data_XN3
#
_chem_comp.id XN3
_chem_comp.name "N-[2(R)-HYDROXY-1(S)-INDANYL]-5-[(2(S)-TERTIARY BUTYLAMINOCARBONYL)-4(BENZO[1,3]DIOXOL-5-YLMETHYL)-PIPERAZINO]-4(S)-HYDROXY-2(R)-PHENYLMETHYLPENTANAMIDE"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C38 H48 N4 O6"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "ANALOGUE OF INDINAVIR DRUG"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2001-11-02
_chem_comp.pdbx_modified_date 2021-03-01
_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 656.811
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code XN3
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details ?
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 1K6P
_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.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
XN3 N1 N1 N 0 1 N N N 2.987 -5.221 16.433 0.792 -0.232 4.823 N1 XN3 1
XN3 C1 C1 C 0 1 N N N 4.424 -5.136 15.883 1.947 -0.633 4.009 C1 XN3 2
XN3 C2 C2 C 0 1 N N S 5.274 -4.003 16.455 1.933 0.132 2.685 C2 XN3 3
XN3 C3 C3 C 0 1 N N N 6.589 -4.107 15.780 3.159 -0.227 1.885 C3 XN3 4
XN3 O1 O1 O 0 1 N N N 6.690 -3.717 14.587 3.040 -0.731 0.789 O1 XN3 5
XN3 N2 N2 N 0 1 N N N 7.625 -4.613 16.505 4.386 0.011 2.389 N2 XN3 6
XN3 C4 C4 C 0 1 N N N 9.044 -4.825 16.155 5.577 -0.337 1.611 C4 XN3 7
XN3 C5 C5 C 0 1 N N N 9.776 -5.467 17.364 6.831 0.034 2.404 C5 XN3 8
XN3 C6 C6 C 0 1 N N N 9.731 -3.618 15.929 5.565 0.429 0.287 C6 XN3 9
XN3 C7 C7 C 0 1 N N N 9.271 -5.728 14.980 5.579 -1.841 1.329 C7 XN3 10
XN3 N3 N3 N 0 1 N N N 4.408 -2.732 16.155 0.730 -0.223 1.923 N3 XN3 11
XN3 C8 C8 C 0 1 N N N 2.977 -2.721 16.623 -0.423 0.178 2.736 C8 XN3 12
XN3 C9 C9 C 0 1 N N N 2.304 -3.992 16.089 -0.410 -0.587 4.060 C9 XN3 13
XN3 C10 C10 C 0 1 N N N 5.034 -1.478 16.685 0.721 0.630 0.728 C10 XN3 14
XN3 C11 C11 C 0 1 N N S 5.031 -0.404 15.652 -0.342 0.129 -0.249 C11 XN3 15
XN3 O2 O2 O 0 1 N N N 5.026 0.651 16.597 -1.639 0.320 0.319 O2 XN3 16
XN3 C12 C12 C 0 1 N N N 6.260 -0.144 14.795 -0.240 0.911 -1.560 C12 XN3 17
XN3 C13 C13 C 0 1 N N R 6.247 0.968 13.736 -1.181 0.294 -2.597 C13 XN3 18
XN3 C14 C14 C 0 1 N N N 7.676 1.026 12.987 -2.632 0.546 -2.183 C14 XN3 19
XN3 C15 C15 C 0 1 Y N N 7.708 2.134 11.912 -3.558 -0.093 -3.185 C15 XN3 20
XN3 C16 C16 C 0 1 Y N N 7.564 3.576 12.269 -3.878 -1.433 -3.073 C16 XN3 21
XN3 C17 C17 C 0 1 Y N N 7.586 4.581 11.223 -4.728 -2.020 -3.992 C17 XN3 22
XN3 C18 C18 C 0 1 Y N N 7.753 4.151 9.811 -5.258 -1.266 -5.022 C18 XN3 23
