data_A1APF
#
_chem_comp.id A1APF
_chem_comp.name "(5P)-2-amino-5-(1-methyl-1H-pyrazol-4-yl)-N-{(1R,2S)-2-[(4'-{2-[4-(2-oxoethyl)piperazin-1-yl]propan-2-yl}[1,1'-biphenyl]-4-yl)methoxy]cyclopentyl}pyridine-3-carboxamide"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C37 H45 N7 O3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2024-04-22
_chem_comp.pdbx_modified_date 2024-10-04
_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 635.798
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code A1APF
_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 9BHI
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
_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
A1APF N1 N1 N 0 1 Y N N N N N -34.386 -10.944 -9.309 -7.981 -3.602 2.696 N1 A1APF 1
A1APF N3 N2 N 0 1 N N N N N N -40.056 -8.641 -4.618 -6.372 -0.245 -4.078 N3 A1APF 2
A1APF C4 C1 C 0 1 Y N N N N N -37.297 -10.396 -7.099 -7.325 -2.283 -0.626 C4 A1APF 3
A1APF C5 C2 C 0 1 Y N N N N N -37.725 -9.082 -7.222 -7.526 -2.817 -1.897 C5 A1APF 4
A1APF C6 C3 C 0 1 Y N N N N N -39.184 -9.251 -5.428 -6.688 -0.920 -2.913 C6 A1APF 5
A1APF C7 C4 C 0 1 Y N N N N N -38.806 -10.610 -5.240 -6.454 -0.309 -1.669 C7 A1APF 6
A1APF C8 C5 C 0 1 Y N N N N N -37.862 -11.180 -6.097 -6.780 -1.006 -0.502 C8 A1APF 7
A1APF C10 C6 C 0 1 N N S N N N -39.029 -13.100 -2.367 -4.977 2.922 -0.328 C10 A1APF 8
A1APF C13 C7 C 0 1 N N N N N N -37.578 -13.003 -0.422 -4.446 4.544 1.415 C13 A1APF 9
A1APF C15 C8 C 0 1 N N N N N N -40.960 -11.465 -0.609 -2.065 2.352 1.854 C15 A1APF 10
A1APF C17 C9 C 0 1 Y N N N N N -42.707 -13.128 0.086 0.277 3.222 1.709 C17 A1APF 11
A1APF C20 C10 C 0 1 Y N N N N N -43.990 -11.249 1.642 1.158 0.835 0.608 C20 A1APF 12
A1APF C21 C11 C 0 1 Y N N N N N -42.846 -10.910 0.946 -0.173 0.997 0.935 C21 A1APF 13
A1APF C22 C12 C 0 1 Y N N N N N -45.776 -12.874 2.270 3.487 1.714 0.463 C22 A1APF 14
A1APF C24 C13 C 0 1 Y N N N N N -47.368 -14.506 3.061 5.266 0.372 -0.430 C24 A1APF 15
A1APF C26 C14 C 0 1 Y N N N N N -47.798 -12.186 3.394 5.713 2.603 0.330 C26 A1APF 16
A1APF C28 C15 C 0 1 N N N N N N -49.523 -13.857 4.235 7.604 1.249 -0.592 C28 A1APF 17
A1APF N N3 N 0 1 Y N N N N N -34.709 -12.197 -8.910 -8.422 -4.660 1.892 N A1APF 18
A1APF C C16 C 0 1 N N N N N N -33.969 -13.342 -9.429 -8.984 -5.926 2.369 C A1APF 19
A1APF O O1 O 0 1 N N N N N N -40.547 -11.255 -3.767 -5.683 1.680 -2.615 O A1APF 20
A1APF C1 C17 C 0 1 Y N N N N N -35.764 -12.208 -8.086 -8.239 -4.313 0.601 C1 A1APF 21
A1APF C11 C18 C 0 1 N N N N N N -38.330 -14.457 -2.208 -6.098 3.975 -0.288 C11 A1APF 22
