data_XN1
#
_chem_comp.id XN1
_chem_comp.name
;N-[2-HYDROXY-1-INDANYL]-5-[(2-TERTIARYBUTYLAMINOCARBONYL)-4(3-PYRIDYLMETHYL)PIPERAZINO]-4-HYDROXY-2-(1-PHENYLETHYL)-PEN
TANAMIDE
;
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C37 H49 N5 O4"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "ANALOGUE OF INDINAVIR"
_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 627.816
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code XN1
_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 1K6T
_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
XN1 N1 N1 N 0 1 N N N 3.182 -5.332 16.303 0.509 2.365 -4.638 N1 XN1 1
XN1 C1 C1 C 0 1 N N N 4.602 -5.146 15.800 -0.058 1.023 -4.814 C1 XN1 2
XN1 C2 C2 C 0 1 N N S 5.403 -3.997 16.407 -1.151 0.787 -3.771 C2 XN1 3
XN1 C3 C3 C 0 1 N N N 6.737 -4.025 15.740 -1.780 -0.562 -4.001 C3 XN1 4
XN1 O1 O1 O 0 1 N N N 6.850 -3.583 14.580 -1.742 -1.406 -3.130 O1 XN1 5
XN1 N2 N2 N 0 1 N N N 7.760 -4.533 16.439 -2.386 -0.832 -5.174 N2 XN1 6
XN1 C4 C4 C 0 1 N N N 9.173 -4.700 16.090 -2.998 -2.145 -5.398 C4 XN1 7
XN1 C5 C5 C 0 1 N N N 9.907 -5.365 17.282 -3.611 -2.189 -6.799 C5 XN1 8
XN1 C6 C6 C 0 1 N N N 9.829 -3.480 15.872 -1.930 -3.233 -5.274 C6 XN1 9
XN1 C7 C7 C 0 1 N N N 9.411 -5.586 14.916 -4.091 -2.382 -4.354 C7 XN1 10
XN1 N3 N3 N 0 1 N N N 4.490 -2.776 16.122 -0.566 0.829 -2.425 N3 XN1 11
XN1 C8 C8 C 0 1 N N N 3.061 -2.859 16.566 0.001 2.172 -2.249 C8 XN1 12
XN1 C9 C9 C 0 1 N N N 2.439 -4.142 16.032 1.093 2.408 -3.292 C9 XN1 13
XN1 C10 C10 C 0 1 N N N 5.012 -1.489 16.657 -1.682 0.715 -1.476 C10 XN1 14
XN1 C11 C11 C 0 1 N N S 4.997 -0.437 15.604 -1.164 0.926 -0.052 C11 XN1 15
XN1 O2 O2 O 0 1 N N N 5.122 0.614 16.527 -0.787 2.294 0.119 O2 XN1 16
XN1 C12 C12 C 0 1 N N N 6.166 -0.263 14.636 -2.265 0.571 0.948 C12 XN1 17
XN1 C13 C13 C 0 1 N N S 6.137 0.819 13.537 -1.711 0.668 2.371 C13 XN1 18
XN1 C14 C14 C 0 1 N N S 7.494 0.777 12.692 -2.853 0.499 3.376 C14 XN1 19
XN1 C15 C15 C 0 1 Y N N 7.493 1.843 11.587 -2.341 0.764 4.768 C15 XN1 20
XN1 C16 C16 C 0 1 Y N N 7.326 3.273 11.893 -2.413 -0.225 5.730 C16 XN1 21
XN1 C17 C17 C 0 1 Y N N 7.318 4.233 10.823 -1.943 0.017 7.008 C17 XN1 22
XN1 C18 C18 C 0 1 Y N N 7.481 3.766 9.441 -1.401 1.249 7.322 C18 XN1 23
XN1 C19 C19 C 0 1 Y N N 7.648 2.351 9.153 -1.328 2.238 6.360 C19 XN1 24
XN1 C20 C20 C 0 1 Y N N 7.653 1.404 10.220 -1.794 1.994 5.081 C20 XN1 25
