data_XK8
# 
_chem_comp.id                                    XK8 
_chem_comp.name                                  "3-[2-(3-{[2,4-diamino-6-(4-hydroxybutyl)pyrimidin-5-yl]oxy}propoxy)phenyl]propanoic acid" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C20 H28 N4 O5" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2022-11-23 
_chem_comp.pdbx_modified_date                    2023-12-08 
_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                        404.460 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     XK8 
_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        8F84 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
# 
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 
XK8 C1  C1  C 0 1 Y N N N N N -0.940 -9.186  13.040 5.883  -1.649 -0.019 C1  XK8 1  
XK8 C2  C2  C 0 1 Y N N N N N -0.492 -11.354 12.498 3.970  -2.064 1.199  C2  XK8 2  
XK8 C3  C3  C 0 1 Y N N N N N -0.652 -11.731 13.883 3.349  -0.982 0.563  C3  XK8 3  
XK8 C4  C4  C 0 1 N N N N N N -1.127 -14.189 13.659 1.032  -1.338 0.155  C4  XK8 4  
XK8 C5  C5  C 0 1 N N N N N N -0.724 -15.436 14.408 -0.328 -0.748 0.533  C5  XK8 5  
XK8 C6  C6  C 0 1 N N N N N N -0.967 -15.384 15.896 -1.433 -1.492 -0.221 C6  XK8 6  
XK8 C7  C7  C 0 1 Y N N N N N -2.787 -15.152 17.460 -3.799 -1.493 -0.454 C7  XK8 7  
XK8 C10 C8  C 0 1 Y N N N N N -3.759 -14.981 20.042 -6.028 -2.607 -1.655 C10 XK8 8  
XK8 C11 C9  C 0 1 Y N N N N N -4.621 -14.896 18.964 -6.175 -1.566 -0.759 C11 XK8 9  
XK8 C12 C10 C 0 1 Y N N N N N -4.167 -14.976 17.649 -5.064 -1.007 -0.157 C12 XK8 10 
XK8 C13 C11 C 0 1 N N N N N N -5.113 -14.882 16.462 -5.226 0.128  0.820  C13 XK8 11 
XK8 C14 C12 C 0 1 N N N N N N -6.472 -15.531 16.676 -5.046 1.460  0.089  C14 XK8 12 
XK8 C15 C13 C 0 1 N N N N N N -7.448 -15.250 15.544 -5.208 2.596  1.067  C15 XK8 13 
XK8 C16 C14 C 0 1 Y N N N N N -1.002 -10.719 14.771 4.072  -0.267 -0.376 C16 XK8 14 
XK8 C17 C15 C 0 1 N N N N N N -1.244 -10.963 16.235 3.447  0.906  -1.087 C17 XK8 15 
XK8 C18 C16 C 0 1 N N N N N N -2.709 -11.170 16.616 3.819  2.200  -0.359 C18 XK8 16 
XK8 C19 C17 C 0 1 N N N N N N -2.922 -11.550 18.073 3.279  3.398  -1.142 C19 XK8 17 
XK8 C20 C18 C 0 1 N N N N N N -2.479 -10.510 19.070 3.650  4.692  -0.414 C20 XK8 18 
XK8 C8  C19 C 0 1 Y N N N N N -1.922 -15.238 18.540 -3.653 -2.538 -1.354 C8  XK8 19 
XK8 C9  C20 C 0 1 Y N N N N N -2.416 -15.152 19.827 -4.767 -3.093 -1.953 C9  XK8 20 
XK8 N1  N1  N 0 1 N N N N N N -1.078 -7.908  12.627 7.194  -1.985 -0.320 N1  XK8 21 
XK8 N2  N2  N 0 1 Y N N N N N -0.623 -10.088 12.102 5.225  -2.363 0.883  N2  XK8 22 
XK8 N3  N3  N 0 1 N N N N N N -0.150 -12.254 11.536 3.286  -2.810 2.148  N3  XK8 23 
XK8 N4  N4  N 0 1 Y N N N N N -1.140 -9.444  14.350 5.323  -0.620 -0.636 N4  XK8 24 
XK8 O1  O1  O 0 1 N N N N N N -0.574 -13.045 14.339 2.064  -0.644 0.859  O1  XK8 25 
XK8 O2  O2  O 0 1 N N N N N N -2.373 -15.226 16.157 -2.704 -0.941 0.132  O2  XK8 26 
XK8 O3  O3  O 0 1 N N N N N N -8.607 -15.708 15.651 -5.092 3.865  0.647  O3  XK8 27 