A1APF C12 C19 C 0 1 N N N N N N -37.797 -14.461 -0.784 -5.937 4.740 1.043 C12 A1APF 23
A1APF C14 C20 C 0 1 N N S N N N -38.767 -12.301 -1.070 -4.173 3.083 0.979 C14 A1APF 24
A1APF C16 C21 C 0 1 Y N N N N N -42.191 -11.841 0.156 -0.613 2.185 1.489 C16 A1APF 25
A1APF C18 C22 C 0 1 Y N N N N N -43.851 -13.471 0.784 1.608 3.075 1.377 C18 A1APF 26
A1APF C19 C23 C 0 1 Y N N N N N -44.515 -12.535 1.574 2.057 1.878 0.823 C19 A1APF 27
A1APF C2 C24 C 0 1 Y N N N N N -36.177 -10.904 -7.923 -7.694 -3.062 0.584 C2 A1APF 28
A1APF C23 C25 C 0 1 Y N N N N N -46.178 -14.195 2.430 3.936 0.517 -0.091 C23 A1APF 29
A1APF C25 C26 C 0 1 Y N N N N N -48.199 -13.506 3.555 6.153 1.412 -0.220 C25 A1APF 30
A1APF C27 C27 C 0 1 Y N N N N N -46.608 -11.876 2.764 4.385 2.759 0.672 C27 A1APF 31
A1APF C29 C28 C 0 1 N N N N N N -50.384 -14.329 3.131 7.845 1.848 -1.980 C29 A1APF 32
A1APF C3 C29 C 0 1 Y N N N N N -35.276 -10.169 -8.712 -7.545 -2.645 1.920 C3 A1APF 33
A1APF C30 C30 C 0 1 N N N N N N -50.164 -12.732 4.983 8.479 1.971 0.434 C30 A1APF 34
A1APF C31 C31 C 0 1 N N N N N N -50.421 -15.847 5.608 7.846 -0.762 0.736 C31 A1APF 35
A1APF C32 C32 C 0 1 N N N N N N -49.991 -17.065 6.401 8.133 -2.263 0.662 C32 A1APF 36
A1APF C33 C33 C 0 1 N N N N N N -48.926 -17.784 8.511 9.816 -3.905 0.081 C33 A1APF 37
A1APF C34 C34 C 0 1 N N N N N N -47.893 -17.505 9.526 11.273 -4.068 -0.269 C34 A1APF 38
A1APF C35 C35 C 0 1 N N N N N N -48.005 -15.839 7.239 9.574 -1.895 -1.248 C35 A1APF 39
A1APF C36 C36 C 0 1 N N N N N N -48.404 -14.617 6.428 9.287 -0.393 -1.174 C36 A1APF 40
A1APF C9 C37 C 0 1 N N N N N N -39.382 -11.420 -4.113 -5.873 1.045 -1.596 C9 A1APF 41
A1APF N2 N4 N 0 1 Y N N N N N -38.631 -8.514 -6.418 -7.208 -2.136 -2.979 N2 A1APF 42
A1APF N4 N5 N 0 1 N N N N N N -38.604 -12.353 -3.548 -5.553 1.577 -0.400 N4 A1APF 43
A1APF N5 N6 N 0 1 N N N N N N -49.228 -15.014 5.228 7.947 -0.180 -0.610 N5 A1APF 44
A1APF N6 N7 N 0 1 N N N N N N -49.241 -16.610 7.621 9.473 -2.476 0.098 N6 A1APF 45
A1APF O1 O2 O 0 1 N N N N N N -39.923 -12.363 -0.233 -2.779 2.886 0.737 O1 A1APF 46
A1APF O2 O3 O 0 1 N N N N N N -47.273 -18.334 10.121 12.004 -4.689 0.464 O2 A1APF 47
A1APF H33 H1 H 0 1 N N N N N N -40.159 -7.686 -4.897 -6.344 0.724 -4.085 H33 A1APF 48
A1APF H32 H2 H 0 1 N N N N N N -40.942 -9.102 -4.674 -6.178 -0.742 -4.889 H32 A1APF 49
A1APF H51 H3 H 0 1 N N N N N N -37.302 -8.482 -8.014 -7.949 -3.806 -1.997 H51 A1APF 50
A1APF H81 H4 H 0 1 N N N N N N -37.574 -12.215 -5.984 -6.613 -0.566 0.471 H81 A1APF 51
A1APF H101 H5 H 0 0 N N N N N N -40.111 -13.284 -2.434 -4.330 3.098 -1.188 H101 A1APF 52