XN1 C21 C21 C 0 1 N N N 4.951 0.612 12.533 -0.687 -0.415 2.587 C21 XN1 26
XN1 O3 O3 O 0 1 N N N 4.483 -0.537 12.198 -0.426 -1.190 1.691 O3 XN1 27
XN1 N4 N4 N 0 1 N N N 4.516 1.759 12.058 -0.062 -0.524 3.776 N4 XN1 28
XN1 C22 C22 C 0 1 N N S 3.453 1.892 11.081 0.932 -1.579 3.986 C22 XN1 29
XN1 C23 C23 C 0 1 N N R 3.415 3.282 10.476 0.980 -1.982 5.475 C23 XN1 30
XN1 O4 O4 O 0 1 N N N 3.703 4.274 11.447 0.568 -0.896 6.309 O4 XN1 31
XN1 C24 C24 C 0 1 N N N 2.050 3.398 9.854 2.475 -2.303 5.684 C24 XN1 32
XN1 C25 C25 C 0 1 Y N N 1.053 2.685 10.729 3.206 -1.478 4.647 C25 XN1 33
XN1 C26 C26 C 0 1 Y N N -0.321 2.701 10.957 4.541 -1.120 4.563 C26 XN1 34
XN1 C27 C27 C 0 1 Y N N -0.856 1.797 11.936 4.989 -0.349 3.509 C27 XN1 35
XN1 C28 C28 C 0 1 Y N N 0.003 0.888 12.675 4.103 0.067 2.533 C28 XN1 36
XN1 C29 C29 C 0 1 Y N N 1.394 0.860 12.457 2.771 -0.289 2.615 C29 XN1 37
XN1 C30 C30 C 0 1 Y N N 1.999 1.696 11.532 2.320 -1.062 3.669 C30 XN1 38
XN1 C31 C31 C 0 1 N N N 2.496 -6.492 15.704 1.624 2.479 -5.587 C31 XN1 39
XN1 C32 C32 C 0 1 Y N N 3.118 -7.880 15.876 2.497 1.254 -5.486 C32 XN1 40
XN1 C33 C33 C 0 1 Y N N 3.268 -8.508 17.162 3.562 1.225 -4.606 C33 XN1 41
XN1 N5 N5 N 0 1 Y N N 3.858 -9.824 17.371 4.326 0.154 -4.508 N5 XN1 42
XN1 C34 C34 C 0 1 Y N N 4.294 -10.471 16.149 4.115 -0.917 -5.246 C34 XN1 43
XN1 C35 C35 C 0 1 Y N N 4.172 -9.899 14.836 3.072 -0.958 -6.152 C35 XN1 44
XN1 C36 C36 C 0 1 Y N N 3.575 -8.582 14.706 2.244 0.145 -6.279 C36 XN1 45
XN1 C37 C37 C 0 1 N N N 8.885 0.784 13.310 -3.972 1.490 3.047 C37 XN1 46
XN1 H11A 1H1 H 0 0 N N N 4.595 -5.050 14.689 -0.486 0.938 -5.813 H11A XN1 47
XN1 H12 2H1 H 0 1 N N N 5.168 -6.099 15.920 0.727 0.278 -4.691 H12 XN1 48
XN1 H2 H2 H 0 1 N N N 5.635 -4.014 17.497 -1.912 1.562 -3.860 H2 XN1 49
XN1 HN2 HN2 H 0 1 N N N 7.420 -4.830 17.353 -2.417 -0.158 -5.871 HN2 XN1 50
XN1 H51 1H5 H 0 1 N N N 9.430 -6.323 17.595 -4.067 -3.166 -6.965 H51 XN1 51
XN1 H52 2H5 H 0 1 N N N 10.982 -5.492 17.016 -4.372 -1.414 -6.887 H52 XN1 52
XN1 H53 3H5 H 0 1 N N N 9.767 -4.803 18.235 -2.832 -2.020 -7.542 H53 XN1 53
XN1 H61 1H6 H 0 1 N N N 9.713 -2.802 16.750 -1.151 -3.064 -6.017 H61 XN1 54
XN1 H62 2H6 H 0 1 N N N 10.904 -3.607 15.606 -1.493 -3.201 -4.276 H62 XN1 55
XN1 H63 3H6 H 0 1 N N N 9.297 -2.873 15.102 -2.385 -4.209 -5.440 H63 XN1 56