XN3 C19 C19 C 0 1 Y N N 7.895 2.718 9.474 -4.940 0.073 -5.134 C19 XN3 24
XN3 C20 C20 C 0 1 Y N N 7.872 1.729 10.518 -4.093 0.661 -4.212 C20 XN3 25
XN3 C21 C21 C 0 1 N N N 5.136 0.742 12.627 -0.925 0.921 -3.943 C21 XN3 26
XN3 O3 O3 O 0 1 N N N 4.774 -0.409 12.158 -0.706 2.111 -4.026 O3 XN3 27
XN3 N4 N4 N 0 1 N N N 4.646 1.895 12.231 -0.941 0.160 -5.055 N4 XN3 28
XN3 C22 C22 C 0 1 N N S 3.633 2.075 11.211 -0.581 0.746 -6.349 C22 XN3 29
XN3 C23 C23 C 0 1 N N R 3.599 3.499 10.677 -1.275 -0.019 -7.495 C23 XN3 30
XN3 O4 O4 O 0 1 N N N 3.736 4.453 11.726 -1.540 -1.371 -7.115 O4 XN3 31
XN3 C24 C24 C 0 1 N N N 2.302 3.578 9.921 -0.220 0.041 -8.620 C24 XN3 32
XN3 C25 C25 C 0 1 Y N N 1.255 2.845 10.718 1.108 0.179 -7.910 C25 XN3 33
XN3 C26 C26 C 0 1 Y N N -0.140 2.839 10.859 2.398 -0.032 -8.369 C26 XN3 34
XN3 C27 C27 C 0 1 Y N N -0.724 1.905 11.805 3.476 0.160 -7.527 C27 XN3 35
XN3 C28 C28 C 0 1 Y N N 0.109 0.984 12.599 3.268 0.565 -6.222 C28 XN3 36
XN3 C29 C29 C 0 1 Y N N 1.518 0.980 12.465 1.983 0.777 -5.762 C29 XN3 37
XN3 C30 C30 C 0 1 Y N N 2.167 1.848 11.576 0.901 0.586 -6.604 C30 XN3 38
XN3 C31 C31 C 0 1 N N N 2.237 -6.357 15.862 0.802 -1.086 6.018 C31 XN3 39
XN3 C32 C32 C 0 1 Y N N 2.785 -7.749 16.170 -0.363 -0.726 6.902 C32 XN3 40
XN3 C33 C33 C 0 1 Y N N 2.627 -8.346 17.497 -1.578 -1.366 6.737 C33 XN3 41
XN3 C34 C34 C 0 1 Y N N 3.824 -10.363 16.761 -2.510 -0.069 8.525 C34 XN3 42
XN3 C35 C35 C 0 1 Y N N 4.019 -9.841 15.442 -1.286 0.575 8.691 C35 XN3 43
XN3 C36 C36 C 0 1 Y N N 3.485 -8.508 15.132 -0.214 0.238 7.880 C36 XN3 44
XN3 O5 O5 O 0 1 N N N 4.418 -11.636 16.810 -3.393 0.430 9.438 O5 XN3 45
XN3 C38 C38 C 0 1 N N N 5.050 -12.091 15.549 -2.819 1.670 9.891 C38 XN3 46
XN3 O6 O6 O 0 1 N N N 4.711 -10.844 14.773 -1.403 1.477 9.708 O6 XN3 47
XN3 C37 C37 C 0 1 Y N N 3.134 -9.674 17.873 -2.650 -1.039 7.546 C37 XN3 48
XN3 H11A 1H1 H 0 0 N N N 4.406 -5.077 14.770 1.896 -1.703 3.810 H11A XN3 49
XN3 H12 2H1 H 0 1 N N N 4.945 -6.112 16.019 2.867 -0.408 4.549 H12 XN3 50
XN3 H2 H2 H 0 1 N N N 5.511 -4.002 17.545 1.932 1.203 2.886 H2 XN3 51
XN3 HN2 HN2 H 0 1 N N N 7.294 -4.867 17.436 4.480 0.414 3.266 HN2 XN3 52
XN3 H51 1H5 H 0 1 N N N 9.281 -6.404 17.710 7.718 -0.225 1.826 H51 XN3 53
XN3 H52 2H5 H 0 1 N N N 10.847 -5.627 17.100 6.830 1.105 2.605 H52 XN3 54
XN3 H53 3H5 H 0 1 N N N 9.655 -4.870 18.298 6.840 -0.512 3.347 H53 XN3 55
XN3 H61 1H6 H 0 1 N N N 9.632 -2.931 16.802 5.563 1.500 0.488 H61 XN3 56
