data_XN2
#
_chem_comp.id XN2
_chem_comp.name
;N-[2-HYDROXY-1-INDANYL]-5-[(2-TERTIARYBUTYLAMINOCARBONYL)-4(BENZO[1,3]DIOXOL-5-YLMETHYL)-PIPERAZINO]-4-HYDROXY-2-(1-PHE
NYLETHYL)-PENTANAMIDE
;
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C39 H50 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 2001-11-05
_chem_comp.pdbx_modified_date 2020-06-17
_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 670.837
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code XN2
_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 1K6V
_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
XN2 N1 N1 N 0 1 N N N 3.118 -5.284 16.285 -0.481 2.517 -4.309 N1 XN2 1
XN2 C1 C1 C 0 1 N N N 4.586 -5.168 15.716 -0.964 1.139 -4.454 C1 XN2 2
XN2 C2 C2 C 0 1 N N S 5.384 -4.013 16.309 -1.920 0.805 -3.308 C2 XN2 3
XN2 C3 C3 C 0 1 N N N 6.711 -4.050 15.650 -2.469 -0.584 -3.501 C3 XN2 4
XN2 O1 O1 O 0 1 N N N 6.784 -3.698 14.415 -2.276 -1.434 -2.658 O1 XN2 5
XN2 N2 N2 N 0 1 N N N 7.799 -4.446 16.411 -3.173 -0.883 -4.611 N2 XN2 6
XN2 C4 C4 C 0 1 N N N 9.245 -4.568 16.053 -3.707 -2.234 -4.798 C4 XN2 7
XN2 C5 C5 C 0 1 N N N 10.049 -5.068 17.284 -4.460 -2.305 -6.128 C5 XN2 8
XN2 C6 C6 C 0 1 N N N 9.837 -3.326 15.749 -2.554 -3.240 -4.810 C6 XN2 9
XN2 C7 C7 C 0 1 N N N 9.530 -5.506 14.912 -4.663 -2.568 -3.652 C7 XN2 10
XN2 N3 N3 N 0 1 N N N 4.472 -2.771 16.007 -1.201 0.873 -2.030 N3 XN2 11
XN2 C8 C8 C 0 1 N N N 3.022 -2.764 16.440 -0.718 2.252 -1.885 C8 XN2 12
XN2 C9 C9 C 0 1 N N N 2.406 -4.057 15.871 0.237 2.585 -3.031 C9 XN2 13
XN2 C10 C10 C 0 1 N N N 5.092 -1.507 16.561 -2.199 0.662 -0.973 C10 XN2 14
XN2 C11 C11 C 0 1 N N S 5.037 -0.433 15.553 -1.550 0.891 0.393 C11 XN2 15
XN2 O2 O2 O 0 1 N N N 5.191 0.590 16.510 -1.259 2.281 0.555 O2 XN2 16
XN2 C12 C12 C 0 1 N N N 6.197 -0.217 14.654 -2.510 0.439 1.495 C12 XN2 17
XN2 C13 C13 C 0 1 N N S 6.150 0.869 13.593 -1.818 0.558 2.855 C13 XN2 18
XN2 C14 C14 C 0 1 N N S 7.587 0.864 12.798 -2.831 0.289 3.968 C14 XN2 19
XN2 C15 C15 C 0 1 Y N N 7.548 1.976 11.672 -2.196 0.571 5.305 C15 XN2 20
XN2 C16 C16 C 0 1 Y N N 7.335 3.476 11.991 -2.092 -0.434 6.248 C16 XN2 21
XN2 C17 C17 C 0 1 Y N N 7.297 4.460 10.893 -1.509 -0.174 7.474 C17 XN2 22
XN2 C18 C18 C 0 1 Y N N 7.467 3.973 9.458 -1.029 1.090 7.758 C18 XN2 23
XN2 C19 C19 C 0 1 Y N N 7.673 2.509 9.160 -1.132 2.095 6.815 C19 XN2 24
XN2 C20 C20 C 0 1 Y N N 7.711 1.532 10.253 -1.711 1.835 5.587 C20 XN2 25
XN2 C21 C21 C 0 1 N N N 4.997 0.611 12.505 -0.699 -0.448 2.939 C21 XN2 26