XN1 H71 1H7 H 0 1 N N N 8.831 -5.229 14.034 -4.852 -1.606 -4.443 H71 XN1 57
XN1 H72 2H7 H 0 1 N N N 10.486 -5.713 14.650 -4.547 -3.358 -4.521 H72 XN1 58
XN1 H73 3H7 H 0 1 N N N 8.928 -6.579 15.072 -3.654 -2.350 -3.356 H73 XN1 59
XN1 H81 1H8 H 0 1 N N N 2.476 -1.955 16.277 -0.784 2.917 -2.372 H81 XN1 60
XN1 H82 2H8 H 0 1 N N N 2.957 -2.768 17.673 0.428 2.257 -1.250 H82 XN1 61
XN1 H91 1H9 H 0 1 N N N 1.394 -4.247 16.406 1.549 3.384 -3.126 H91 XN1 62
XN1 H92 2H9 H 0 1 N N N 2.246 -4.050 14.938 1.855 1.633 -3.203 H92 XN1 63
XN1 H101 1H10 H 0 0 N N N 6.025 -1.609 17.107 -2.128 -0.275 -1.557 H101 XN1 64
XN1 H102 2H10 H 0 0 N N N 4.460 -1.167 17.571 -2.433 1.472 -1.705 H102 XN1 65
XN1 H11 H11 H 0 1 N N N 4.154 -0.589 14.891 -0.298 0.287 0.117 H11 XN1 66
XN1 HO2 HO2 H 0 1 N N N 5.112 1.285 15.855 -1.595 2.819 0.040 HO2 XN1 67
XN1 H121 1H12 H 0 0 N N N 6.359 -1.246 14.147 -2.611 -0.445 0.762 H121 XN1 68
XN1 H122 2H12 H 0 0 N N N 7.094 -0.120 15.237 -3.098 1.265 0.834 H122 XN1 69
XN1 H13 H13 H 0 1 N N N 6.011 1.798 14.056 -1.244 1.643 2.513 H13 XN1 70
XN1 H141 1H14 H 0 0 N N N 7.399 -0.288 12.377 -3.240 -0.517 3.318 H141 XN1 71
XN1 H16 H16 H 0 1 N N N 7.206 3.627 12.931 -2.836 -1.188 5.485 H16 XN1 72
XN1 H17 H17 H 0 1 N N N 7.190 5.303 11.057 -1.999 -0.756 7.760 H17 XN1 73
XN1 H18 H18 H 0 1 N N N 7.478 4.488 8.607 -1.034 1.438 8.320 H18 XN1 74
XN1 H19 H19 H 0 1 N N N 7.772 1.993 8.117 -0.905 3.201 6.605 H19 XN1 75
XN1 H20 H20 H 0 1 N N N 7.781 0.333 9.988 -1.737 2.767 4.329 H20 XN1 76
XN1 HN4 HN4 H 0 1 N N N 5.011 2.558 12.454 -0.271 0.094 4.493 HN4 XN1 77
XN1 H22 H22 H 0 1 N N N 3.740 1.057 10.400 0.701 -2.445 3.367 H22 XN1 78
XN1 H23 H23 H 0 1 N N N 4.200 3.444 9.701 0.365 -2.863 5.658 H23 XN1 79
XN1 HO4 HO4 H 0 1 N N N 3.679 5.145 11.068 0.619 -1.210 7.222 HO4 XN1 80
XN1 H241 1H24 H 0 0 N N N 2.030 3.032 8.801 2.788 -2.013 6.687 H241 XN1 81
XN1 H242 2H24 H 0 0 N N N 1.762 4.457 9.656 2.660 -3.365 5.522 H242 XN1 82
XN1 H26 H26 H 0 1 N N N -0.957 3.399 10.387 5.234 -1.444 5.325 H26 XN1 83
XN1 H27 H27 H 0 1 N N N -1.943 1.801 12.123 6.031 -0.071 3.447 H27 XN1 84
XN1 H28 H28 H 0 1 N N N -0.414 0.197 13.426 4.451 0.670 1.708 H28 XN1 85
XN1 H29 H29 H 0 1 N N N 2.029 0.162 13.028 2.079 0.036 1.852 H29 XN1 86
XN1 H311 1H31 H 0 0 N N N 2.340 -6.298 14.617 1.232 2.563 -6.601 H311 XN1 87
XN1 H312 2H31 H 0 0 N N N 1.444 -6.519 16.072 2.214 3.365 -5.351 H312 XN1 88