XN3 H62 2H6 H 0 1 N N N 10.802 -3.778 15.665 6.451 0.169 -0.291 H62 XN3 57
XN3 H63 3H6 H 0 1 N N N 9.215 -3.002 15.156 4.671 0.164 -0.277 H63 XN3 58
XN3 H71 1H7 H 0 1 N N N 8.705 -5.359 14.093 5.588 -2.387 2.272 H71 XN3 59
XN3 H72 2H7 H 0 1 N N N 10.342 -5.888 14.716 4.686 -2.106 0.764 H72 XN3 60
XN3 H73 3H7 H 0 1 N N N 8.762 -6.707 15.140 6.466 -2.101 0.751 H73 XN3 61
XN3 H81 1H8 H 0 1 N N N 2.434 -1.790 16.337 -1.343 -0.046 2.197 H81 XN3 62
XN3 H82 2H8 H 0 1 N N N 2.883 -2.612 17.729 -0.373 1.248 2.936 H82 XN3 63
XN3 H91 1H9 H 0 1 N N N 1.239 -4.035 16.416 -0.409 -1.658 3.860 H91 XN3 64
XN3 H92 2H9 H 0 1 N N N 2.162 -3.922 14.985 -1.296 -0.327 4.639 H92 XN3 65
XN3 H101 1H10 H 0 0 N N N 6.059 -1.665 17.081 0.495 1.657 1.016 H101 XN3 66
XN3 H102 2H10 H 0 0 N N N 4.547 -1.142 17.630 1.700 0.595 0.249 H102 XN3 67
XN3 H11 H11 H 0 1 N N N 4.249 -0.593 14.880 -0.184 -0.931 -0.446 H11 XN3 68
XN3 HO2 HO2 H 0 1 N N N 5.024 1.336 15.938 -1.738 1.268 0.477 HO2 XN3 69
XN3 H121 1H12 H 0 0 N N N 6.548 -1.099 14.297 -0.522 1.949 -1.386 H121 XN3 70
XN3 H122 2H12 H 0 0 N N N 7.129 0.027 15.472 0.784 0.870 -1.929 H122 XN3 71
XN3 H13 H13 H 0 1 N N N 6.026 1.918 14.277 -1.001 -0.779 -2.657 H13 XN3 72
XN3 H141 1H14 H 0 0 N N N 7.952 0.034 12.559 -2.809 0.116 -1.198 H141 XN3 73
XN3 H142 2H14 H 0 0 N N N 8.513 1.140 13.715 -2.818 1.620 -2.150 H142 XN3 74
XN3 H16 H16 H 0 1 N N N 7.440 3.902 13.315 -3.463 -2.021 -2.268 H16 XN3 75
XN3 H17 H17 H 0 1 N N N 7.479 5.645 11.494 -4.977 -3.067 -3.905 H17 XN3 76
XN3 H18 H18 H 0 1 N N N 7.772 4.903 9.005 -5.922 -1.725 -5.741 H18 XN3 77
XN3 H19 H19 H 0 1 N N N 8.020 2.383 8.431 -5.354 0.662 -5.939 H19 XN3 78
XN3 H20 H20 H 0 1 N N N 7.980 0.664 10.251 -3.844 1.709 -4.299 H20 XN3 79
XN3 HN4 HN4 H 0 1 N N N 5.067 2.677 12.733 -1.191 -0.775 -4.999 HN4 XN3 80
XN3 H22 H22 H 0 1 N N N 3.971 1.282 10.504 -0.859 1.800 -6.376 H22 XN3 81
XN3 H23 H23 H 0 1 N N N 4.454 3.745 10.005 -2.193 0.483 -7.798 H23 XN3 82
XN3 HO4 HO4 H 0 1 N N N 3.715 5.342 11.393 -1.907 -1.813 -7.893 HO4 XN3 83
XN3 H241 1H24 H 0 0 N N N 2.389 3.203 8.875 -0.241 -0.876 -9.209 H241 XN3 84
XN3 H242 2H24 H 0 0 N N N 2.006 4.626 9.680 -0.399 0.905 -9.260 H242 XN3 85
XN3 H26 H26 H 0 1 N N N -0.748 3.534 10.256 2.561 -0.348 -9.389 H26 XN3 86
XN3 H27 H27 H 0 1 N N N -1.821 1.895 11.923 4.480 -0.006 -7.888 H27 XN3 87
XN3 H28 H28 H 0 1 N N N -0.336 0.275 13.317 4.110 0.715 -5.562 H28 XN3 88
XN3 H29 H29 H 0 1 N N N 2.125 0.284 13.068 1.822 1.093 -4.742 H29 XN3 89