XN2 O3 O3 O 0 1 N N N 4.651 -0.542 12.012 -0.478 -1.188 2.003 O3 XN2 27
XN2 N4 N4 N 0 1 N N N 4.461 1.752 12.151 0.054 -0.526 4.053 N4 XN2 28
XN2 C22 C22 C 0 1 N N S 3.419 1.890 11.155 1.141 -1.505 4.135 C22 XN2 29
XN2 C23 C23 C 0 1 N N R 3.430 3.272 10.534 1.375 -1.924 5.602 C23 XN2 30
XN2 O4 O4 O 0 1 N N N 3.710 4.288 11.495 0.974 -0.885 6.497 O4 XN2 31
XN2 C24 C24 C 0 1 N N N 2.100 3.384 9.835 2.903 -2.134 5.646 C24 XN2 32
XN2 C25 C25 C 0 1 Y N N 1.054 2.722 10.670 3.458 -1.241 4.557 C25 XN2 33
XN2 C26 C26 C 0 1 Y N N -0.360 2.771 10.835 4.747 -0.782 4.342 C26 XN2 34
XN2 C27 C27 C 0 1 Y N N -0.973 1.876 11.843 5.023 0.035 3.264 C27 XN2 35
XN2 C28 C28 C 0 1 Y N N -0.150 0.933 12.679 4.010 0.396 2.395 C28 XN2 36
XN2 C29 C29 C 0 1 Y N N 1.287 0.882 12.513 2.724 -0.060 2.608 C29 XN2 37
XN2 C30 C30 C 0 1 Y N N 1.954 1.715 11.564 2.445 -0.881 3.686 C30 XN2 38
XN2 C31 C31 C 0 1 N N N 2.408 -6.407 15.697 0.516 2.729 -5.367 C31 XN2 39
XN2 C32 C32 C 0 1 Y N N 2.958 -7.777 16.044 1.482 1.572 -5.384 C32 XN2 40
XN2 C33 C33 C 0 1 Y N N 2.752 -8.297 17.426 1.220 0.467 -6.172 C33 XN2 41
XN2 C34 C34 C 0 1 Y N N 3.975 -10.400 16.841 3.254 -0.555 -5.421 C34 XN2 42
XN2 C35 C35 C 0 1 Y N N 4.219 -9.965 15.465 3.518 0.557 -4.628 C35 XN2 43
XN2 C36 C36 C 0 1 Y N N 3.702 -8.623 15.045 2.630 1.622 -4.617 C36 XN2 44
XN2 O5 O5 O 0 1 N N N 4.542 -11.657 16.990 4.269 -1.454 -5.263 O5 XN2 45
XN2 C38 C38 C 0 1 N N N 5.209 -12.201 15.787 4.949 -1.058 -4.058 C38 XN2 46
XN2 O6 O6 O 0 1 N N N 4.922 -11.017 14.900 4.698 0.357 -3.973 O6 XN2 47
XN2 C37 C37 C 0 1 Y N N 3.240 -9.621 17.906 2.103 -0.596 -6.192 C37 XN2 48
XN2 C39 C39 C 0 1 N N N 8.810 0.899 13.231 -4.049 1.196 3.780 C39 XN2 49
XN2 H11A 1H1 H 0 0 N N N 4.573 -5.106 14.603 -1.487 1.035 -5.405 H11A XN2 50
XN2 H12 2H1 H 0 1 N N N 5.134 -6.131 15.843 -0.117 0.453 -4.431 H12 XN2 51
XN2 H2 H2 H 0 1 N N N 5.607 -4.022 17.402 -2.741 1.522 -3.301 H2 XN2 52
XN2 HN2 HN2 H 0 1 N N N 7.496 -4.678 17.357 -3.327 -0.203 -5.285 HN2 XN2 53
XN2 H51 1H5 H 0 1 N N N 9.637 -6.018 17.697 -4.857 -3.311 -6.267 H51 XN2 54
XN2 H52 2H5 H 0 1 N N N 11.128 -5.159 17.017 -5.281 -1.588 -6.119 H52 XN2 55
XN2 H53 3H5 H 0 1 N N N 9.891 -4.422 18.179 -3.778 -2.067 -6.945 H53 XN2 56
XN2 H61 1H6 H 0 1 N N N 9.691 -2.599 16.582 -1.873 -3.002 -5.627 H61 XN2 57
XN2 H62 2H6 H 0 1 N N N 10.916 -3.417 15.482 -2.018 -3.190 -3.863 H62 XN2 58
XN2 H63 3H6 H 0 1 N N N 9.270 -2.798 14.947 -2.951 -4.246 -4.950 H63 XN2 59