A1APF H131 H6 H 0 0 N N N N N N -37.583 -12.862 0.669 -3.815 5.238 0.859 H131 A1APF 53
A1APF H132 H7 H 0 0 N N N N N N -36.628 -12.632 -0.835 -4.294 4.662 2.488 H132 A1APF 54
A1APF H151 H8 H 0 0 N N N N N N -41.151 -11.546 -1.689 -2.485 1.383 2.125 H151 A1APF 55
A1APF H152 H9 H 0 0 N N N N N N -40.668 -10.433 -0.365 -2.151 3.034 2.700 H152 A1APF 56
A1APF H171 H10 H 0 0 N N N N N N -42.209 -13.870 -0.521 -0.072 4.149 2.139 H171 A1APF 57
A1APF H201 H11 H 0 0 N N N N N N -44.484 -10.504 2.248 1.500 -0.093 0.175 H201 A1APF 58
A1APF H211 H12 H 0 0 N N N N N N -42.457 -9.905 1.019 -0.873 0.194 0.757 H211 A1APF 59
A1APF H241 H13 H 0 0 N N N N N N -47.657 -15.541 3.172 5.615 -0.555 -0.860 H241 A1APF 60
A1APF H261 H14 H 0 0 N N N N N N -48.426 -11.390 3.767 6.410 3.412 0.492 H261 A1APF 61
A1APF HC3 H15 H 0 1 N N N N N N -33.193 -12.992 -10.126 -8.182 -6.650 2.511 HC3 A1APF 62
A1APF HC1 H16 H 0 1 N N N N N N -33.497 -13.882 -8.595 -9.496 -5.761 3.317 HC1 A1APF 63
A1APF HC2 H17 H 0 1 N N N N N N -34.660 -14.016 -9.957 -9.693 -6.308 1.635 HC2 A1APF 64
A1APF H11 H18 H 0 1 N N N N N N -36.210 -13.080 -7.632 -8.480 -4.915 -0.262 H11 A1APF 65
A1APF H111 H19 H 0 0 N N N N N N -39.045 -15.280 -2.355 -5.995 4.662 -1.128 H111 A1APF 66
A1APF H112 H20 H 0 0 N N N N N N -37.505 -14.554 -2.930 -7.071 3.486 -0.322 H112 A1APF 67
A1APF H121 H21 H 0 0 N N N N N N -38.528 -14.920 -0.102 -6.581 4.310 1.810 H121 A1APF 68
A1APF H122 H22 H 0 0 N N N N N N -36.849 -15.016 -0.731 -6.160 5.797 0.904 H122 A1APF 69
A1APF H141 H23 H 0 0 N N N N N N -38.504 -11.262 -1.318 -4.533 2.386 1.736 H141 A1APF 70
A1APF H181 H24 H 0 0 N N N N N N -44.235 -14.478 0.716 2.301 3.886 1.545 H181 A1APF 71
A1APF H231 H25 H 0 0 N N N N N N -45.551 -14.991 2.056 3.244 -0.296 -0.256 H231 A1APF 72
A1APF H271 H26 H 0 0 N N N N N N -46.319 -10.841 2.654 4.042 3.689 1.101 H271 A1APF 73
A1APF H292 H27 H 0 0 N N N N N N -51.371 -14.608 3.529 8.895 1.729 -2.249 H292 A1APF 74
A1APF H293 H28 H 0 0 N N N N N N -50.501 -13.526 2.389 7.222 1.333 -2.711 H293 A1APF 75
A1APF H291 H29 H 0 0 N N N N N N -49.920 -15.205 2.653 7.591 2.908 -1.967 H291 A1APF 76
A1APF H31 H30 H 0 1 N N N N N N -35.307 -9.095 -8.819 -7.142 -1.698 2.247 H31 A1APF 77
A1APF H302 H31 H 0 0 N N N N N N -51.105 -13.080 5.434 8.224 3.031 0.447 H302 A1APF 78
A1APF H301 H32 H 0 0 N N N N N N -49.484 -12.384 5.775 8.307 1.544 1.422 H301 A1APF 79
A1APF H303 H33 H 0 0 N N N N N N -50.374 -11.904 4.290 9.528 1.852 0.165 H303 A1APF 80
A1APF H312 H34 H 0 0 N N N N N N -50.939 -16.175 4.694 6.842 -0.602 1.127 H312 A1APF 81
