data_S5R
# 
_chem_comp.id                                    S5R 
_chem_comp.name                                  "(2~{R})-2-methyl-2-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]-3-oxidanyl-propanoic acid" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C12 H19 N2 O8 P" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-04-10 
_chem_comp.pdbx_modified_date                    2024-04-05 
_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                        350.262 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     S5R 
_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        8IYT 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBJ 
# 
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 
S5R C21 C1  C 0 1 Y N N N N N 36.519 9.513  46.328 -0.232 3.694  0.371  C21 S5R 1  
S5R N   N1  N 0 1 N N N N N N 37.457 7.395  49.927 -1.839 -0.477 0.170  N   S5R 2  
S5R CA  C2  C 0 1 N N R N N N 37.628 6.641  51.195 -2.642 -1.599 -0.336 CA  S5R 3  
S5R C2  C3  C 0 1 N N N N N N 38.955 6.885  51.895 -1.754 -2.531 -1.162 C2  S5R 4  
S5R CB  C4  C 0 1 N N N N N N 37.431 5.170  50.817 -3.773 -1.060 -1.214 CB  S5R 5  
S5R OG  O1  O 0 1 N N N N N N 36.256 5.220  49.971 -4.534 -0.101 -0.477 OG  S5R 6  
S5R C   C5  C 0 1 N N N N N N 36.478 7.032  52.096 -3.228 -2.361 0.825  C   S5R 7  
S5R O   O2  O 0 1 N N N N N N 35.725 7.980  51.764 -4.327 -2.854 0.732  O   S5R 8  
S5R OXT O3  O 0 1 N N N N N N 36.252 6.371  53.137 -2.528 -2.492 1.963  OXT S5R 9  
S5R O3P O4  O 0 1 N N N N N N 43.285 8.849  48.711 3.980  -1.713 -1.474 O3P S5R 10 
S5R P   P1  P 0 1 N N N N N N 42.215 9.580  49.454 3.987  -1.204 -0.084 P   S5R 11 
S5R O1P O5  O 0 1 N N N N N N 42.646 10.846 50.107 3.537  -2.379 0.920  O1P S5R 12 
S5R O2P O6  O 0 1 N N N N N N 41.547 8.664  50.458 5.470  -0.709 0.298  O2P S5R 13 
S5R O4P O7  O 0 1 N N N N N N 41.097 9.895  48.373 2.961  0.031  0.040  O4P S5R 14 
S5R C5A C6  C 0 1 N N N N N N 39.970 10.784 48.651 1.584  -0.061 -0.334 C5A S5R 15 
S5R C5  C7  C 0 1 Y N N N N N 38.791 10.270 47.869 0.909  1.265  -0.094 C5  S5R 16 
S5R C6  C8  C 0 1 Y N N N N N 38.347 10.962 46.732 1.625  2.332  0.416  C6  S5R 17 
S5R N1  N2  N 0 1 Y N N N N N 37.277 10.591 46.004 1.045  3.497  0.630  N1  S5R 18 
S5R C4  C9  C 0 1 Y N N N N N 37.969 9.133  48.347 -0.436 1.429  -0.380 C4  S5R 19 
S5R C4A C10 C 0 1 N N N N N N 38.408 8.420  49.598 -1.251 0.290  -0.937 C4A S5R 20 
S5R C3  C11 C 0 1 Y N N N N N 36.849 8.730  47.530 -1.017 2.671  -0.142 C3  S5R 21 
S5R O3  O8  O 0 1 N N N N N N 36.064 7.699  47.853 -2.333 2.878  -0.408 O3  S5R 22 
S5R C2A C12 C 0 1 N N N N N N 35.335 9.152  45.506 -0.848 5.043  0.640  C2A S5R 23 
S5R H1  H1  H 0 1 N N N N N N 36.557 7.829  49.962 -1.125 -0.801 0.805  H1  S5R 24 
S5R H3  H3  H 0 1 N N N N N N 38.997 6.291  52.820 -0.948 -2.914 -0.536 H3  S5R 25 
S5R H4  H4  H 0 1 N N N N N N 39.780 6.588  51.231 -2.350 -3.363 -1.537 H4  S5R 26 
S5R H5  H5  H 0 1 N N N N N N 39.049 7.953  52.141 -1.331 -1.980 -2.001 H5  S5R 27 
S5R H6  H6  H 0 1 N N N N N N 37.253 4.551  51.708 -3.351 -0.586 -2.100 H6  S5R 28 
S5R H7  H7  H 0 1 N N N N N N 38.301 4.781  50.267 -4.421 -1.883 -1.517 H7  S5R 29 
S5R H8  H8  H 0 1 N N N N N N 36.041 4.343  49.675 -5.270 0.283  -0.974 H8  S5R 30 
S5R H9  H9  H 0 1 N N N N N N 35.475 6.710  53.566 -2.945 -2.989 2.680  H9  S5R 31 
S5R H10 H10 H 0 1 N N N N N N 43.570 10.991 49.939 3.519  -2.115 1.850  H10 S5R 32 
S5R H11 H11 H 0 1 N N N N N N 41.944 7.802  50.414 6.142  -1.403 0.245  H11 S5R 33 
