1.203 S1   SXD 22 
SXD C1   C1   C 0 1 N N N N N N 4.976  -14.950 -5.717 -6.813  0.001  -0.080 C1   SXD 23 
SXD C2   C2   C 0 1 N N N N N N 3.759  -15.847 -5.439 -8.128  0.081  -0.858 C2   SXD 24 
SXD C3   C3   C 0 1 N N N N N N 3.908  -17.273 -5.975 -9.240  0.486  0.075  C3   SXD 25 
SXD O3   O3   O 0 1 N N N N N N 4.759  -18.054 -5.490 -9.005  0.689  1.242  O3   SXD 26 
SXD C4   C4   C 0 1 N N N N N N 3.041  -17.715 -7.147 -10.645 0.637  -0.448 C4   SXD 27 
SXD C5   C5   C 0 1 N N N N N N 1.610  -18.115 -6.798 -11.559 1.046  0.679  C5   SXD 28 
SXD O5   O5   O 0 1 N N N N N N 1.287  -19.319 -6.696 -11.115 1.199  1.791  O5   SXD 29 
SXD C6   C6   C 0 1 N N N N N N 0.578  -17.021 -6.637 -13.027 1.264  0.417  C6   SXD 30 
SXD H28  H28  H 0 1 N N N N N N 2.607  -12.794 0.793  5.377   0.151  -0.452 H28  SXD 31 
SXD H28A H28A H 0 0 N N N N N N 3.764  -14.172 1.056  7.077   -0.377 -0.484 H28A SXD 32 
SXD H30  H30  H 0 1 N N N N N N 2.224  -15.257 2.109  7.113   -1.593 3.047  H30  SXD 33 
SXD H30A H30A H 0 0 N N N N N N 0.880  -16.114 1.280  8.083   -1.469 1.560  H30A SXD 34 
SXD H30B H30B H 0 0 N N N N N N 0.679  -14.401 1.782  7.653   0.001  2.468  H30B SXD 35 
SXD H31  H31  H 0 1 N N N N N N -0.061 -13.841 -0.097 5.287   0.677  2.659  H31  SXD 36 
SXD H31A H31A H 0 0 N N N N N N 0.530  -14.645 -1.591 4.054   -0.033 1.589  H31A SXD 37 
SXD H31B H31B H 0 0 N N N N N N 1.181  -13.039 -1.117 4.652   -0.952 2.991  H31B SXD 38 
SXD H32  H32  H 0 1 N N N N N N 2.932  -15.549 -1.622 5.312   -2.852 1.702  H32  SXD 39 
SXD HO33 HO33 H 0 0 N N N N N N 0.852  -17.018 -0.259 6.971   -2.361 -0.629 HO33 SXD 40 
SXD HN36 HN36 H 0 0 N N N N N N 4.589  -15.284 0.537  3.109   -1.542 1.365  HN36 SXD 41 
SXD H37  H37  H 0 1 N N N N N N 5.648  -17.969 0.895  2.193   -1.000 -1.251 H37  SXD 42 
SXD H37A H37A H 0 0 N N N N N N 5.084  -17.152 2.434  1.873   -2.713 -0.888 H37A SXD 43 
SXD H38  H38  H 0 1 N N N N N N 6.661  -15.317 1.989  0.632   -2.050 1.153  H38  SXD 44 
SXD H38A H38A H 0 0 N N N N N N 7.497  -16.959 2.087  0.952   -0.337 0.791  H38A SXD 45 
SXD HN41 HN41 H 0 0 N N N N N N 5.803  -16.325 -0.765 -1.711  -0.744 0.893  HN41 SXD 46 
SXD H42  H42  H 0 1 N N N N N N 7.608  -16.867 -2.650 -2.626  -0.202 -1.723 H42  SXD 47 
SXD H42A H42A H 0 0 N N N N N N 7.992  -15.129 -2.279 -2.945  -1.915 -1.360 H42A SXD 48 
SXD H43  H43  H 0 1 N N N N N N 5.827  -14.435 -2.925 -4.187  -1.252 0.681  H43  SXD 49 
SXD H43A H43A H 0 0 N N N N N N 5.233  -16.159 -3.036 -3.867  0.461  0.319  H43A SXD 50 
SXD H1   H1   H 0 1 N N N N N N 4.745  -13.945 -5.334 -6.906  -0.738 0.716  H1   SXD 51 
SXD H1A  H1A  H 0 1 N N N N N N 5.146  -14.983 -6.803 -6.587  0.975  0.354  H1A  SXD 52 
SXD H2   H2   H 0 1 N N N N N N 3.620  -15.905 -4.349 -8.035  0.820  -1.654 H2   SXD 53 
SXD H2A  H2A  H 0 1 N N N N N N 2.900  -15.395 -5.957 -8.354  -0.893 -1.291 H2A  SXD 54 
SXD H4   H4   H 0 1 N N N N N N 3.518  -18.619 -7.553 -10.663 1.401  -1.225 H4   SXD 55 
SXD H4A  H4A  H 0 1 N N N N N N 2.985  -16.873 -7.852 -10.982 -0.313 -0.863 H4A  SXD 56 
SXD H6   H6   H 0 1 N N N N N N 0.985  -16.074 -7.022 -13.151 2.055  -0.323 H6   SXD 57 
SXD H6A  H6A  H 0 1 N N N N N N -0.329 -17.287 -7.200 -13.470 0.342  0.040  H6A  SXD 58 
SXD H6B  H6B  H 0 1 N N N N N N 0.327  -16.906 -5.572 -13.523 1.552  1.344  H6B  SXD 59 
SXD HO25 HO25 H 0 0 N N N N N N 4.606  -11.588 1.104  9.152   2.004  -0.730 HO25 SXD 60 
SXD HO26 HO26 H 0 0 N N N N N N 6.797  -13.587 -0.254 7.573   4.661  -0.086 HO26 SXD 61 
# 
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 
SXD P24  O25  SING N N 1  
SXD O25  HO25 SING N N 2  
SXD O23  P24  DOUB N N 3  
SXD O27  P24  SING N N 4  
SXD P24  O26  SING N N 5  
SXD O26  HO26 SING N N 6  
SXD O27  C28  SING N N 7  