XN1 H33 H33 H 0 1 N N N 2.909 -7.947 18.041 3.766 2.085 -3.986 H33 XN1 89
XN1 H34 H34 H 0 1 N N N 4.752 -11.472 16.224 4.765 -1.774 -5.141 H34 XN1 90
XN1 H35 H35 H 0 1 N N N 4.527 -10.455 13.952 2.904 -1.840 -6.753 H35 XN1 91
XN1 H36 H36 H 0 1 N N N 3.468 -8.113 13.714 1.421 0.141 -6.978 H36 XN1 92
XN1 H371 1H37 H 0 0 N N N 8.925 -0.063 14.034 -3.601 2.508 3.163 H371 XN1 93
XN1 H372 2H37 H 0 0 N N N 9.831 0.755 12.721 -4.302 1.337 2.020 H372 XN1 94
XN1 H373 3H37 H 0 0 N N N 8.942 1.677 13.975 -4.810 1.329 3.725 H373 XN1 95
# #
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
XN1 N1 C1 SING N N 1
XN1 N1 C9 SING N N 2
XN1 N1 C31 SING N N 3
XN1 C1 C2 SING N N 4
XN1 C1 H11A SING N N 5
XN1 C1 H12 SING N N 6
XN1 C2 C3 SING N N 7
XN1 C2 N3 SING N N 8
XN1 C2 H2 SING N N 9
XN1 C3 O1 DOUB N N 10
XN1 C3 N2 SING N N 11
XN1 N2 C4 SING N N 12
XN1 N2 HN2 SING N N 13
XN1 C4 C5 SING N N 14
XN1 C4 C6 SING N N 15
XN1 C4 C7 SING N N 16
XN1 C5 H51 SING N N 17
XN1 C5 H52 SING N N 18
XN1 C5 H53 SING N N 19
XN1 C6 H61 SING N N 20
XN1 C6 H62 SING N N 21
XN1 C6 H63 SING N N 22
XN1 C7 H71 SING N N 23
XN1 C7 H72 SING N N 24
XN1 C7 H73 SING N N 25
XN1 N3 C8 SING N N 26
XN1 N3 C10 SING N N 27
XN1 C8 C9 SING N N 28
XN1 C8 H81 SING N N 29
XN1 C8 H82 SING N N 30
XN1 C9 H91 SING N N 31
XN1 C9 H92 SING N N 32
XN1 C10 C11 SING N N 33
XN1 C10 H101 SING N N 34
XN1 C10 H102 SING N N 35
XN1 C11 O2 SING N N 36
XN1 C11 C12 SING N N 37
XN1 C11 H11 SING N N 38
XN1 O2 HO2 SING N N 39
XN1 C12 C13 SING N N 40
XN1 C12 H121 SING N N 41
XN1 C12 H122 SING N N 42
XN1 C13 C14 SING N N 43
XN1 C13 C21 SING N N 44
XN1 C13 H13 SING N N 45
XN1 C14 C15 SING N N 46
XN1 C14 C37 SING N N 47
XN1 C14 H141 SING N N 48
XN1 C15 C16 DOUB Y N 49
XN1 C15 C20 SING Y N 50
XN1 C16 C17 SING Y N 51
XN1 C16 H16 SING N N 52
XN1 C17 C18 DOUB Y N 53
XN1 C17 H17 SING N N 54
XN1 C18 C19 SING Y N 55
XN1 C18 H18 SING N N 56
XN1 C19 C20 DOUB Y N 57
XN1 C19 H19 SING N N 58
XN1 C20 H20 SING N N 59
XN1 C21 O3 DOUB N N 60
XN1 C21 N4 SING N N 61
XN1 N4 C22 SING N N 62
XN1 N4 HN4 SING N N 63
XN1 C22 C23 SING N N 64
XN1 C22 C30 SING N N 65
XN1 C22 H22 SING N N 66
XN1 C23 O4 SING N N 67
XN1 C23 C24 SING N N 68
XN1 C23 H23 SING N N 69
XN1 O4 HO4 SING N N 70
XN1 C24 C25 SING N N 71
XN1 C24 H241 SING N N 72
XN1 C24 H242 SING N N 73
XN1 C25 C26 DOUB Y N 74