XN2 H71 1H7 H 0 1 N N N 8.932 -5.219 14.016 -5.484 -1.851 -3.643 H71 XN2 60
XN2 H72 2H7 H 0 1 N N N 10.609 -5.597 14.645 -5.060 -3.574 -3.791 H72 XN2 61
XN2 H73 3H7 H 0 1 N N N 9.096 -6.512 15.119 -4.127 -2.518 -2.704 H73 XN2 62
XN2 H81 1H8 H 0 1 N N N 2.473 -1.840 16.143 -1.566 2.937 -1.909 H81 XN2 63
XN2 H82 2H8 H 0 1 N N N 2.886 -2.653 17.541 -0.195 2.355 -0.935 H82 XN2 64
XN2 H91 1H9 H 0 1 N N N 1.323 -4.124 16.128 0.634 3.591 -2.891 H91 XN2 65
XN2 H92 2H9 H 0 1 N N N 2.330 -4.001 14.760 1.058 1.869 -3.039 H92 XN2 66
XN2 H101 1H10 H 0 0 N N N 6.129 -1.679 16.932 -2.577 -0.358 -1.029 H101 XN2 67
XN2 H102 2H10 H 0 0 N N N 4.623 -1.199 17.525 -3.023 1.362 -1.106 H102 XN2 68
XN2 H11 H11 H 0 1 N N N 4.179 -0.565 14.854 -0.626 0.316 0.457 H11 XN2 69
XN2 HO2 HO2 H 0 1 N N N 5.156 1.282 15.860 -2.108 2.744 0.572 HO2 XN2 70
XN2 H121 1H12 H 0 0 N N N 6.440 -1.184 14.156 -2.798 -0.597 1.324 H121 XN2 71
XN2 H122 2H12 H 0 0 N N N 7.103 -0.055 15.283 -3.399 1.070 1.484 H122 XN2 72
XN2 H13 H13 H 0 1 N N N 5.943 1.838 14.104 -1.411 1.563 2.969 H13 XN2 73
XN2 H141 1H14 H 0 0 N N N 7.523 -0.238 12.638 -3.146 -0.753 3.929 H141 XN2 74
XN2 H16 H16 H 0 1 N N N 7.208 3.851 13.021 -2.467 -1.422 6.026 H16 XN2 75
XN2 H17 H17 H 0 1 N N N 7.146 5.525 11.137 -1.429 -0.960 8.211 H17 XN2 76
XN2 H18 H18 H 0 1 N N N 7.441 4.692 8.622 -0.574 1.293 8.716 H18 XN2 77
XN2 H19 H19 H 0 1 N N N 7.798 2.147 8.126 -0.757 3.084 7.036 H19 XN2 78
XN2 H20 H20 H 0 1 N N N 7.862 0.467 10.009 -1.791 2.621 4.850 H20 XN2 79
XN2 HN4 HN4 H 0 1 N N N 4.860 2.543 12.657 -0.123 0.065 4.801 HN4 XN2 80
XN2 H22 H22 H 0 1 N N N 3.698 1.037 10.493 0.910 -2.378 3.524 H22 XN2 81
XN2 H23 H23 H 0 1 N N N 4.254 3.421 9.798 0.849 -2.852 5.828 H23 XN2 82
XN2 HO4 HO4 H 0 1 N N N 3.717 5.155 11.106 1.145 -1.207 7.393 HO4 XN2 83
XN2 H241 1H24 H 0 0 N N N 2.131 2.981 8.796 3.298 -1.836 6.617 H241 XN2 84
XN2 H242 2H24 H 0 0 N N N 1.839 4.439 9.586 3.148 -3.177 5.442 H242 XN2 85
XN2 H26 H26 H 0 1 N N N -0.950 3.466 10.214 5.538 -1.064 5.020 H26 XN2 86
XN2 H27 H27 H 0 1 N N N -2.068 1.913 11.974 6.029 0.391 3.100 H27 XN2 87
XN2 H28 H28 H 0 1 N N N -0.609 0.266 13.428 4.224 1.036 1.552 H28 XN2 88
XN2 H29 H29 H 0 1 N N N 1.889 0.190 13.126 1.933 0.222 1.929 H29 XN2 89
XN2 H311 1H31 H 0 0 N N N 2.352 -6.287 14.590 0.013 2.797 -6.332 H311 XN2 90
XN2 H312 2H31 H 0 0 N N N 1.325 -6.353 15.956 1.059 3.653 -5.173 H312 XN2 91
XN2 H33 H33 H 0 1 N N N 2.203 -7.661 18.140 0.323 0.433 -6.773 H33 XN2 92
