data_Y8P
# 
_chem_comp.id                                    Y8P 
_chem_comp.name                                  "(3~{S},4~{S})-4-methyl-3-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]cyclohexene-1-carboxylic acid" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C16 H25 N2 O7 P" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2021-02-10 
_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                        388.353 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     ? 
_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        7LOM 
_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 
Y8P C18 C1  C 0 1 N N N N N N -2.266 -54.631 -77.625 0.478  1.452  0.403  C18 Y8P 1  
Y8P C17 C2  C 0 1 Y N N N N N -1.820 -52.595 -76.137 -1.976 0.938  0.526  C17 Y8P 2  
Y8P C16 C3  C 0 1 Y N N N N N -2.194 -53.943 -76.250 -0.964 1.800  0.137  C16 Y8P 3  
Y8P C13 C4  C 0 1 Y N N N N N -2.117 -52.798 -73.751 -3.543 2.505  -0.381 C13 Y8P 4  
Y8P C12 C5  C 0 1 Y N N N N N -1.779 -52.023 -74.861 -3.293 1.301  0.259  C12 Y8P 5  
Y8P C11 C6  C 0 1 N N N N N N -0.650 -48.095 -80.646 0.668  -3.827 -1.145 C11 Y8P 6  
Y8P C01 C7  C 0 1 N N N N N N -0.957 -48.345 -78.032 0.335  -2.795 1.106  C01 Y8P 7  
Y8P C02 C8  C 0 1 N N R N N N -1.221 -47.558 -79.336 1.092  -2.685 -0.219 C02 Y8P 8  
Y8P C03 C9  C 0 1 N N N N N N -1.577 -46.072 -79.214 2.574  -2.772 0.039  C03 Y8P 9  
Y8P C06 C10 C 0 1 N N R N N N -0.183 -49.673 -78.088 -1.169 -2.707 0.844  C06 Y8P 10 
Y8P C08 C11 C 0 1 N N S N N N 0.286  -50.174 -79.476 -1.593 -3.849 -0.082 C08 Y8P 11 
Y8P C09 C12 C 0 1 N N N N N N -1.433 -51.717 -77.399 -1.659 -0.365 1.214  C09 Y8P 12 
Y8P O40 O1  O 0 1 N N N N N N -0.968 -54.966 -78.070 1.319  2.497  -0.091 O40 Y8P 13 
Y8P O42 O2  O 0 1 N N N N N N -0.878 -54.204 -80.557 3.313  2.264  1.439  O42 Y8P 14 
Y8P O43 O3  O 0 1 N N N N N N -1.823 -56.426 -80.054 3.497  1.243  -0.862 O43 Y8P 15 
Y8P O44 O4  O 0 1 N N N N N N 0.603  -56.036 -79.806 3.534  3.848  -0.513 O44 Y8P 16 
Y8P P41 P1  P 0 1 N N N N N N -0.771 -55.415 -79.659 2.924  2.459  0.024  P41 Y8P 17 
Y8P C10 C13 C 0 1 N N N N N N -0.481 -49.644 -80.683 -0.837 -3.739 -1.408 C10 Y8P 18 
Y8P C15 C14 C 0 1 Y N N N N N -2.512 -54.648 -75.088 -1.293 2.984  -0.498 C15 Y8P 19 
Y8P C20 C15 C 0 1 N N N N N N -2.069 -52.146 -72.339 -4.964 2.912  -0.676 C20 Y8P 20 
Y8P C21 C16 C 0 1 N N N N N N 1.192  -51.492 -79.531 -3.098 -3.761 -0.345 C21 Y8P 21 
Y8P N07 N1  N 0 1 N N N N N N -0.401 -50.694 -76.972 -1.481 -1.420 0.208  N07 Y8P 22 
Y8P N14 N2  N 0 1 Y N N N N N -2.473 -54.068 -73.885 -2.551 3.298  -0.735 N14 Y8P 23 
Y8P O04 O5  O 0 1 N N N N N N -1.478 -45.506 -78.095 3.439  -2.698 -0.984 O04 Y8P 24 
Y8P O05 O6  O 0 1 N N N N N N -1.963 -45.427 -80.220 2.983  -2.908 1.168  O05 Y8P 25 
Y8P O19 O7  O 0 1 N N N N N N -1.407 -50.686 -74.702 -4.319 0.486  0.622  O19 Y8P 26 
Y8P H1  H1  H 0 1 N N N N N N -2.734 -53.948 -78.349 0.632  1.338  1.476  H1  Y8P 27 
Y8P H2  H2  H 0 1 N N N N N N -2.870 -55.547 -77.542 0.725  0.518  -0.101 H2  Y8P 28 