SXD C29  C28  SING N N 8  
SXD C28  H28A SING N N 9  
SXD C28  H28  SING N N 10 
SXD C31  C29  SING N N 11 
SXD C32  C29  SING N N 12 
SXD C29  C30  SING N N 13 
SXD H30  C30  SING N N 14 
SXD C30  H30B SING N N 15 
SXD C30  H30A SING N N 16 
SXD H31  C31  SING N N 17 
SXD H31B C31  SING N N 18 
SXD C31  H31A SING N N 19 
SXD H32  C32  SING N N 20 
SXD O33  C32  SING N N 21 
SXD C32  C34  SING N N 22 
SXD O33  HO33 SING N N 23 
SXD C34  O35  DOUB N N 24 
SXD C34  N36  SING N N 25 
SXD HN36 N36  SING N N 26 
SXD N36  C37  SING N N 27 
SXD H37A C37  SING N N 28 
SXD C37  C38  SING N N 29 
SXD C37  H37  SING N N 30 
SXD C39  C38  SING N N 31 
SXD C38  H38  SING N N 32 
SXD C38  H38A SING N N 33 
SXD N41  C39  SING N N 34 
SXD O40  C39  DOUB N N 35 
SXD C42  N41  SING N N 36 
SXD N41  HN41 SING N N 37 
SXD C43  C42  SING N N 38 
SXD H42A C42  SING N N 39 
SXD H42  C42  SING N N 40 
SXD S1   C43  SING N N 41 
SXD C43  H43A SING N N 42 
SXD C43  H43  SING N N 43 
SXD C1   S1   SING N N 44 
SXD H1   C1   SING N N 45 
SXD C1   C2   SING N N 46 
SXD C1   H1A  SING N N 47 
SXD C3   C2   SING N N 48 
SXD H2   C2   SING N N 49 
SXD C2   H2A  SING N N 50 
SXD C4   C3   SING N N 51 
SXD C3   O3   DOUB N N 52 
SXD H4A  C4   SING N N 53 
SXD H4   C4   SING N N 54 
SXD C4   C5   SING N N 55 
SXD C5   O5   DOUB N N 56 
SXD C5   C6   SING N N 57 
SXD H6B  C6   SING N N 58 
SXD H6   C6   SING N N 59 
SXD C6   H6A  SING N N 60 
# 
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 
SXD SMILES           ACDLabs              10.04 "O=C(NCCSCCC(=O)CC(=O)C)CCNC(=O)C(O)C(C)(C)COP(=O)(O)O"                                                                                                                   
SXD SMILES_CANONICAL CACTVS               3.341 "CC(=O)CC(=O)CCSCCNC(=O)CCNC(=O)[C@@H](O)C(C)(C)CO[P](O)(O)=O"                                                                                                            
SXD SMILES           CACTVS               3.341 "CC(=O)CC(=O)CCSCCNC(=O)CCNC(=O)[CH](O)C(C)(C)CO[P](O)(O)=O"                                                                                                              
SXD SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC(=O)CC(=O)CCSCCNC(=O)CCNC(=O)[C@H](C(C)(C)COP(=O)(O)O)O"                                                                                                               
SXD SMILES           "OpenEye OEToolkits" 1.5.0 "CC(=O)CC(=O)CCSCCNC(=O)CCNC(=O)C(C(C)(C)COP(=O)(O)O)O"                                                                                                                   
SXD InChI            InChI                1.03  "InChI=1S/C17H31N2O9PS/c1-12(20)10-13(21)5-8-30-9-7-18-14(22)4-6-19-16(24)15(23)17(2,3)11-28-29(25,26)27/h15,23H,4-11H2,1-3H3,(H,18,22)(H,19,24)(H2,25,26,27)/t15-/m1/s1" 
SXD InChIKey         InChI                1.03  SGRFVRXXQNAKSR-OAHLLOKOSA-N                                                                                                                                               
# 
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 
SXD "SYSTEMATIC NAME" ACDLabs              10.04 "N-{2-[(3,5-dioxohexyl)sulfanyl]ethyl}-N~3~-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alaninamide"              
SXD "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(3S)-4-[[3-[2-(3,5-dioxohexylsulfanyl)ethylamino]-3-oxo-propyl]amino]-3-hydroxy-2,2-dimethyl-4-oxo-butyl] dihydrogen phosphate" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
SXD "Create component"  2009-04-02 RCSB 
SXD "Modify descriptor" 2011-06-04 RCSB 
SXD "Modify PCM"        2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            SXD 
_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      ? 
# 
