data_A1D5X
#
_chem_comp.id A1D5X
_chem_comp.name "~{tert}-butyl 4-[6-[(6-cyanopyridin-3-yl)methylcarbamoyl]-5-oxidanyl-1,7-naphthyridin-2-yl]piperazine-1-carboxylate"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C25 H27 N7 O4"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2024-02-04
_chem_comp.pdbx_modified_date 2024-12-13
_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 489.526
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code A1D5X
_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 8Y0V
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBC
_chem_comp.pdbx_pcm ?
#
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_n_terminal_atom_flag
_chem_comp_atom.pdbx_backbone_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
A1D5X C1 C1 C 0 1 N N N N N N -24.676 -26.303 -1.014 -4.094 -1.781 -0.394 C1 A1D5X 1
A1D5X C2 C2 C 0 1 N N N N N N -25.880 -26.951 -3.077 -6.429 -1.104 -0.555 C2 A1D5X 2
A1D5X C3 C3 C 0 1 Y N N N N N -25.371 -26.805 -4.493 -7.255 0.136 -0.330 C3 A1D5X 3
A1D5X C4 C4 C 0 1 Y N N N N N -26.040 -27.406 -5.550 -7.467 1.031 -1.364 C4 A1D5X 4
A1D5X C5 C5 C 0 1 Y N N N N N -24.562 -26.566 -7.087 -8.736 2.399 -0.005 C5 A1D5X 5
A1D5X C6 C6 C 0 1 N N N N N N -24.176 -26.469 -8.485 -9.511 3.594 0.149 C6 A1D5X 6
A1D5X C7 C7 C 0 1 Y N N N N N -23.827 -25.923 -6.109 -8.568 1.538 1.079 C7 A1D5X 7
A1D5X C8 C8 C 0 1 Y N N N N N -24.252 -26.051 -4.800 -7.815 0.388 0.914 C8 A1D5X 8
A1D5X C9 C9 C 0 1 Y N N N N N -23.652 -26.746 -0.018 -2.680 -1.490 -0.100 C9 A1D5X 9
A1D5X C10 C10 C 0 1 Y N N N N N -22.936 -27.936 -0.190 -1.728 -2.499 -0.241 C10 A1D5X 10
A1D5X N1 N1 N 0 1 N N N N N N -24.829 -27.106 -2.077 -5.023 -0.814 -0.262 N1 A1D5X 11
A1D5X C11 C11 C 0 1 Y N N N N N -21.961 -28.307 0.794 -0.382 -2.195 0.047 C11 A1D5X 12
A1D5X C12 C12 C 0 1 Y N N N N N -21.166 -29.468 0.727 0.641 -3.152 -0.069 C12 A1D5X 13
A1D5X O1 O1 O 0 1 N N N N N N -25.310 -25.271 -0.785 -4.422 -2.893 -0.762 O1 A1D5X 14
A1D5X N2 N2 N 0 1 Y N N N N N -25.654 -27.302 -6.832 -8.186 2.118 -1.181 N2 A1D5X 15
A1D5X C13 C13 C 0 1 Y N N N N N -20.259 -29.733 1.709 1.916 -2.771 0.230 C13 A1D5X 16
A1D5X N3 N3 N 0 1 N N N N N N -23.913 -26.383 -9.595 -10.126 4.541 0.272 N3 A1D5X 17
A1D5X N4 N4 N 0 1 N N N N N N -19.253 -29.021 3.816 3.472 -1.081 0.939 N4 A1D5X 18
A1D5X C14 C14 C 0 1 Y N N N N N -20.144 -28.828 2.801 2.172 -1.455 0.639 C14 A1D5X 19
A1D5X C15 C15 C 0 1 N N N N N N -18.607 -30.280 4.163 3.534 0.329 1.346 C15 A1D5X 20
A1D5X C16 C16 C 0 1 N N N N N N -17.100 -30.139 4.069 4.948 0.653 1.840 C16 A1D5X 21
A1D5X C17 C17 C 0 1 N N N N N N -15.701 -29.150 5.855 6.846 1.130 0.362 C17 A1D5X 22
A1D5X C18 C18 C 0 1 N N N N N N -14.340 -27.780 7.413 8.698 1.738 -1.014 C18 A1D5X 23
A1D5X C19 C19 C 0 1 N N N N N N -14.770 -28.592 8.617 9.556 2.146 0.186 C19 A1D5X 24
A1D5X N5 N5 N 0 1 N N N N N N -16.643 -29.024 4.891 5.908 0.264 0.796 N5 A1D5X 25
A1D5X C20 C20 C 0 1 N N N N N N -14.342 -26.302 7.736 7.982 2.970 -1.570 C20 A1D5X 26