XN2 H36 H36 H 0 1 N N N 3.867 -8.263 14.015 2.835 2.489 -4.007 H36 XN2 93
XN2 H381 1H38 H 0 0 N N N 4.883 -13.205 15.427 4.529 -1.574 -3.194 H381 XN2 94
XN2 H382 2H38 H 0 0 N N N 6.272 -12.522 15.889 6.018 -1.253 -4.139 H382 XN2 95
XN2 H37 H37 H 0 1 N N N 3.076 -9.984 18.935 1.896 -1.458 -6.808 H37 XN2 96
XN2 H391 1H39 H 0 0 N N N 8.880 0.044 13.943 -3.744 2.238 3.879 H391 XN2 97
XN2 H392 2H39 H 0 0 N N N 9.786 0.896 12.691 -4.473 1.034 2.790 H392 XN2 98
XN2 H393 3H39 H 0 0 N N N 8.852 1.804 13.880 -4.796 0.963 4.539 H393 XN2 99
# #
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
XN2 N1 C1 SING N N 1
XN2 N1 C9 SING N N 2
XN2 N1 C31 SING N N 3
XN2 C1 C2 SING N N 4
XN2 C1 H11A SING N N 5
XN2 C1 H12 SING N N 6
XN2 C2 C3 SING N N 7
XN2 C2 N3 SING N N 8
XN2 C2 H2 SING N N 9
XN2 C3 O1 DOUB N N 10
XN2 C3 N2 SING N N 11
XN2 N2 C4 SING N N 12
XN2 N2 HN2 SING N N 13
XN2 C4 C5 SING N N 14
XN2 C4 C6 SING N N 15
XN2 C4 C7 SING N N 16
XN2 C5 H51 SING N N 17
XN2 C5 H52 SING N N 18
XN2 C5 H53 SING N N 19
XN2 C6 H61 SING N N 20
XN2 C6 H62 SING N N 21
XN2 C6 H63 SING N N 22
XN2 C7 H71 SING N N 23
XN2 C7 H72 SING N N 24
XN2 C7 H73 SING N N 25
XN2 N3 C8 SING N N 26
XN2 N3 C10 SING N N 27
XN2 C8 C9 SING N N 28
XN2 C8 H81 SING N N 29
XN2 C8 H82 SING N N 30
XN2 C9 H91 SING N N 31
XN2 C9 H92 SING N N 32
XN2 C10 C11 SING N N 33
XN2 C10 H101 SING N N 34
XN2 C10 H102 SING N N 35
XN2 C11 O2 SING N N 36
XN2 C11 C12 SING N N 37
XN2 C11 H11 SING N N 38
XN2 O2 HO2 SING N N 39
XN2 C12 C13 SING N N 40
XN2 C12 H121 SING N N 41
XN2 C12 H122 SING N N 42
XN2 C13 C14 SING N N 43
XN2 C13 C21 SING N N 44
XN2 C13 H13 SING N N 45
XN2 C14 C15 SING N N 46
XN2 C14 C39 SING N N 47
XN2 C14 H141 SING N N 48
XN2 C15 C16 DOUB Y N 49
XN2 C15 C20 SING Y N 50
XN2 C16 C17 SING Y N 51
XN2 C16 H16 SING N N 52
XN2 C17 C18 DOUB Y N 53
XN2 C17 H17 SING N N 54
XN2 C18 C19 SING Y N 55
XN2 C18 H18 SING N N 56
XN2 C19 C20 DOUB Y N 57
XN2 C19 H19 SING N N 58
XN2 C20 H20 SING N N 59
XN2 C21 O3 DOUB N N 60
XN2 C21 N4 SING N N 61
XN2 N4 C22 SING N N 62
XN2 N4 HN4 SING N N 63
XN2 C22 C23 SING N N 64
XN2 C22 C30 SING N N 65
XN2 C22 H22 SING N N 66
XN2 C23 O4 SING N N 67
XN2 C23 C24 SING N N 68
XN2 C23 H23 SING N N 69
XN2 O4 HO4 SING N N 70
XN2 C24 C25 SING N N 71
XN2 C24 H241 SING N N 72
XN2 C24 H242 SING N N 73
XN2 C25 C26 DOUB Y N 74
XN2 C25 C30 SING Y N 75
XN2 C26 C27 SING Y N 76
XN2 C26 H26 SING N N 77
XN2 C27 C28 DOUB Y N 78
XN2 C27 H27 SING N N 79
XN2 C28 C29 SING Y N 80
XN2 C28 H28 SING N N 81