XN3 H311 1H31 H 0 0 N N N 2.137 -6.227 14.759 0.721 -2.131 5.718 H311 XN3 90
XN3 H312 2H31 H 0 0 N N N 1.167 -6.296 16.170 1.733 -0.936 6.565 H312 XN3 91
XN3 H33 H33 H 0 1 N N N 2.092 -7.758 18.262 -1.689 -2.122 5.974 H33 XN3 92
XN3 H36 H36 H 0 1 N N N 3.609 -8.079 14.124 0.736 0.733 8.011 H36 XN3 93
XN3 H381 1H38 H 0 0 N N N 4.726 -13.071 15.128 -3.174 2.501 9.282 H381 XN3 94
XN3 H382 2H38 H 0 0 N N N 6.119 -12.407 15.586 -3.050 1.837 10.943 H382 XN3 95
XN3 H37 H37 H 0 1 N N N 3.010 -10.106 18.880 -3.598 -1.540 7.414 H37 XN3 96
# #
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
XN3 N1 C1 SING N N 1
XN3 N1 C9 SING N N 2
XN3 N1 C31 SING N N 3
XN3 C1 C2 SING N N 4
XN3 C1 H11A SING N N 5
XN3 C1 H12 SING N N 6
XN3 C2 C3 SING N N 7
XN3 C2 N3 SING N N 8
XN3 C2 H2 SING N N 9
XN3 C3 O1 DOUB N N 10
XN3 C3 N2 SING N N 11
XN3 N2 C4 SING N N 12
XN3 N2 HN2 SING N N 13
XN3 C4 C5 SING N N 14
XN3 C4 C6 SING N N 15
XN3 C4 C7 SING N N 16
XN3 C5 H51 SING N N 17
XN3 C5 H52 SING N N 18
XN3 C5 H53 SING N N 19
XN3 C6 H61 SING N N 20
XN3 C6 H62 SING N N 21
XN3 C6 H63 SING N N 22
XN3 C7 H71 SING N N 23
XN3 C7 H72 SING N N 24
XN3 C7 H73 SING N N 25
XN3 N3 C8 SING N N 26
XN3 N3 C10 SING N N 27
XN3 C8 C9 SING N N 28
XN3 C8 H81 SING N N 29
XN3 C8 H82 SING N N 30
XN3 C9 H91 SING N N 31
XN3 C9 H92 SING N N 32
XN3 C10 C11 SING N N 33
XN3 C10 H101 SING N N 34
XN3 C10 H102 SING N N 35
XN3 C11 O2 SING N N 36
XN3 C11 C12 SING N N 37
XN3 C11 H11 SING N N 38
XN3 O2 HO2 SING N N 39
XN3 C12 C13 SING N N 40
XN3 C12 H121 SING N N 41
XN3 C12 H122 SING N N 42
XN3 C13 C14 SING N N 43
XN3 C13 C21 SING N N 44
XN3 C13 H13 SING N N 45
XN3 C14 C15 SING N N 46
XN3 C14 H141 SING N N 47
XN3 C14 H142 SING N N 48
XN3 C15 C16 DOUB Y N 49
XN3 C15 C20 SING Y N 50
XN3 C16 C17 SING Y N 51
XN3 C16 H16 SING N N 52
XN3 C17 C18 DOUB Y N 53
XN3 C17 H17 SING N N 54
XN3 C18 C19 SING Y N 55
XN3 C18 H18 SING N N 56
XN3 C19 C20 DOUB Y N 57
XN3 C19 H19 SING N N 58
XN3 C20 H20 SING N N 59
XN3 C21 O3 DOUB N N 60
XN3 C21 N4 SING N N 61
XN3 N4 C22 SING N N 62
XN3 N4 HN4 SING N N 63
XN3 C22 C23 SING N N 64
XN3 C22 C30 SING N N 65
XN3 C22 H22 SING N N 66
XN3 C23 O4 SING N N 67
XN3 C23 C24 SING N N 68
XN3 C23 H23 SING N N 69
XN3 O4 HO4 SING N N 70
XN3 C24 C25 SING N N 71
XN3 C24 H241 SING N N 72
XN3 C24 H242 SING N N 73
XN3 C25 C26 DOUB Y N 74
XN3 C25 C30 SING Y N 75
XN3 C26 C27 SING Y N 76
XN3 C26 H26 SING N N 77
XN3 C27 C28 DOUB Y N 78
XN3 C27 H27 SING N N 79
