data_SY6
# 
_chem_comp.id                                    SY6 
_chem_comp.name                                  "N-[(6-cyanopyridin-3-yl)methyl]-5-oxidanyl-2-[(3R)-3-oxidanylpyrrolidin-1-yl]-1,7-naphthyridine-6-carboxamide" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C20 H18 N6 O3" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-04-18 
_chem_comp.pdbx_modified_date                    2024-04-12 
_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                        390.395 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     SY6 
_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        8J1K 
_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 
SY6 C1  C1  C 0 1 N N N N N N -16.698 -27.785 5.114  -7.654 1.408  -0.978 C1  SY6 1  
SY6 C2  C2  C 0 1 N N R N N N -16.770 -29.282 4.855  -7.701 1.399  0.564  C2  SY6 2  
SY6 C3  C3  C 0 1 N N N N N N -18.171 -29.505 4.303  -6.299 0.930  1.006  C3  SY6 3  
SY6 N4  N1  N 0 1 N N N N N N -18.400 -28.264 3.568  -5.413 1.270  -0.137 N4  SY6 4  
SY6 C5  C4  C 0 1 N N N N N N -17.514 -27.185 3.987  -6.226 0.947  -1.340 C5  SY6 5  
SY6 O6  O1  O 0 1 N N N N N N -16.616 -29.988 6.076  -8.698 0.484  1.024  O6  SY6 6  
SY6 C7  C5  C 0 1 Y N N N N N -19.314 -28.106 2.567  -4.250 0.518  -0.107 C7  SY6 7  
SY6 C8  C6  C 0 1 Y N N N N N -19.411 -29.059 1.514  -4.340 -0.880 -0.081 C8  SY6 8  
SY6 C9  C7  C 0 1 Y N N N N N -20.314 -28.846 0.522  -3.203 -1.633 -0.057 C9  SY6 9  
SY6 C10 C8  C 0 1 Y N N N N N -21.123 -27.684 0.555  -1.966 -0.966 -0.059 C10 SY6 10 
SY6 C11 C9  C 0 1 Y N N N N N -20.969 -26.780 1.632  -1.940 0.451  -0.086 C11 SY6 11 
SY6 N12 N2  N 0 1 Y N N N N N -20.049 -27.010 2.620  -3.084 1.136  -0.109 N12 SY6 12 
SY6 C13 C10 C 0 1 Y N N N N N -21.762 -25.618 1.691  -0.689 1.104  -0.087 C13 SY6 13 
SY6 N14 N3  N 0 1 Y N N N N N -22.670 -25.317 0.773  0.420  0.414  -0.064 N14 SY6 14 
SY6 C15 C11 C 0 1 Y N N N N N -22.849 -26.151 -0.266 0.442  -0.922 -0.038 C15 SY6 15 
SY6 C16 C12 C 0 1 Y N N N N N -22.104 -27.357 -0.420 -0.740 -1.662 -0.035 C16 SY6 16 
SY6 O17 O2  O 0 1 N N N N N N -22.288 -28.195 -1.459 -0.712 -3.016 -0.008 O17 SY6 17 
SY6 C18 C13 C 0 1 N N N N N N -23.887 -25.742 -1.257 1.737  -1.625 -0.014 C18 SY6 18 
SY6 N19 N4  N 0 1 N N N N N N -24.032 -26.563 -2.306 2.886  -0.921 -0.017 N19 SY6 19 
SY6 C20 C14 C 0 1 N N N N N N -25.117 -26.487 -3.276 4.173  -1.620 0.007  C20 SY6 20 
SY6 C21 C15 C 0 1 Y N N N N N -24.616 -26.297 -4.690 5.293  -0.612 -0.002 C21 SY6 21 
SY6 C22 C16 C 0 1 Y N N N N N -25.192 -26.979 -5.750 5.802  -0.121 1.189  C22 SY6 22 
