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
#