data_R1O
# 
_chem_comp.id                                    R1O 
_chem_comp.name                                  "N~2~-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-D-lysine" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C14 H24 N3 O7 P" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2022-06-15 
_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                        377.330 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     R1O 
_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        8D88 
_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 
R1O N1  N1  N 0 1 N N N N N N 34.837 -8.990  26.594 1.330  0.415  -0.244 N1  R1O 1  
R1O N3  N2  N 0 1 N N N N N N 29.111 -9.018  29.896 7.623  0.270  1.681  N3  R1O 2  
R1O C4  C1  C 0 1 Y N N N N N 36.414 -7.206  25.890 -0.125 -1.479 -0.691 C4  R1O 3  
R1O C5  C2  C 0 1 Y N N N N N 37.618 -7.034  26.610 -1.408 -1.362 -0.184 C5  R1O 4  
R1O C6  C3  C 0 1 Y N N N N N 38.793 -6.823  25.906 -2.024 -2.474 0.359  C6  R1O 5  
R1O C7  C4  C 0 1 Y N N N N N 37.662 -6.886  23.813 -0.187 -3.793 -0.078 C7  R1O 6  
R1O C8  C5  C 0 1 Y N N N N N 36.444 -7.059  24.456 0.495  -2.724 -0.638 C8  R1O 7  
R1O C10 C6  C 0 1 N N N N N N 37.634 -7.043  28.112 -2.125 -0.036 -0.222 C10 R1O 8  
R1O C13 C7  C 0 1 N N N N N N 30.982 -10.100 28.676 5.454  1.099  0.901  C13 R1O 9  
R1O C1  C8  C 0 1 N N N N N N 33.713 -10.928 25.449 1.094  2.762  -0.827 C1  R1O 10 
R1O C11 C9  C 0 1 N N N N N N 32.372 -9.202  26.730 3.238  1.914  0.086  C11 R1O 11 
R1O C12 C10 C 0 1 N N N N N N 32.358 -9.960  28.053 4.248  0.767  0.021  C12 R1O 12 
R1O C14 C11 C 0 1 N N N N N N 30.415 -8.806  29.222 6.465  -0.048 0.835  C14 R1O 13 
R1O C2  C12 C 0 1 N N R N N N 33.626 -9.451  25.882 2.031  1.583  -0.794 C2  R1O 14 
R1O C3  C13 C 0 1 N N N N N N 35.111 -7.546  26.579 0.580  -0.290 -1.292 C3  R1O 15 
R1O C9  C14 C 0 1 N N N N N N 37.766 -6.837  22.315 0.472  -5.147 -0.014 C9  R1O 16 
R1O N2  N3  N 0 1 Y N N N N N 38.779 -6.755  24.570 -1.406 -3.638 0.399  N2  R1O 17 
R1O O1  O1  O 0 1 N N N N N N 33.809 -11.782 26.354 1.521  3.946  -1.294 O1  R1O 18 
R1O O2  O2  O 0 1 N N N N N N 33.703 -11.174 24.220 -0.042 2.643  -0.433 O2  R1O 19 
R1O O3  O3  O 0 1 N N N N N N 35.387 -7.104  23.790 1.752  -2.888 -1.128 O3  R1O 20 
R1O O4  O4  O 0 1 N N N N N N 37.337 -8.326  28.655 -3.423 -0.179 0.358  O4  R1O 21 
R1O O5  O5  O 0 1 N N N N N N 36.880 -10.004 30.411 -4.687 1.640  -0.851 O5  R1O 22 
R1O O6  O6  O 0 1 N N N N N N 36.666 -7.537  30.942 -5.865 0.492  1.063  O6  R1O 23 
R1O O7  O7  O 0 1 N N N N N N 38.941 -8.550  30.560 -3.872 2.155  1.482  O7  R1O 24 
R1O P1  P1  P 0 1 N N N N N N 37.458 -8.611  30.235 -4.467 1.040  0.484  P1  R1O 25 
R1O H1  H1  H 0 1 N N N N N N 34.750 -9.271  27.550 1.973  -0.207 0.221  H1  R1O 26 
R1O H3  H3  H 0 1 N N N N N N 28.768 -8.145  30.243 7.336  0.464  2.628  H3  R1O 27 
R1O H4  H4  H 0 1 N N N N N N 28.456 -9.397  29.243 8.305  -0.473 1.654  H4  R1O 28 
R1O H6  H6  H 0 1 N N N N N N 39.726 -6.713  26.439 -3.025 -2.388 0.757  H6  R1O 29 
R1O H8  H8  H 0 1 N N N N N N 38.633 -6.738  28.456 -1.554 0.702  0.341  H8  R1O 30 
R1O H9  H9  H 0 1 N N N N N N 36.885 -6.324  28.477 -2.224 0.293  -1.257 H9  R1O 31 
R1O H10 H10 H 0 1 N N N N N N 30.293 -10.482 27.909 5.923  2.016  0.545  H10 R1O 32 
R1O H11 H11 H 0 1 N N N N N N 31.049 -10.823 29.502 5.126  1.235  1.931  H11 R1O 33 
R1O H12 H12 H 0 1 N N N N N N 32.309 -8.126  26.947 2.909  2.050  1.117  H12 R1O 34 
R1O H13 H13 H 0 1 N N N N N N 31.492 -9.510  26.146 3.706  2.832  -0.270 H13 R1O 35 
R1O H14 H14 H 0 1 N N N N N N 32.761 -10.968 27.877 4.576  0.631  -1.010 H14 R1O 36 
R1O H15 H15 H 0 1 N N N N N N 33.005 -9.425  28.764 3.780  -0.150 0.377  H15 R1O 37 
R1O H16 H16 H 0 1 N N N N N N 31.126 -8.383  29.947 6.793  -0.184 -0.195 H16 R1O 38 
R1O H17 H17 H 0 1 N N N N N N 30.276 -8.099  28.391 5.996  -0.966 1.191  H17 R1O 39 
R1O H18 H18 H 0 1 N N N N N N 33.524 -8.851  24.966 2.370  1.360  -1.806 H18 R1O 40 
R1O H19 H19 H 0 1 N N N N N N 35.158 -7.186  27.617 -0.155 0.385  -1.730 H19 R1O 41 