XN1 C25 C30 SING Y N 75
XN1 C26 C27 SING Y N 76
XN1 C26 H26 SING N N 77
XN1 C27 C28 DOUB Y N 78
XN1 C27 H27 SING N N 79
XN1 C28 C29 SING Y N 80
XN1 C28 H28 SING N N 81
XN1 C29 C30 DOUB Y N 82
XN1 C29 H29 SING N N 83
XN1 C31 C32 SING N N 84
XN1 C31 H311 SING N N 85
XN1 C31 H312 SING N N 86
XN1 C32 C33 DOUB Y N 87
XN1 C32 C36 SING Y N 88
XN1 C33 N5 SING Y N 89
XN1 C33 H33 SING N N 90
XN1 N5 C34 DOUB Y N 91
XN1 C34 C35 SING Y N 92
XN1 C34 H34 SING N N 93
XN1 C35 C36 DOUB Y N 94
XN1 C35 H35 SING N N 95
XN1 C36 H36 SING N N 96
XN1 C37 H371 SING N N 97
XN1 C37 H372 SING N N 98
XN1 C37 H373 SING N N 99
# #
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
XN1 SMILES ACDLabs 10.04 "O=C(NC2c1ccccc1CC2O)C(C(c3ccccc3)C)CC(O)CN5C(C(=O)NC(C)(C)C)CN(Cc4cnccc4)CC5"
XN1 SMILES_CANONICAL CACTVS 3.341 "C[C@@H]([C@H](C[C@H](O)CN1CCN(C[C@H]1C(=O)NC(C)(C)C)Cc2cccnc2)C(=O)N[C@@H]3[C@H](O)Cc4ccccc34)c5ccccc5"
XN1 SMILES CACTVS 3.341 "C[CH]([CH](C[CH](O)CN1CCN(C[CH]1C(=O)NC(C)(C)C)Cc2cccnc2)C(=O)N[CH]3[CH](O)Cc4ccccc34)c5ccccc5"
XN1 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)Cc3cccnc3)O)C(=O)N[C@H]4c5ccccc5C[C@H]4O"
XN1 SMILES "OpenEye OEToolkits" 1.5.0 "CC(c1ccccc1)C(CC(CN2CCN(CC2C(=O)NC(C)(C)C)Cc3cccnc3)O)C(=O)NC4c5ccccc5CC4O"
XN1 InChI InChI 1.03 "InChI=1S/C37H49N5O4/c1-25(27-12-6-5-7-13-27)31(35(45)39-34-30-15-9-8-14-28(30)19-33(34)44)20-29(43)23-42-18-17-41(22-26-11-10-16-38-21-26)24-32(42)36(46)40-37(2,3)4/h5-16,21,25,29,31-34,43-44H,17-20,22-24H2,1-4H3,(H,39,45)(H,40,46)/t25-,29+,31+,32+,33-,34+/m1/s1"
XN1 InChIKey InChI 1.03 AITMPVIQUIXEST-FGUNTGOFSA-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
XN1 "SYSTEMATIC NAME" ACDLabs 10.04 "(2S)-N-tert-butyl-1-[(2S,4S,5S)-2-hydroxy-4-{[(1S,2R)-2-hydroxy-2,3-dihydro-1H-inden-1-yl]carbamoyl}-5-phenylhexyl]-4-(pyridin-3-ylmethyl)piperazine-2-carboxamide (non-preferred name)"
XN1 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(1S,2S,4R)-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]-4-(pyridin-3-ylmethyl)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
XN1 "Create component" 2001-11-05 RCSB
XN1 "Modify descriptor" 2011-06-04 RCSB
XN1 "Modify synonyms" 2020-06-05 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id XN1
_pdbx_chem_comp_synonyms.name "ANALOGUE OF INDINAVIR"
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
##