data_XV9 # _chem_comp.id XV9 _chem_comp.name "(phenylmethyl) ~{N}-[(2~{S})-1-[[(2~{S})-1-[[(2~{S})-1-[[iminomethyl-(phenylmethyl)amino]-methyl-amino]-1-oxidanylidene-3-phenyl-propan-2-yl]amino]-3,3-dimethyl-1-oxidanylidene-butan-2-yl]amino]-1-oxidanylidene-butan-2-yl]carbamate" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C36 H46 N6 O5" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2023-11-14 _chem_comp.pdbx_modified_date 2024-09-27 _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 642.788 _chem_comp.one_letter_code ? _chem_comp.three_letter_code XV9 _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 8QDC _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBE _chem_comp.pdbx_pcm Y # 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 _chem_comp_atom.pdbx_n_terminal_atom_flag _chem_comp_atom.pdbx_backbone_atom_flag _chem_comp_atom.pdbx_c_terminal_atom_flag XV9 N1 N1 N 0 1 N N N 75.732 -3.296 2.277 -0.714 -0.506 -0.297 N1 XV9 1 N N N XV9 N3 N2 N 0 1 N N N 72.743 -0.516 6.762 6.333 -1.450 0.677 N3 XV9 2 N N N XV9 C4 C1 C 0 1 N N N 76.494 -3.121 1.196 -2.005 -0.593 0.079 C4 XV9 3 N N N XV9 C5 C2 C 0 1 N N S 74.686 -2.354 2.631 0.276 -1.428 0.266 C5 XV9 4 N N N XV9 C6 C3 C 0 1 N N N 73.273 -2.926 2.314 0.276 -2.729 -0.538 C6 XV9 5 N N N XV9 C7 C4 C 0 1 N N N 73.073 -4.222 3.101 1.312 -3.691 0.048 C7 XV9 6 N N N XV9 C8 C5 C 0 1 N N N 73.163 -3.220 0.817 -1.111 -3.371 -0.471 C8 XV9 7 N N N XV9 C10 C6 C 0 1 N N N 74.898 -1.982 4.118 1.643 -0.797 0.201 C10 XV9 8 N N N XV9 C13 C7 C 0 1 Y N N 77.142 0.619 4.691 3.048 1.420 1.753 C13 XV9 9 N N N XV9 C15 C8 C 0 1 Y N N 79.363 -0.330 4.750 0.871 2.388 1.986 C15 XV9 10 N N N XV9 C17 C9 C 0 1 Y N N 78.324 0.108 2.648 2.571 3.546 0.762 C17 XV9 11 N N N XV9 C20 C10 C 0 1 N N N 73.040 -1.949 6.806 7.367 -2.484 0.759 C20 XV9 12 N N N XV9 C21 C11 C 0 1 N N N 70.381 0.143 6.890 6.744 0.061 -1.249 C21 XV9 13 N N N XV9 C22 C12 C 0 1 Y N N 69.831 -1.136 6.313 5.408 0.529 -1.766 C22 XV9 14 N N N XV9 C24 C13 C 0 1 Y N N 68.870 -2.360 4.472 3.312 0.055 -2.822 C24 XV9 15 N N N XV9 C26 C14 C 0 1 Y N N 69.309 -3.478 6.531 3.824 2.288 -2.125 C26 XV9 16 N N N XV9 C28 C15 C 0 1 N N N 71.907 0.305 8.884 6.885 0.851 1.072 C28 XV9 17 N N N XV9 N N3 N 0 1 N N N 77.705 -4.287 -0.495 -4.343 0.057 0.063 N XV9 18 N N N XV9 C C16 C 0 1 N N N 76.620 -4.666 -1.200 -5.457 0.386 -0.621 C XV9 19 N N N XV9 O O1 O 0 1 N N N 75.562 -5.006 -0.714 -5.367 0.928 -1.705 O XV9 20 N N N XV9 C1 C17 C 0 1 N N S 77.587 -4.158 0.949 -3.024 0.355 -0.500 C1 XV9 21 N N N XV9 C11 C18 C 0 1 N N S 74.915 -0.084 5.658 3.984 -0.701 0.873 C11 XV9 22 N N N XV9 C12 C19 C 0 1 N N N 75.900 1.074 5.410 4.014 0.297 2.032 C12 XV9 23 N N N XV9 C14 C20 C 0 1 Y N N 78.245 0.160 5.407 1.757 1.358 2.242 C14 XV9 24 N N N XV9 C16 C21 C 0 1 Y N N 79.400 -0.358 3.375 1.276 3.480 1.241 C16 XV9 25 N N N XV9 C18 C22 C 0 1 Y N N 77.206 0.591 3.308 3.455 2.514 1.013 C18 XV9 26 N N N XV9 C19 C23 C 0 1 N N N 73.631 0.420 6.317 5.072 -1.726 1.064 C19 XV9 27 N N N XV9 C2 C24 C 0 1 N N N 78.904 -3.733 1.585 -2.635 1.794 -0.155 C2 XV9 28 N N N XV9 C23 C25 C 0 1 Y N N 69.358 -1.180 5.007 4.538 -0.374 -2.348 C23 XV9 29 N N N XV9 C25 C26 C 0 1 Y N N 68.845 -3.509 5.233 2.956 1.386 -2.713 C25 XV9 30 N N N XV9 C27 C27 C 0 1 Y N N 69.798 -2.300 7.067 5.050 1.859 -1.652 C27 XV9 31 N N N XV9 C3 C28 C 0 1 N N N 80.034 -4.647 1.247 -3.597 2.762 -0.846 C3 XV9 32 N N N XV9 C32 C29 C 0 1 N N N 75.769 -5.036 -3.385 -7.826 0.494 -0.896 C32 XV9 33 N N N XV9 C33 C30 C 0 1 Y N N 74.677 -3.991 -3.318 -9.085 0.112 -0.162 C33 XV9 34 N N N XV9 C34 C31 C 0 1 Y N N 73.346 -4.357 -3.467 -9.647 -1.137 -0.356 C34 XV9 35 N N N XV9 C35 C32 C 0 1 Y N N 72.344 -3.398 -3.378 -10.802 -1.487 0.317 C35 XV9 36 N N N XV9 C36 C33 C 0 1 Y N N 72.658 -2.078 -3.143 -11.396 -0.589 1.184 C36 XV9 37 N N N XV9 C37 C34 C 0 1 Y N N 73.978 -1.710 -2.997 -10.834 0.658 1.379 C37 XV9 38 N N N XV9 C38 C35 C 0 1 Y N N 74.990 -2.659 -3.083 -9.676 1.007 0.710 C38 XV9 39 N N N XV9 C9 C36 C 0 1 N N N 72.191 -1.924 2.708 0.628 -2.428 -1.996 C9 XV9 40 N N N XV9 N2 N4 N 0 1 N N N 74.553 -0.722 4.404 2.682 -1.372 0.840 N2 XV9 41 N N N XV9 N4 N5 N 0 1 N N N 71.686 -0.036 7.558 6.654 -0.175 0.194 N4 XV9 42 N N N XV9 N6 N6 N 0 1 N N N 71.097 1.002 9.565 7.181 2.029 0.626 N6 XV9 43 N N N XV9 O3 O2 O 0 1 N N N 73.406 1.612 6.410 4.813 -2.799 1.568 O3 XV9 44 N N N XV9 O4 O3 O 0 1 N N N 75.326 -2.773 4.954 1.809 0.228 -0.425 O4 XV9 45 N N N XV9 O5 O4 O 0 1 N N N 76.351 -2.178 0.422 -2.348 -1.434 0.882 O5 XV9 