XK8 O4  O4  O 0 1 N N N N N N -7.046 -14.580 14.566 -5.443 2.363  2.229  O4  XK8 28 
XK8 O5  O5  O 0 1 N N N N N N -2.584 -10.973 20.411 3.146  5.811  -1.145 O5  XK8 29 
XK8 H1  H1  H 0 1 N N N N N N -2.224 -14.110 13.633 1.058  -2.394 0.423  H1  XK8 30 
XK8 H2  H2  H 0 1 N N N N N N -0.738 -14.232 12.631 1.189  -1.231 -0.918 H2  XK8 31 
XK8 H3  H3  H 0 1 N N N N N N -1.295 -16.282 13.997 -0.485 -0.855 1.606  H3  XK8 32 
XK8 H4  H4  H 0 1 N N N N N N 0.350  -15.603 14.242 -0.353 0.308  0.265  H4  XK8 33 
XK8 H5  H5  H 0 1 N N N N N N -0.613 -16.318 16.356 -1.276 -1.385 -1.294 H5  XK8 34 
XK8 H6  H6  H 0 1 N N N N N N -0.418 -14.533 16.326 -1.408 -2.548 0.047  H6  XK8 35 
XK8 H7  H7  H 0 1 N N N N N N -4.142 -14.913 21.049 -6.898 -3.043 -2.124 H7  XK8 36 
XK8 H8  H8  H 0 1 N N N N N N -5.677 -14.764 19.147 -7.161 -1.188 -0.528 H8  XK8 37 
XK8 H9  H9  H 0 1 N N N N N N -4.632 -15.371 15.602 -6.221 0.088  1.263  H9  XK8 38 
XK8 H10 H10 H 0 1 N N N N N N -5.274 -13.818 16.236 -4.475 0.041  1.606  H10 XK8 39 
XK8 H11 H11 H 0 1 N N N N N N -6.901 -15.146 17.613 -4.051 1.501  -0.353 H11 XK8 40 
XK8 H12 H12 H 0 1 N N N N N N -6.332 -16.619 16.757 -5.797 1.548  -0.696 H12 XK8 41 
XK8 H13 H13 H 0 1 N N N N N N -0.683 -11.862 16.529 3.815  0.947  -2.112 H13 XK8 42 
XK8 H14 H14 H 0 1 N N N N N N -0.864 -10.095 16.794 2.363  0.792  -1.094 H14 XK8 43 
XK8 H15 H15 H 0 1 N N N N N N -3.253 -10.234 16.420 3.384  2.192  0.640  H15 XK8 44 
XK8 H16 H16 H 0 1 N N N N N N -3.120 -11.972 15.986 4.904  2.275  -0.283 H16 XK8 45 
XK8 H17 H17 H 0 1 N N N N N N -3.996 -11.734 18.225 3.714  3.406  -2.141 H17 XK8 46 
XK8 H18 H18 H 0 1 N N N N N N -2.360 -12.475 18.271 2.194  3.323  -1.218 H18 XK8 47 
XK8 H19 H19 H 0 1 N N N N N N -1.430 -10.248 18.867 3.215  4.684  0.585  H19 XK8 48 
XK8 H20 H20 H 0 1 N N N N N N -3.109 -9.616  18.953 4.735  4.767  -0.338 H20 XK8 49 
XK8 H21 H21 H 0 1 N N N N N N -0.863 -15.372 18.375 -2.669 -2.918 -1.587 H21 XK8 50 
XK8 H22 H22 H 0 1 N N N N N N -1.741 -15.220 20.668 -4.655 -3.907 -2.653 H22 XK8 51 
XK8 H23 H23 H 0 1 N N N N N N -0.911 -7.855  11.642 7.688  -1.468 -0.976 H23 XK8 52 
XK8 H24 H24 H 0 1 N N N N N N -2.006 -7.592  12.825 7.616  -2.736 0.124  H24 XK8 53 
XK8 H25 H25 H 0 1 N N N N N N -0.052 -11.784 10.659 2.371  -2.584 2.376  H25 XK8 54 
XK8 H26 H26 H 0 1 N N N N N N 0.717  -12.689 11.779 3.724  -3.559 2.583  H26 XK8 55 
XK8 H27 H27 H 0 1 N N N N N N -9.115 -15.467 14.885 -5.204 4.559  1.311  H27 XK8 56 
XK8 H28 H28 H 0 1 N N N N N N -2.296 -10.290 21.006 3.345  6.667  -0.741 H28 XK8 57 
# 
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 
XK8 N3  C2  SING N N 1  
XK8 N2  C2  DOUB Y N 2  
XK8 N2  C1  SING Y N 3  
XK8 C2  C3  SING Y N 4  
XK8 N1  C1  SING N N 5  
XK8 C1  N4  DOUB Y N 6  
XK8 C4  O1  SING N N 7  
XK8 C4  C5  SING N N 8  
XK8 C3  O1  SING N N 9  
XK8 C3  C16 DOUB Y N 10 
XK8 N4  C16 SING Y N 11 
XK8 C5  C6  SING N N 12 
XK8 O4  C15 DOUB N N 13 
XK8 C16 C17 SING N N 14 
XK8 C15 O3  SING N N 15 
XK8 C15 C14 SING N N 16 
XK8 C6  O2  SING N N 17 