XN2 C29 C30 DOUB Y N 82
XN2 C29 H29 SING N N 83
XN2 C31 C32 SING N N 84
XN2 C31 H311 SING N N 85
XN2 C31 H312 SING N N 86
XN2 C32 C33 DOUB Y N 87
XN2 C32 C36 SING Y N 88
XN2 C33 C37 SING Y N 89
XN2 C33 H33 SING N N 90
XN2 C34 C35 SING Y N 91
XN2 C34 O5 SING N N 92
XN2 C34 C37 DOUB Y N 93
XN2 C35 C36 DOUB Y N 94
XN2 C35 O6 SING N N 95
XN2 C36 H36 SING N N 96
XN2 O5 C38 SING N N 97
XN2 C38 O6 SING N N 98
XN2 C38 H381 SING N N 99
XN2 C38 H382 SING N N 100
XN2 C37 H37 SING N N 101
XN2 C39 H391 SING N N 102
XN2 C39 H392 SING N N 103
XN2 C39 H393 SING N N 104
# #
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
XN2 SMILES ACDLabs 10.04 "O=C(NC2c1ccccc1CC2O)C(C(c3ccccc3)C)CC(O)CN4C(C(=O)NC(C)(C)C)CN(CC4)Cc5ccc6OCOc6c5"
XN2 SMILES_CANONICAL CACTVS 3.341 "C[C@@H]([C@H](C[C@H](O)CN1CCN(C[C@H]1C(=O)NC(C)(C)C)Cc2ccc3OCOc3c2)C(=O)N[C@@H]4[C@H](O)Cc5ccccc45)c6ccccc6"
XN2 SMILES CACTVS 3.341 "C[CH]([CH](C[CH](O)CN1CCN(C[CH]1C(=O)NC(C)(C)C)Cc2ccc3OCOc3c2)C(=O)N[CH]4[CH](O)Cc5ccccc45)c6ccccc6"
XN2 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C[C@H](c1ccccc1)[C@H](C[C@@H](C[N@@]2CC[N@](C[C@H]2C(=O)NC(C)(C)C)Cc3ccc4c(c3)OCO4)O)C(=O)N[C@H]5c6ccccc6C[C@H]5O"
XN2 SMILES "OpenEye OEToolkits" 1.5.0 "CC(c1ccccc1)C(CC(CN2CCN(CC2C(=O)NC(C)(C)C)Cc3ccc4c(c3)OCO4)O)C(=O)NC5c6ccccc6CC5O"
XN2 InChI InChI 1.03 "InChI=1S/C39H50N4O6/c1-25(27-10-6-5-7-11-27)31(37(46)40-36-30-13-9-8-12-28(30)19-33(36)45)20-29(44)22-43-17-16-42(23-32(43)38(47)41-39(2,3)4)21-26-14-15-34-35(18-26)49-24-48-34/h5-15,18,25,29,31-33,36,44-45H,16-17,19-24H2,1-4H3,(H,40,46)(H,41,47)/t25-,29+,31+,32+,33-,36+/m1/s1"
XN2 InChIKey InChI 1.03 MJIRDPUZGGHJMX-OIVSQUILSA-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
XN2 "SYSTEMATIC NAME" ACDLabs 10.04 "(2S)-4-(1,3-benzodioxol-5-ylmethyl)-N-tert-butyl-1-[(2S,4S,5S)-2-hydroxy-4-{[(1S,2R)-2-hydroxy-2,3-dihydro-1H-inden-1-yl]carbamoyl}-5-phenylhexyl]piperazine-2-carboxamide (non-preferred name)"
XN2 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(1S,2S,4R)-4-(1,3-benzodioxol-5-ylmethyl)-N-tert-butyl-1-[(2S,4S,5S)-2-hydroxy-4-[[(1S,2R)-2-hydroxy-2,3-dihydro-1H-inden-1-yl]carbamoyl]-5-phenyl-hexyl]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
XN2 "Create component" 2001-11-05 RCSB
XN2 "Modify descriptor" 2011-06-04 RCSB
XN2 "Modify synonyms" 2020-06-05 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id XN2
_pdbx_chem_comp_synonyms.name "ANALOGUE OF INDINAVIR DRUG"
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
##