46 N N N XV9 O6 O5 O 0 1 N N N 76.885 -4.676 -2.521 -6.670 0.112 -0.104 O6 XV9 47 N N N XV9 H10 H1 H 0 1 N N N 75.885 -4.096 2.858 -0.441 0.164 -0.942 H10 XV9 48 N N N XV9 H1 H2 H 0 1 N N N 74.815 -1.438 2.036 0.024 -1.642 1.304 H1 XV9 49 N N N XV9 H11 H3 H 0 1 N N N 73.152 -4.013 4.178 1.058 -3.910 1.085 H11 XV9 50 N N N XV9 H12 H4 H 0 1 N N N 72.078 -4.636 2.879 1.316 -4.616 -0.529 H12 XV9 51 N N N XV9 H13 H5 H 0 1 N N N 73.845 -4.950 2.811 2.300 -3.231 0.005 H13 XV9 52 N N N XV9 H15 H6 H 0 1 N N N 72.164 -3.624 0.595 -1.849 -2.686 -0.888 H15 XV9 53 N N N XV9 H14 H7 H 0 1 N N N 73.317 -2.291 0.249 -1.111 -4.298 -1.044 H14 XV9 54 N N N XV9 H16 H8 H 0 1 N N N 73.928 -3.956 0.531 -1.362 -3.586 0.568 H16 XV9 55 N N N XV9 H24 H9 H 0 1 N N N 80.207 -0.691 5.319 -0.138 2.340 2.368 H24 XV9 56 N N N XV9 H26 H10 H 0 1 N N N 78.353 0.096 1.568 2.890 4.401 0.184 H26 XV9 57 N N N XV9 H28 H11 H 0 1 N N N 72.169 -2.493 7.201 7.851 -2.437 1.735 H28 XV9 58 N N N XV9 H30 H12 H 0 1 N N N 73.266 -2.308 5.791 6.912 -3.466 0.627 H30 XV9 59 N N N XV9 H29 H13 H 0 1 N N N 73.908 -2.124 7.459 8.109 -2.320 -0.022 H29 XV9 60 N N N XV9 H31 H14 H 0 1 N N N 70.502 0.871 6.074 7.024 -0.864 -1.752 H31 XV9 61 N N N XV9 H32 H15 H 0 1 N N N 69.662 0.533 7.626 7.497 0.824 -1.446 H32 XV9 62 N N N XV9 H34 H16 H 0 1 N N N 68.508 -2.380 3.455 2.633 -0.650 -3.278 H34 XV9 63 N N N XV9 H36 H17 H 0 1 N N N 69.291 -4.376 7.131 3.544 3.327 -2.036 H36 XV9 64 N N N XV9 H3 H18 H 0 1 N N N 72.813 -0.040 9.359 6.819 0.677 2.135 H3 XV9 65 N N N XV9 H4 H19 H 0 1 N N N 78.573 -4.099 -0.955 -4.415 -0.376 0.928 H4 XV9 66 N N N XV9 H H20 H 0 1 N N N 77.273 -5.118 1.386 -3.056 0.237 -1.583 H XV9 67 N N N XV9 H2 H21 H 0 1 N N N 75.393 -0.816 6.325 4.144 -0.172 -0.066 H2 XV9 68 N N N XV9 H21 H22 H 0 1 N N N 76.190 1.506 6.379 5.020 0.701 2.138 H21 XV9 69 N N N XV9 H22 H23 H 0 1 N N N 75.399 1.841 4.801 3.727 -0.208 2.954 H22 XV9 70 N N N XV9 H23 H24 H 0 1 N N N 78.229 0.186 6.487 1.439 0.506 2.824 H23 XV9 71 N N N XV9 H25 H25 H 0 1 N N N 80.270 -0.744 2.865 0.586 4.286 1.045 H25 XV9 72 N N N XV9 H27 H26 H 0 1 N N N 76.367 0.953 2.732 4.465 2.562 0.631 H27 XV9 73 N N N XV9 H5 H27 H 0 1 N N N 79.154 -2.721 1.233 -2.689 1.936 0.924 H5 XV9 74 N N N XV9 H6 H28 H 0 1 N N N 