XK8 O2  C7  SING N N 18 
XK8 C17 C18 SING N N 19 
XK8 C13 C14 SING N N 20 
XK8 C13 C12 SING N N 21 
XK8 C18 C19 SING N N 22 
XK8 C7  C12 DOUB Y N 23 
XK8 C7  C8  SING Y N 24 
XK8 C12 C11 SING Y N 25 
XK8 C19 C20 SING N N 26 
XK8 C8  C9  DOUB Y N 27 
XK8 C11 C10 DOUB Y N 28 
XK8 C20 O5  SING N N 29 
XK8 C9  C10 SING Y N 30 
XK8 C4  H1  SING N N 31 
XK8 C4  H2  SING N N 32 
XK8 C5  H3  SING N N 33 
XK8 C5  H4  SING N N 34 
XK8 C6  H5  SING N N 35 
XK8 C6  H6  SING N N 36 
XK8 C10 H7  SING N N 37 
XK8 C11 H8  SING N N 38 
XK8 C13 H9  SING N N 39 
XK8 C13 H10 SING N N 40 
XK8 C14 H11 SING N N 41 
XK8 C14 H12 SING N N 42 
XK8 C17 H13 SING N N 43 
XK8 C17 H14 SING N N 44 
XK8 C18 H15 SING N N 45 
XK8 C18 H16 SING N N 46 
XK8 C19 H17 SING N N 47 
XK8 C19 H18 SING N N 48 
XK8 C20 H19 SING N N 49 
XK8 C20 H20 SING N N 50 
XK8 C8  H21 SING N N 51 
XK8 C9  H22 SING N N 52 
XK8 N1  H23 SING N N 53 
XK8 N1  H24 SING N N 54 
XK8 N3  H25 SING N N 55 
XK8 N3  H26 SING N N 56 
XK8 O3  H27 SING N N 57 
XK8 O5  H28 SING N N 58 
# 
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 
XK8 SMILES           ACDLabs              12.01 "Nc1nc(CCCCO)c(OCCCOc2ccccc2CCC(=O)O)c(N)n1"                                                                                                                   
XK8 InChI            InChI                1.06  "InChI=1S/C20H28N4O5/c21-19-18(15(7-3-4-11-25)23-20(22)24-19)29-13-5-12-28-16-8-2-1-6-14(16)9-10-17(26)27/h1-2,6,8,25H,3-5,7,9-13H2,(H,26,27)(H4,21,22,23,24)" 
XK8 InChIKey         InChI                1.06  KIVXGXPLHYMNPB-UHFFFAOYSA-N                                                                                                                                    
XK8 SMILES_CANONICAL CACTVS               3.385 "Nc1nc(N)c(OCCCOc2ccccc2CCC(O)=O)c(CCCCO)n1"                                                                                                                   
XK8 SMILES           CACTVS               3.385 "Nc1nc(N)c(OCCCOc2ccccc2CCC(O)=O)c(CCCCO)n1"                                                                                                                   
XK8 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1ccc(c(c1)CCC(=O)O)OCCCOc2c(nc(nc2N)N)CCCCO"                                                                                                                 
XK8 SMILES           "OpenEye OEToolkits" 2.0.7 "c1ccc(c(c1)CCC(=O)O)OCCCOc2c(nc(nc2N)N)CCCCO"                                                                                                                 
# 
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 
XK8 "SYSTEMATIC NAME" ACDLabs              12.01 "3-[2-(3-{[2,4-diamino-6-(4-hydroxybutyl)pyrimidin-5-yl]oxy}propoxy)phenyl]propanoic acid"    
XK8 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "3-[2-[3-[2,4-bis(azanyl)-6-(4-oxidanylbutyl)pyrimidin-5-yl]oxypropoxy]phenyl]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 
XK8 "Create component" 2022-11-23 RCSB 
XK8 "Initial release"  2023-12-13 RCSB 
# 