R1O H20 H20 H 0 1 N N N N N N 34.291 -7.038  26.051 1.268  -0.629 -2.066 H20 R1O 42 
R1O H21 H21 H 0 1 N N N N N N 38.817 -6.690  22.024 1.021  -5.239 0.924  H21 R1O 43 
R1O H22 H22 H 0 1 N N N N N N 37.397 -7.783  21.891 -0.289 -5.925 -0.067 H22 R1O 44 
R1O H23 H23 H 0 1 N N N N N N 37.160 -6.002  21.933 1.162  -5.256 -0.851 H23 R1O 45 
R1O H24 H24 H 0 1 N N N N N N 33.873 -12.648 25.968 0.883  4.673  -1.296 H24 R1O 46 
R1O H25 H25 H 0 1 N N N N N N 35.924 -7.930  31.386 -6.543 1.174  1.165  H25 R1O 47 
R1O H26 H26 H 0 1 N N N N N N 39.244 -9.412  30.820 -3.703 1.830  2.377  H26 R1O 48 
R1O H2  H2  H 0 1 N N N N N N 34.648 -7.226  24.375 1.781  -3.137 -2.062 H2  R1O 49 
# 
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 
R1O C9  C7  SING N N 1  
R1O O3  C8  SING N N 2  
R1O C7  C8  DOUB Y N 3  
R1O C7  N2  SING Y N 4  
R1O O2  C1  DOUB N N 5  
R1O C8  C4  SING Y N 6  
R1O N2  C6  DOUB Y N 7  
R1O C1  C2  SING N N 8  
R1O C1  O1  SING N N 9  
R1O C2  N1  SING N N 10 
R1O C2  C11 SING N N 11 
R1O C4  C3  SING N N 12 
R1O C4  C5  DOUB Y N 13 
R1O C6  C5  SING Y N 14 
R1O C3  N1  SING N N 15 
R1O C5  C10 SING N N 16 
R1O C11 C12 SING N N 17 
R1O C12 C13 SING N N 18 
R1O C10 O4  SING N N 19 
R1O O4  P1  SING N N 20 
R1O C13 C14 SING N N 21 
R1O C14 N3  SING N N 22 
R1O P1  O5  DOUB N N 23 
R1O P1  O7  SING N N 24 
R1O P1  O6  SING N N 25 
R1O N1  H1  SING N N 26 
R1O N3  H3  SING N N 27 
R1O N3  H4  SING N N 28 
R1O C6  H6  SING N N 29 
R1O C10 H8  SING N N 30 
R1O C10 H9  SING N N 31 
R1O C13 H10 SING N N 32 
R1O C13 H11 SING N N 33 
R1O C11 H12 SING N N 34 
R1O C11 H13 SING N N 35 
R1O C12 H14 SING N N 36 
R1O C12 H15 SING N N 37 
R1O C14 H16 SING N N 38 
R1O C14 H17 SING N N 39 
R1O C2  H18 SING N N 40 
R1O C3  H19 SING N N 41 
R1O C3  H20 SING N N 42 
R1O C9  H21 SING N N 43 
R1O C9  H22 SING N N 44 
R1O C9  H23 SING N N 45 
R1O O1  H24 SING N N 46 
R1O O6  H25 SING N N 47 
R1O O7  H26 SING N N 48 
R1O O3  H2  SING N N 49 
# 
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 
R1O SMILES           ACDLabs              12.01 "Oc1c(CNC(CCCCN)C(=O)O)c(cnc1C)COP(=O)(O)O"                                                                                                                 
R1O InChI            InChI                1.03  "InChI=1S/C14H24N3O7P/c1-9-13(18)11(10(6-16-9)8-24-25(21,22)23)7-17-12(14(19)20)4-2-3-5-15/h6,12,17-18H,2-5,7-8,15H2,1H3,(H,19,20)(H2,21,22,23)/t12-/m1/s1" 
R1O InChIKey         InChI                1.03  GQMAOPRRHWJXFB-GFCCVEGCSA-N                                                                                                                                 
R1O SMILES_CANONICAL CACTVS               3.385 "Cc1ncc(CO[P](O)(O)=O)c(CN[C@H](CCCCN)C(O)=O)c1O"                                                                                                           
R1O SMILES           CACTVS               3.385 "Cc1ncc(CO[P](O)(O)=O)c(CN[CH](CCCCN)C(O)=O)c1O"                                                                                                            
R1O SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "Cc1c(c(c(cn1)COP(=O)(O)O)CN[C@H](CCCCN)C(=O)O)O"                                                                                                           
R1O SMILES           "OpenEye OEToolkits" 2.0.7 "Cc1c(c(c(cn1)COP(=O)(O)O)CNC(CCCCN)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 
R1O "SYSTEMATIC NAME" ACDLabs              12.01 "N~2~-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-D-lysine"                       
R1O "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(2~{R})-6-azanyl-2-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]hexanoic 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 
R1O "Create component" 2022-06-15 RCSB 
R1O "Initial release"  2022-11-16 RCSB 
R1O "Modify PCM"       2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            R1O 
_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               C3 
_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      ? 
# 