Y8P H3  H3  H 0 1 N N N N N N 0.337  -47.637 -80.805 1.207  -3.748 -2.089 H3  Y8P 29 
Y8P H4  H4  H 0 1 N N N N N N -1.326 -47.802 -81.463 0.899  -4.782 -0.673 H4  Y8P 30 
Y8P H5  H5  H 0 1 N N N N N N -0.395 -47.676 -77.364 0.567  -3.750 1.578  H5  Y8P 31 
Y8P H6  H6  H 0 1 N N N N N N 0.787  -49.287 -77.742 -1.708 -2.786 1.788  H6  Y8P 32 
Y8P H7  H7  H 0 1 N N N N N N 1.126  -49.469 -79.565 -1.362 -4.804 0.390  H7  Y8P 33 
Y8P H8  H8  H 0 1 N N N N N N -2.327 -51.204 -77.783 -0.741 -0.256 1.792  H8  Y8P 34 
Y8P H9  H9  H 0 1 N N N N N N -1.014 -52.362 -78.185 -2.478 -0.633 1.881  H9  Y8P 35 
Y8P H10 H10 H 0 1 N N N N N N -2.330 -56.088 -80.783 3.279  1.305  -1.802 H10 Y8P 36 
Y8P H11 H11 H 0 1 N N N N N N 1.112  -55.535 -80.432 4.499  3.896  -0.473 H11 Y8P 37 
Y8P H12 H12 H 0 1 N N N N N N -1.478 -50.108 -80.699 -1.068 -2.784 -1.879 H12 Y8P 38 
Y8P H13 H13 H 0 1 N N N N N N 0.066  -49.918 -81.597 -1.139 -4.552 -2.067 H13 Y8P 39 
Y8P H14 H14 H 0 1 N N N N N N -2.796 -55.687 -75.163 -0.508 3.660  -0.803 H14 Y8P 40 
Y8P H15 H15 H 0 1 N N N N N N -2.361 -52.888 -71.582 -5.360 3.483  0.164  H15 Y8P 41 
Y8P H16 H16 H 0 1 N N N N N N -1.048 -51.794 -72.132 -4.987 3.526  -1.576 H16 Y8P 42 
Y8P H17 H17 H 0 1 N N N N N N -2.764 -51.294 -72.305 -5.573 2.021  -0.829 H17 Y8P 43 
Y8P H18 H18 H 0 1 N N N N N N 1.641  -51.670 -78.543 -3.329 -2.806 -0.817 H18 Y8P 44 
Y8P H19 H19 H 0 1 N N N N N N 0.569  -52.354 -79.812 -3.400 -4.575 -1.004 H19 Y8P 45 
Y8P H20 H20 H 0 1 N N N N N N 1.989  -51.358 -80.277 -3.637 -3.839 0.600  H20 Y8P 46 
Y8P H21 H21 H 0 1 N N N N N N 0.463  -51.158 -76.774 -0.770 -1.166 -0.461 H21 Y8P 47 
Y8P H23 H23 H 0 1 N N N N N N -1.731 -44.594 -78.177 4.380  -2.758 -0.769 H23 Y8P 48 
Y8P H24 H24 H 0 1 N N N N N N -1.431 -50.458 -73.780 -4.662 0.658  1.510  H24 Y8P 49 
Y8P H22 H22 H 0 1 N N N N N N -1.939 -48.566 -77.588 0.637  -1.981 1.765  H22 Y8P 50 
Y8P H25 H25 H 0 1 N N N N N N -2.248 -47.919 -79.491 0.860  -1.730 -0.691 H25 Y8P 51 
# 
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 
Y8P C10 C11 SING N N 1  
Y8P C10 C08 SING N N 2  
Y8P C11 C02 SING N N 3  
Y8P O42 P41 DOUB N N 4  
Y8P O05 C03 DOUB N N 5  
Y8P O43 P41 SING N N 6  
Y8P O44 P41 SING N N 7  
Y8P P41 O40 SING N N 8  
Y8P C21 C08 SING N N 9  
Y8P C08 C06 SING N N 10 
Y8P C02 C03 SING N N 11 
Y8P C02 C01 SING N N 12 
Y8P C03 O04 SING N N 13 
Y8P C06 C01 SING N N 14 
Y8P C06 N07 SING N N 15 
Y8P O40 C18 SING N N 16 
Y8P C18 C16 SING N N 17 
Y8P C09 N07 SING N N 18 
Y8P C09 C17 SING N N 19 
Y8P C16 C17 DOUB Y N 20 
Y8P C16 C15 SING Y N 21 
Y8P C17 C12 SING Y N 22 
Y8P C15 N14 DOUB Y N 23 
Y8P C12 O19 SING N N 24 
Y8P C12 C13 DOUB Y N 25 
Y8P N14 C13 SING Y N 26 
Y8P C13 C20 SING N N 27 
Y8P C18 H1  SING N N 28 
Y8P C18 H2  SING N N 29 
Y8P C11 H3  SING N N 30 
Y8P C11 H4  SING N N 31 
Y8P C01 H5  SING N N 32 
Y8P C06 H6  SING N N 33 
Y8P C08 H7  SING N N 34 
Y8P C09 H8  SING N N 35 
Y8P C09 H9  SING N N 36 
Y8P O43 H10 SING N N 37 