SY6 N23 N5  N 0 1 Y N N N N N -24.793 -26.844 -7.021 6.779  0.760  1.194  N23 SY6 23 
SY6 C24 C17 C 0 1 Y N N N N N -23.781 -25.999 -7.289 7.315  1.213  0.067  C24 SY6 24 
SY6 C25 C18 C 0 1 Y N N N N N -23.150 -25.273 -6.293 6.851  0.761  -1.169 C25 SY6 25 
SY6 C26 C19 C 0 1 Y N N N N N -23.579 -25.433 -4.987 5.827  -0.170 -1.204 C26 SY6 26 
SY6 C27 C20 C 0 1 N N N N N N -23.396 -25.862 -8.679 8.376  2.172  0.120  C27 SY6 27 
SY6 O28 O3  O 0 1 N N N N N N -24.512 -24.701 -1.048 1.768  -2.841 0.009  O28 SY6 28 
SY6 N29 N6  N 0 1 N N N N N N -23.039 -25.613 -9.759 9.219  2.933  0.162  N29 SY6 29 
SY6 H1  H1  H 0 1 N N N N N N -15.657 -27.430 5.077  -8.390 0.715  -1.384 H1  SY6 30 
SY6 H2  H2  H 0 1 N N N N N N -17.136 -27.535 6.092  -7.833 2.415  -1.356 H2  SY6 31 
SY6 H3  H3  H 0 1 N N N N N N -16.015 -29.578 4.112  -7.905 2.401  0.943  H3  SY6 32 
SY6 H4  H4  H 0 1 N N N N N N -18.905 -29.633 5.112  -5.984 1.465  1.903  H4  SY6 33 
SY6 H5  H5  H 0 1 N N N N N N -18.205 -30.379 3.635  -6.296 -0.145 1.185  H5  SY6 34 
SY6 H6  H6  H 0 1 N N N N N N -16.862 -26.872 3.158  -6.212 -0.126 -1.531 H6  SY6 35 
SY6 H7  H7  H 0 1 N N N N N N -18.094 -26.321 4.343  -5.855 1.493  -2.207 H7  SY6 36 
SY6 H8  H8  H 0 1 N N N N N N -15.741 -29.846 6.416  -9.595 0.703  0.738  H8  SY6 37 
SY6 H9  H9  H 0 1 N N N N N N -18.779 -29.935 1.504  -5.308 -1.360 -0.080 H9  SY6 38 
SY6 H10 H10 H 0 1 N N N N N N -20.414 -29.557 -0.285 -3.252 -2.712 -0.036 H10 SY6 39 
SY6 H11 H11 H 0 1 N N N N N N -21.624 -24.941 2.521  -0.649 2.183  -0.107 H11 SY6 40 
SY6 H12 H12 H 0 1 N N N N N N -21.698 -28.935 -1.378 -0.711 -3.391 0.883  H12 SY6 41 
SY6 H13 H13 H 0 1 N N N N N N -23.346 -27.280 -2.432 2.861  0.048  -0.036 H13 SY6 42 
SY6 H14 H14 H 0 1 N N N N N N -25.766 -25.638 -3.014 4.239  -2.228 0.910  H14 SY6 43 
SY6 H15 H15 H 0 1 N N N N N N -25.698 -27.420 -3.230 4.255  -2.262 -0.870 H15 SY6 44 
SY6 H16 H16 H 0 1 N N N N N N -26.007 -27.656 -5.540 5.391  -0.467 2.126  H16 SY6 45 
SY6 H17 H17 H 0 1 N N N N N N -22.341 -24.597 -6.530 7.287  1.130  -2.086 H17 SY6 46 
SY6 H18 H18 H 0 1 N N N N N N -23.100 -24.878 -4.194 5.448  -0.539 -2.145 H18 SY6 47 
# 
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 
SY6 N29 C27 TRIP N N 1  
SY6 C27 C24 SING N N 2  
SY6 C24 N23 DOUB Y N 3  
SY6 C24 C25 SING Y N 4  
SY6 N23 C22 SING Y N 5  
SY6 C25 C26 DOUB Y N 6  
SY6 C22 C21 DOUB Y N 7  
SY6 C26 C21 SING Y N 8  
SY6 C21 C20 SING N N 9  
SY6 C20 N19 SING N N 10 
SY6 N19 C18 SING N N 11 
SY6 O17 C16 SING N N 12 
SY6 C18 O28 DOUB N N 13 
SY6 C18 C15 SING N N 14 
SY6 C16 C15 DOUB Y N 15 