A1D5X O2 O2 O 0 1 N N N N N N -23.112 -28.745 -1.262 -2.088 -3.741 -0.644 O2 A1D5X 27
A1D5X C21 C21 C 0 1 N N N N N N -12.991 -28.220 6.883 9.593 1.135 -2.099 C21 A1D5X 28
A1D5X C22 C22 C 0 1 N N N N N N -17.315 -27.766 4.584 5.819 -1.094 0.240 C22 A1D5X 29
A1D5X C23 C23 C 0 1 N N N N N N -18.816 -27.939 4.688 4.371 -1.349 -0.191 C23 A1D5X 30
A1D5X C24 C24 C 0 1 Y N N N N N -21.806 -27.437 1.895 -0.060 -0.880 0.466 C24 A1D5X 31
A1D5X C25 C25 C 0 1 Y N N N N N -22.610 -26.270 1.958 -1.098 0.068 0.577 C25 A1D5X 32
A1D5X O3 O3 O 0 1 N N N N N N -15.323 -27.942 6.318 7.716 0.755 -0.594 O3 A1D5X 33
A1D5X O4 O4 O 0 1 N N N N N N -15.279 -30.216 6.251 6.905 2.248 0.833 O4 A1D5X 34
A1D5X N6 N6 N 0 1 Y N N N N N -20.902 -27.710 2.888 1.206 -0.563 0.745 N6 A1D5X 35
A1D5X N7 N7 N 0 1 Y N N N N N -23.500 -25.929 1.044 -2.331 -0.261 0.293 N7 A1D5X 36
A1D5X H2 H1 H 0 1 N N N N N N -26.531 -27.837 -3.034 -6.781 -1.900 0.103 H2 A1D5X 37
A1D5X H3 H2 H 0 1 N N N N N N -26.465 -26.054 -2.826 -6.526 -1.422 -1.593 H3 A1D5X 38
A1D5X H4 H3 H 0 1 N N N N N N -26.921 -27.990 -5.329 -7.036 0.836 -2.335 H4 A1D5X 39
A1D5X H5 H4 H 0 1 N N N N N N -22.952 -25.341 -6.359 -9.018 1.766 2.034 H5 A1D5X 40
A1D5X H6 H5 H 0 1 N N N N N N -23.706 -25.558 -4.009 -7.668 -0.299 1.735 H6 A1D5X 41
A1D5X H1 H6 H 0 1 N N N N N N -24.181 -27.859 -2.192 -4.762 0.074 0.028 H1 A1D5X 42
A1D5X H8 H7 H 0 1 N N N N N N -21.275 -30.149 -0.104 0.423 -4.161 -0.386 H8 A1D5X 43
A1D5X H9 H8 H 0 1 N N N N N N -19.638 -30.615 1.659 2.726 -3.481 0.152 H9 A1D5X 44
A1D5X H11 H9 H 0 1 N N N N N N -18.882 -30.558 5.191 3.292 0.965 0.493 H11 A1D5X 45
A1D5X H10 H10 H 0 1 N N N N N N -18.943 -31.064 3.468 2.818 0.508 2.148 H10 A1D5X 46
A1D5X H12 H11 H 0 1 N N N N N N -16.626 -31.067 4.421 5.032 1.722 2.035 H12 A1D5X 47
A1D5X H13 H12 H 0 1 N N N N N N -16.817 -29.957 3.022 5.153 0.095 2.753 H13 A1D5X 48
A1D5X H15 H13 H 0 1 N N N N N N -14.035 -28.467 9.426 8.919 2.576 0.959 H15 A1D5X 49
A1D5X H14 H14 H 0 1 N N N N N N -15.756 -28.245 8.960 10.067 1.269 0.582 H14 A1D5X 50
A1D5X H16 H15 H 0 1 N N N N N N -14.832 -29.655 8.339 10.293 2.885 -0.129 H16 A1D5X 51
A1D5X H19 H16 H 0 1 N N N N N N -13.628 -26.103 8.549 8.719 3.708 -1.885 H19 A1D5X 52
A1D5X H17 H17 H 0 1 N N N N N N -14.049 -25.731 6.843 7.371 2.680 -2.425 H17 A1D5X 53
A1D5X H18 H18 H 0 1 N N N N N N -15.351 -25.997 8.051 7.344 3.400 -0.798 H18 A1D5X 54
A1D5X H7 H19 H 0 1 N N N N N N -22.535 -29.496 -1.190 -2.066 -3.864 -1.603 H7 A1D5X 55
A1D5X H22 H20 H 0 1 N N N N N N -12.233 -28.113 7.673 10.104 0.258 -1.702 H22 A1D5X 56
A1D5X H21 H21 H 0 1 N N N N N N -13.046 -29.273 6.569 8.982 0.845 -2.953 H21 A1D5X 57
A1D5X H20 H22 H 0 1 N N N N N N -12.714 -27.594 6.022 10.330 1.874 -2.414 H20 A1D5X 58
A1D5X H24 H23 H 0 1 N N N N N N -16.987 -26.995 5.297 6.479 -1.181 -0.623 H24 A1D5X 59
A1D5X H23 H24 H 0 1 N N N N N N -17.055 -27.454 3.562 6.108 -1.821 0.999 H23 A1D5X 60
A1D5X H26 H25 H 0 1 N N N N N N -19.312 -27.005 4.387 4.262 -2.388 -0.504 H26 A1D5X 61