A1APF H311 H35 H 0 0 N N N N N N -51.105 -15.241 6.220 8.573 -0.285 1.394 H311 A1APF 82
A1APF H321 H36 H 0 0 N N N N N N -50.878 -17.640 6.706 8.088 -2.692 1.663 H321 A1APF 83
A1APF H322 H37 H 0 0 N N N N N N -49.339 -17.698 5.781 7.390 -2.744 0.026 H322 A1APF 84
A1APF H332 H38 H 0 0 N N N N N N -48.575 -18.613 7.879 9.205 -4.416 -0.663 H332 A1APF 85
A1APF H331 H39 H 0 0 N N N N N N -49.849 -18.083 9.029 9.628 -4.335 1.064 H331 A1APF 86
A1APF H341 H40 H 0 0 N N N N N N -47.681 -16.470 9.749 11.663 -3.628 -1.175 H341 A1APF 87
A1APF H352 H41 H 0 0 N N N N N N -47.344 -16.480 6.637 8.847 -2.372 -1.905 H352 A1APF 88
A1APF H351 H42 H 0 0 N N N N N N -47.476 -15.519 8.149 10.578 -2.054 -1.639 H351 A1APF 89
A1APF H361 H43 H 0 0 N N N N N N -48.995 -13.940 7.063 10.030 0.088 -0.538 H361 A1APF 90
A1APF H362 H44 H 0 0 N N N N N N -47.496 -14.099 6.086 9.333 0.036 -2.175 H362 A1APF 91
A1APF H41 H45 H 0 1 N N N N N N -37.707 -12.543 -3.946 -5.705 1.071 0.413 H41 A1APF 92
#
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
A1APF N C SING N N 1
A1APF N C1 SING Y N 2
A1APF N N1 SING Y N 3
A1APF O C9 DOUB N N 4
A1APF C1 C2 DOUB Y N 5
A1APF C10 C11 SING N N 6
A1APF C10 C14 SING N N 7
A1APF C10 N4 SING N N 8
A1APF C11 C12 SING N N 9
A1APF C12 C13 SING N N 10
A1APF C13 C14 SING N N 11
A1APF C14 O1 SING N N 12
A1APF C15 C16 SING N N 13
A1APF C15 O1 SING N N 14
A1APF C16 C17 DOUB Y N 15
A1APF C16 C21 SING Y N 16
A1APF C17 C18 SING Y N 17
A1APF C18 C19 DOUB Y N 18
A1APF C19 C20 SING Y N 19
A1APF C19 C22 SING N N 20
A1APF C2 C3 SING Y N 21
A1APF C2 C4 SING N N 22
A1APF C20 C21 DOUB Y N 23
A1APF C22 C23 DOUB Y N 24
A1APF C22 C27 SING Y N 25
A1APF C23 C24 SING Y N 26
A1APF C24 C25 DOUB Y N 27
A1APF C25 C26 SING Y N 28
A1APF C25 C28 SING N N 29
A1APF C26 C27 DOUB Y N 30
A1APF C28 C29 SING N N 31
A1APF C28 C30 SING N N 32
A1APF C28 N5 SING N N 33
A1APF C3 N1 DOUB Y N 34
A1APF C31 C32 SING N N 35
A1APF C31 N5 SING N N 36
A1APF C32 N6 SING N N 37
A1APF C33 C34 SING N N 38
A1APF C33 N6 SING N N 39
A1APF C34 O2 DOUB N N 40
A1APF C35 C36 SING N N 41
A1APF C35 N6 SING N N 42
A1APF C36 N5 SING N N 43
A1APF C4 C5 DOUB Y N 44
A1APF C4 C8 SING Y N 45
A1APF C5 N2 SING Y N 46
A1APF C6 C7 SING Y N 47
A1APF C6 N2 DOUB Y N 48
A1APF C6 N3 SING N N 49
A1APF C7 C8 DOUB Y N 50
A1APF C7 C9 SING N N 51
A1APF C9 N4 SING N N 52
A1APF N3 H33 SING N N 53
A1APF N3 H32 SING N N 54
A1APF C5 H51 SING N N 55
A1APF C8 H81 SING N N 56
A1APF C10 H101 SING N N 57
A1APF C13 H131 SING N N 58
A1APF C13 H132 SING N N 59
A1APF C15 H151 SING N N 60
A1APF C15 H152 SING N N 61