SY6 C16 C10 SING Y N 16 
SY6 C15 N14 SING Y N 17 
SY6 C9  C10 DOUB Y N 18 
SY6 C9  C8  SING Y N 19 
SY6 C10 C11 SING Y N 20 
SY6 N14 C13 DOUB Y N 21 
SY6 C8  C7  DOUB Y N 22 
SY6 C11 C13 SING Y N 23 
SY6 C11 N12 DOUB Y N 24 
SY6 C7  N12 SING Y N 25 
SY6 C7  N4  SING N N 26 
SY6 N4  C5  SING N N 27 
SY6 N4  C3  SING N N 28 
SY6 C5  C1  SING N N 29 
SY6 C3  C2  SING N N 30 
SY6 C2  C1  SING N N 31 
SY6 C2  O6  SING N N 32 
SY6 C1  H1  SING N N 33 
SY6 C1  H2  SING N N 34 
SY6 C2  H3  SING N N 35 
SY6 C3  H4  SING N N 36 
SY6 C3  H5  SING N N 37 
SY6 C5  H6  SING N N 38 
SY6 C5  H7  SING N N 39 
SY6 O6  H8  SING N N 40 
SY6 C8  H9  SING N N 41 
SY6 C9  H10 SING N N 42 
SY6 C13 H11 SING N N 43 
SY6 O17 H12 SING N N 44 
SY6 N19 H13 SING N N 45 
SY6 C20 H14 SING N N 46 
SY6 C20 H15 SING N N 47 
SY6 C22 H16 SING N N 48 
SY6 C25 H17 SING N N 49 
SY6 C26 H18 SING N N 50 
# 
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 
SY6 InChI            InChI                1.06  "InChI=1S/C20H18N6O3/c21-7-13-2-1-12(8-22-13)9-24-20(29)18-19(28)15-3-4-17(25-16(15)10-23-18)26-6-5-14(27)11-26/h1-4,8,10,14,27-28H,5-6,9,11H2,(H,24,29)/t14-/m1/s1" 
SY6 InChIKey         InChI                1.06  ROTOKWNRJPNVEV-CQSZACIVSA-N                                                                                                                                          
SY6 SMILES_CANONICAL CACTVS               3.385 "O[C@@H]1CCN(C1)c2ccc3c(O)c(ncc3n2)C(=O)NCc4ccc(nc4)C#N"                                                                                                             
SY6 SMILES           CACTVS               3.385 "O[CH]1CCN(C1)c2ccc3c(O)c(ncc3n2)C(=O)NCc4ccc(nc4)C#N"                                                                                                               
SY6 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1cc(ncc1CNC(=O)c2c(c3ccc(nc3cn2)N4CC[C@H](C4)O)O)C#N"                                                                                                              
SY6 SMILES           "OpenEye OEToolkits" 2.0.7 "c1cc(ncc1CNC(=O)c2c(c3ccc(nc3cn2)N4CCC(C4)O)O)C#N"                                                                                                                  
# 
_pdbx_chem_comp_identifier.comp_id           SY6 
_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        "~{N}-[(6-cyanopyridin-3-yl)methyl]-5-oxidanyl-2-[(3~{R})-3-oxidanylpyrrolidin-1-yl]-1,7-naphthyridine-6-carboxamide" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
SY6 "Create component" 2023-04-18 PDBJ 
SY6 "Initial release"  2024-04-17 RCSB 
# 