A1D5X H25 H26 H 0 1 N N N N N N -19.084 -28.178 5.728 4.118 -0.691 -1.022 H25 A1D5X 62
A1D5X H27 H27 H 0 1 N N N N N N -22.486 -25.617 2.810 -0.873 1.075 0.895 H27 A1D5X 63
#
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
A1D5X O1 C1 DOUB N N 1
A1D5X C1 N1 SING N N 2
A1D5X C1 C9 SING N N 3
A1D5X N1 C2 SING N N 4
A1D5X C2 C3 SING N N 5
A1D5X C3 C4 DOUB Y N 6
A1D5X C3 C8 SING Y N 7
A1D5X C4 N2 SING Y N 8
A1D5X N2 C5 DOUB Y N 9
A1D5X C5 C6 SING N N 10
A1D5X C5 C7 SING Y N 11
A1D5X C6 N3 TRIP N N 12
A1D5X C7 C8 DOUB Y N 13
A1D5X C9 C10 DOUB Y N 14
A1D5X C9 N7 SING Y N 15
A1D5X C10 O2 SING N N 16
A1D5X C10 C11 SING Y N 17
A1D5X C11 C12 DOUB Y N 18
A1D5X C11 C24 SING Y N 19
A1D5X C12 C13 SING Y N 20
A1D5X C13 C14 DOUB Y N 21
A1D5X C14 N4 SING N N 22
A1D5X C14 N6 SING Y N 23
A1D5X N4 C15 SING N N 24
A1D5X N4 C23 SING N N 25
A1D5X C15 C16 SING N N 26
A1D5X C16 N5 SING N N 27
A1D5X N5 C17 SING N N 28
A1D5X N5 C22 SING N N 29
A1D5X C17 O3 SING N N 30
A1D5X C17 O4 DOUB N N 31
A1D5X O3 C18 SING N N 32
A1D5X C18 C19 SING N N 33
A1D5X C18 C20 SING N N 34
A1D5X C18 C21 SING N N 35
A1D5X C22 C23 SING N N 36
A1D5X N6 C24 DOUB Y N 37
A1D5X C24 C25 SING Y N 38
A1D5X C25 N7 DOUB Y N 39
A1D5X C2 H2 SING N N 40
A1D5X C2 H3 SING N N 41
A1D5X C4 H4 SING N N 42
A1D5X C7 H5 SING N N 43
A1D5X C8 H6 SING N N 44
A1D5X N1 H1 SING N N 45
A1D5X C12 H8 SING N N 46
A1D5X C13 H9 SING N N 47
A1D5X C15 H11 SING N N 48
A1D5X C15 H10 SING N N 49
A1D5X C16 H12 SING N N 50
A1D5X C16 H13 SING N N 51
A1D5X C19 H15 SING N N 52
A1D5X C19 H14 SING N N 53
A1D5X C19 H16 SING N N 54
A1D5X C20 H19 SING N N 55
A1D5X C20 H17 SING N N 56
A1D5X C20 H18 SING N N 57
A1D5X O2 H7 SING N N 58
A1D5X C21 H22 SING N N 59
A1D5X C21 H21 SING N N 60
A1D5X C21 H20 SING N N 61
A1D5X C22 H24 SING N N 62
A1D5X C22 H23 SING N N 63
A1D5X C23 H26 SING N N 64
A1D5X C23 H25 SING N N 65
A1D5X C25 H27 SING N N 66
#
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
A1D5X InChI InChI 1.06 "InChI=1S/C25H27N7O4/c1-25(2,3)36-24(35)32-10-8-31(9-11-32)20-7-6-18-19(30-20)15-28-21(22(18)33)23(34)29-14-16-4-5-17(12-26)27-13-16/h4-7,13,15,33H,8-11,14H2,1-3H3,(H,29,34)"
A1D5X InChIKey InChI 1.06 VXVKDBNSYJRFIQ-UHFFFAOYSA-N
A1D5X SMILES_CANONICAL CACTVS 3.385 "CC(C)(C)OC(=O)N1CCN(CC1)c2ccc3c(O)c(ncc3n2)C(=O)NCc4ccc(nc4)C#N"
A1D5X SMILES CACTVS 3.385 "CC(C)(C)OC(=O)N1CCN(CC1)c2ccc3c(O)c(ncc3n2)C(=O)NCc4ccc(nc4)C#N"
A1D5X SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC(C)(C)OC(=O)N1CCN(CC1)c2ccc3c(n2)cnc(c3O)C(=O)NCc4ccc(nc4)C#N"
A1D5X SMILES "OpenEye OEToolkits" 2.0.7 "CC(C)(C)OC(=O)N1CCN(CC1)c2ccc3c(n2)cnc(c3O)C(=O)NCc4ccc(nc4)C#N"
#
_pdbx_chem_comp_identifier.comp_id A1D5X
_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 "~{tert}-butyl 4-[6-[(6-cyanopyridin-3-yl)methylcarbamoyl]-5-oxidanyl-1,7-naphthyridin-2-yl]piperazine-1-carboxylate"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
A1D5X "Create component" 2024-02-04 PDBC
A1D5X "Initial release" 2024-12-18 RCSB
#