XN3 C28 C29 SING Y N 80
XN3 C28 H28 SING N N 81
XN3 C29 C30 DOUB Y N 82
XN3 C29 H29 SING N N 83
XN3 C31 C32 SING N N 84
XN3 C31 H311 SING N N 85
XN3 C31 H312 SING N N 86
XN3 C32 C33 DOUB Y N 87
XN3 C32 C36 SING Y N 88
XN3 C33 C37 SING Y N 89
XN3 C33 H33 SING N N 90
XN3 C34 C35 SING Y N 91
XN3 C34 O5 SING N N 92
XN3 C34 C37 DOUB Y N 93
XN3 C35 C36 DOUB Y N 94
XN3 C35 O6 SING N N 95
XN3 C36 H36 SING N N 96
XN3 O5 C38 SING N N 97
XN3 C38 O6 SING N N 98
XN3 C38 H381 SING N N 99
XN3 C38 H382 SING N N 100
XN3 C37 H37 SING N N 101
# #
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
XN3 SMILES ACDLabs 10.04 "O=C(NC2c1ccccc1CC2O)C(Cc3ccccc3)CC(O)CN4C(C(=O)NC(C)(C)C)CN(CC4)Cc5ccc6OCOc6c5"
XN3 SMILES_CANONICAL CACTVS 3.341 "CC(C)(C)NC(=O)[C@@H]1CN(CCN1C[C@@H](O)C[C@@H](Cc2ccccc2)C(=O)N[C@@H]3[C@H](O)Cc4ccccc34)Cc5ccc6OCOc6c5"
XN3 SMILES CACTVS 3.341 "CC(C)(C)NC(=O)[CH]1CN(CCN1C[CH](O)C[CH](Cc2ccccc2)C(=O)N[CH]3[CH](O)Cc4ccccc34)Cc5ccc6OCOc6c5"
XN3 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC(C)(C)NC(=O)[C@@H]1C[N@@](CC[N@]1C[C@H](C[C@@H](Cc2ccccc2)C(=O)N[C@H]3c4ccccc4C[C@H]3O)O)Cc5ccc6c(c5)OCO6"
XN3 SMILES "OpenEye OEToolkits" 1.5.0 "CC(C)(C)NC(=O)C1CN(CCN1CC(CC(Cc2ccccc2)C(=O)NC3c4ccccc4CC3O)O)Cc5ccc6c(c5)OCO6"
XN3 InChI InChI 1.03 "InChI=1S/C38H48N4O6/c1-38(2,3)40-37(46)31-23-41(21-26-13-14-33-34(18-26)48-24-47-33)15-16-42(31)22-29(43)19-28(17-25-9-5-4-6-10-25)36(45)39-35-30-12-8-7-11-27(30)20-32(35)44/h4-14,18,28-29,31-32,35,43-44H,15-17,19-24H2,1-3H3,(H,39,45)(H,40,46)/t28-,29+,31+,32-,35+/m1/s1"
XN3 InChIKey InChI 1.03 BJZTWVIYUGVEFV-OQOOGSQVSA-N
# #
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
XN3 "SYSTEMATIC NAME" ACDLabs 10.04 "(2S)-4-(1,3-benzodioxol-5-ylmethyl)-1-[(2S,4R)-4-benzyl-2-hydroxy-5-{[(1S,2R)-2-hydroxy-2,3-dihydro-1H-inden-1-yl]amino}-5-oxopentyl]-N-tert-butylpiperazine-2-carboxamide (non-preferred name)"
XN3 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(1S,2S,4R)-4-(1,3-benzodioxol-5-ylmethyl)-N-tert-butyl-1-[(2S,4R)-2-hydroxy-5-[[(1S,2R)-2-hydroxy-2,3-dihydro-1H-inden-1-yl]amino]-5-oxo-4-(phenylmethyl)pentyl]piperazine-2-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
XN3 "Create component" 2001-11-02 RCSB
XN3 "Modify descriptor" 2011-06-04 RCSB
XN3 "Modify synonyms" 2021-03-01 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id XN3
_pdbx_chem_comp_synonyms.name "ANALOGUE OF INDINAVIR DRUG"
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
##