Y8P O44 H11 SING N N 38 
Y8P C10 H12 SING N N 39 
Y8P C10 H13 SING N N 40 
Y8P C15 H14 SING N N 41 
Y8P C20 H15 SING N N 42 
Y8P C20 H16 SING N N 43 
Y8P C20 H17 SING N N 44 
Y8P C21 H18 SING N N 45 
Y8P C21 H19 SING N N 46 
Y8P C21 H20 SING N N 47 
Y8P N07 H21 SING N N 48 
Y8P O04 H23 SING N N 49 
Y8P O19 H24 SING N N 50 
Y8P C01 H22 SING N N 51 
Y8P C02 H25 SING N N 52 
# 
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 
Y8P SMILES           ACDLabs              12.01 "Oc1c(CNC2CC(CCC2C)C(=O)O)c(cnc1C)COP(=O)(O)O"                                                                                                                               
Y8P InChI            InChI                1.03  "InChI=1S/C16H25N2O7P/c1-9-3-4-11(16(20)21)5-14(9)18-7-13-12(8-25-26(22,23)24)6-17-10(2)15(13)19/h6,9,11,14,18-19H,3-5,7-8H2,1-2H3,(H,20,21)(H2,22,23,24)/t9-,11?,14+/m0/s1" 
Y8P InChIKey         InChI                1.03  VMGXIUNFRDERKW-FGBBXPCBSA-N                                                                                                                                                  
Y8P SMILES_CANONICAL CACTVS               3.385 "C[C@H]1CC[C@H](C[C@H]1NCc2c(O)c(C)ncc2CO[P](O)(O)=O)C(O)=O"                                                                                                                 
Y8P SMILES           CACTVS               3.385 "C[CH]1CC[CH](C[CH]1NCc2c(O)c(C)ncc2CO[P](O)(O)=O)C(O)=O"                                                                                                                    
Y8P SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "Cc1c(c(c(cn1)COP(=O)(O)O)CN[C@@H]2CC(CC[C@@H]2C)C(=O)O)O"                                                                                                                   
Y8P SMILES           "OpenEye OEToolkits" 2.0.7 "Cc1c(c(c(cn1)COP(=O)(O)O)CNC2CC(CCC2C)C(=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 
Y8P "SYSTEMATIC NAME" ACDLabs              12.01 "(1R,3R,4S)-3-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]-4-methylcyclohexane-1-carboxylic acid" 
Y8P "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(3~{R},4~{S})-4-methyl-3-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]cyclohexane-1-carboxylic 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 
Y8P "Create component"   2021-02-10 RCSB 
Y8P "Modify value order" 2021-08-17 RCSB 
Y8P "Initial release"    2021-08-25 RCSB 
Y8P "Modify PCM"         2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            Y8P 
_pdbx_chem_comp_pcm.modified_residue_id                LYS 
_pdbx_chem_comp_pcm.type                               None 
_pdbx_chem_comp_pcm.category                           "Covalent chemical modification" 
_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               C21 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom   NZ 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession     ? 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession      ? 
# 