A1APF C17 H171 SING N N 62
A1APF C20 H201 SING N N 63
A1APF C21 H211 SING N N 64
A1APF C24 H241 SING N N 65
A1APF C26 H261 SING N N 66
A1APF C HC3 SING N N 67
A1APF C HC1 SING N N 68
A1APF C HC2 SING N N 69
A1APF C1 H11 SING N N 70
A1APF C11 H111 SING N N 71
A1APF C11 H112 SING N N 72
A1APF C12 H121 SING N N 73
A1APF C12 H122 SING N N 74
A1APF C14 H141 SING N N 75
A1APF C18 H181 SING N N 76
A1APF C23 H231 SING N N 77
A1APF C27 H271 SING N N 78
A1APF C29 H292 SING N N 79
A1APF C29 H293 SING N N 80
A1APF C29 H291 SING N N 81
A1APF C3 H31 SING N N 82
A1APF C30 H302 SING N N 83
A1APF C30 H301 SING N N 84
A1APF C30 H303 SING N N 85
A1APF C31 H312 SING N N 86
A1APF C31 H311 SING N N 87
A1APF C32 H321 SING N N 88
A1APF C32 H322 SING N N 89
A1APF C33 H332 SING N N 90
A1APF C33 H331 SING N N 91
A1APF C34 H341 SING N N 92
A1APF C35 H352 SING N N 93
A1APF C35 H351 SING N N 94
A1APF C36 H361 SING N N 95
A1APF C36 H362 SING N N 96
A1APF N4 H41 SING N N 97
#
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
A1APF SMILES ACDLabs 12.01 "Cn1cc(cn1)c1cnc(N)c(c1)C(=O)NC1CCCC1OCc1ccc(cc1)c1ccc(cc1)C(C)(C)N1CCN(CC=O)CC1"
A1APF InChI InChI 1.06 "InChI=1S/C37H45N7O3/c1-37(2,44-17-15-43(16-18-44)19-20-45)31-13-11-28(12-14-31)27-9-7-26(8-10-27)25-47-34-6-4-5-33(34)41-36(46)32-21-29(22-39-35(32)38)30-23-40-42(3)24-30/h7-14,20-24,33-34H,4-6,15-19,25H2,1-3H3,(H2,38,39)(H,41,46)/t33-,34+/m1/s1"
A1APF InChIKey InChI 1.06 YAMLXCAIPJCCJF-NOCHOARKSA-N
A1APF SMILES_CANONICAL CACTVS 3.385 "Cn1cc(cn1)c2cnc(N)c(c2)C(=O)N[C@H]3CCC[C@@H]3OCc4ccc(cc4)c5ccc(cc5)C(C)(C)N6CCN(CC6)CC=O"
A1APF SMILES CACTVS 3.385 "Cn1cc(cn1)c2cnc(N)c(c2)C(=O)N[CH]3CCC[CH]3OCc4ccc(cc4)c5ccc(cc5)C(C)(C)N6CCN(CC6)CC=O"
A1APF SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC(C)(c1ccc(cc1)c2ccc(cc2)CO[C@H]3CCC[C@@H]3NC(=O)c4cc(cnc4N)c5cnn(c5)C)N6CCN(CC6)CC=O"
A1APF SMILES "OpenEye OEToolkits" 2.0.7 "CC(C)(c1ccc(cc1)c2ccc(cc2)COC3CCCC3NC(=O)c4cc(cnc4N)c5cnn(c5)C)N6CCN(CC6)CC=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
A1APF "SYSTEMATIC NAME" ACDLabs 12.01 "(5P)-2-amino-5-(1-methyl-1H-pyrazol-4-yl)-N-{(1R,2S)-2-[(4'-{2-[4-(2-oxoethyl)piperazin-1-yl]propan-2-yl}[1,1'-biphenyl]-4-yl)methoxy]cyclopentyl}pyridine-3-carboxamide"
A1APF "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "2-azanyl-5-(1-methylpyrazol-4-yl)-~{N}-[(1~{S},2~{S})-2-[[4-[4-[2-[4-(2-oxidanylideneethyl)piperazin-1-yl]propan-2-yl]phenyl]phenyl]methoxy]cyclopentyl]pyridine-3-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
A1APF "Create component" 2024-04-22 RCSB
A1APF "Initial release" 2024-10-09 RCSB
#