S5R H12 H12 H 0 1 N N N N N N 40.213 11.809 48.336 1.511  -0.319 -1.390 H12 S5R 34 
S5R H13 H13 H 0 1 N N N N N N 39.741 10.776 49.727 1.096  -0.830 0.264  H13 S5R 35 
S5R H14 H14 H 0 1 N N N N N N 38.894 11.841 46.424 2.675  2.210  0.642  H14 S5R 36 
S5R H15 H15 H 0 1 N N N N N N 39.395 7.964  49.432 -0.609 -0.361 -1.529 H15 S5R 37 
S5R H16 H16 H 0 1 N N N N N N 38.471 9.140  50.427 -2.047 0.687  -1.567 H16 S5R 38 
S5R H17 H17 H 0 1 N N N N N N 36.391 7.287  48.644 -2.509 3.193  -1.306 H17 S5R 39 
S5R H18 H18 H 0 1 N N N N N N 35.229 9.870  44.679 -1.232 5.069  1.660  H18 S5R 40 
S5R H19 H19 H 0 1 N N N N N N 35.467 8.139  45.097 -0.093 5.818  0.516  H19 S5R 41 
S5R H20 H20 H 0 1 N N N N N N 34.432 9.179  46.133 -1.665 5.215  -0.061 H20 S5R 42 
# 
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 
S5R C2A C21 SING N N 1  
S5R N1  C21 DOUB Y N 2  
S5R N1  C6  SING Y N 3  
S5R C21 C3  SING Y N 4  
S5R C6  C5  DOUB Y N 5  
S5R C3  O3  SING N N 6  
S5R C3  C4  DOUB Y N 7  
S5R C5  C4  SING Y N 8  
S5R C5  C5A SING N N 9  
S5R C4  C4A SING N N 10 
S5R O4P C5A SING N N 11 
S5R O4P P   SING N N 12 
S5R O3P P   DOUB N N 13 
S5R P   O1P SING N N 14 
S5R P   O2P SING N N 15 
S5R C4A N   SING N N 16 
S5R N   CA  SING N N 17 
S5R OG  CB  SING N N 18 
S5R CB  CA  SING N N 19 
S5R CA  C2  SING N N 20 
S5R CA  C   SING N N 21 
S5R O   C   DOUB N N 22 
S5R C   OXT SING N N 23 
S5R N   H1  SING N N 24 
S5R C2  H3  SING N N 25 
S5R C2  H4  SING N N 26 
S5R C2  H5  SING N N 27 
S5R CB  H6  SING N N 28 
S5R CB  H7  SING N N 29 
S5R OG  H8  SING N N 30 
S5R OXT H9  SING N N 31 
S5R O1P H10 SING N N 32 
S5R O2P H11 SING N N 33 
S5R C5A H12 SING N N 34 
S5R C5A H13 SING N N 35 
S5R C6  H14 SING N N 36 
S5R C4A H15 SING N N 37 
S5R C4A H16 SING N N 38 
S5R O3  H17 SING N N 39 
S5R C2A H18 SING N N 40 
S5R C2A H19 SING N N 41 
S5R C2A H20 SING N N 42 
# 
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 
S5R InChI            InChI                1.06  "InChI=1S/C12H19N2O8P/c1-7-10(16)9(4-14-12(2,6-15)11(17)18)8(3-13-7)5-22-23(19,20)21/h3,14-16H,4-6H2,1-2H3,(H,17,18)(H2,19,20,21)/t12-/m1/s1" 
S5R InChIKey         InChI                1.06  FVZJSLHHGJVQIU-GFCCVEGCSA-N                                                                                                                   
S5R SMILES_CANONICAL CACTVS               3.385 "Cc1ncc(CO[P](O)(O)=O)c(CN[C@](C)(CO)C(O)=O)c1O"                                                                                              
S5R SMILES           CACTVS               3.385 "Cc1ncc(CO[P](O)(O)=O)c(CN[C](C)(CO)C(O)=O)c1O"                                                                                               
S5R SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "Cc1c(c(c(cn1)COP(=O)(O)O)CN[C@](C)(CO)C(=O)O)O"                                                                                              
S5R SMILES           "OpenEye OEToolkits" 2.0.7 "Cc1c(c(c(cn1)COP(=O)(O)O)CNC(C)(CO)C(=O)O)O"                                                                                                 
# 
_pdbx_chem_comp_identifier.comp_id           S5R 
_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        "(2~{R})-2-methyl-2-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]-3-oxidanyl-propanoic acid" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
S5R "Create component" 2023-04-10 PDBJ 
S5R "Initial release"  2024-04-10 RCSB 
# 