78.778 -3.720 2.678 -1.618 1.987 -0.496 H6 XV9 75 N N N XV9 H33 H29 H 0 1 N N N 69.371 -0.285 4.403 4.816 -1.414 -2.434 H33 XV9 76 N N N XV9 H35 H30 H 0 1 N N N 68.464 -4.429 4.815 1.998 1.721 -3.083 H35 XV9 77 N N N XV9 H37 H31 H 0 1 N N N 70.158 -2.286 8.085 5.727 2.563 -1.192 H37 XV9 78 N N N XV9 H7 H32 H 0 1 N N N 80.954 -4.289 1.733 -3.320 3.787 -0.600 H7 XV9 79 N N N XV9 H9 H33 H 0 1 N N N 79.803 -5.662 1.602 -3.543 2.620 -1.926 H9 XV9 80 N N N XV9 H8 H34 H 0 1 N N N 80.178 -4.664 0.157 -4.614 2.569 -0.505 H8 XV9 81 N N N XV9 H44 H35 H 0 1 N N N 75.361 -6.005 -3.062 -7.794 -0.021 -1.856 H44 XV9 82 N N N XV9 H45 H36 H 0 1 N N N 76.127 -5.117 -4.422 -7.813 1.571 -1.060 H45 XV9 83 N N N XV9 H46 H37 H 0 1 N N N 73.089 -5.389 -3.653 -9.183 -1.838 -1.034 H46 XV9 84 N N N XV9 H47 H38 H 0 1 N N N 71.311 -3.690 -3.494 -11.241 -2.462 0.164 H47 XV9 85 N N N XV9 H48 H39 H 0 1 N N N 71.876 -1.337 -3.074 -12.299 -0.863 1.709 H48 XV9 86 N N N XV9 H49 H40 H 0 1 N N N 74.228 -0.675 -2.814 -11.298 1.360 2.057 H49 XV9 87 N N N XV9 H50 H41 H 0 1 N N N 76.021 -2.360 -2.967 -9.235 1.981 0.865 H50 XV9 88 N N N XV9 H19 H42 H 0 1 N N N 72.265 -1.708 3.784 1.617 -1.971 -2.045 H19 XV9 89 N N N XV9 H18 H43 H 0 1 N N N 72.328 -0.994 2.137 0.628 -3.355 -2.569 H18 XV9 90 N N N XV9 H17 H44 H 0 1 N N N 71.201 -2.348 2.486 -0.109 -1.742 -2.414 H17 XV9 91 N N N XV9 H20 H45 H 0 1 N N N 74.028 -0.201 3.731 2.567 -2.230 1.278 H20 XV9 92 N N N XV9 H43 H46 H 0 1 N N N 71.422 1.147 10.500 7.345 2.756 1.248 H43 XV9 93 N N N # 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 XV9 C34 C35 DOUB Y N 1 XV9 C34 C33 SING Y N 2 XV9 C32 C33 SING N N 3 XV9 C32 O6 SING N N 4 XV9 C35 C36 SING Y N 5 XV9 C33 C38 DOUB Y N 6 XV9 C36 C37 DOUB Y N 7 XV9 C38 C37 SING Y N 8 XV9 O6 C SING N N 9 XV9 C O DOUB N N 10 XV9 C N SING N N 11 XV9 N C1 SING N N 12 XV9 O5 C4 DOUB N N 13 XV9 C8 C6 SING N N 14 XV9 C1 C4 SING N N 15 XV9 C1 C2 SING N N 16 XV9 C4 N1 SING N N 17 XV9 C3 C2 SING N N 18 XV9 N1 C5 SING N N 19 XV9 C6 C5 SING N N 20 XV9 C6 C9 SING N N 21 XV9 C6 C7 SING N N 22 XV9 C5 C10 SING N N 23 XV9 C17 C18 DOUB Y N 24 XV9 C17 C16 SING Y N 25 XV9 C18 C13 SING Y N 26 XV9 C16 C15 DOUB Y N 27 XV9 C10 N2 SING N N 28 XV9 C10 O4 DOUB N N 29 XV9 N2 C11 SING N N 30 XV9 C24 C23 DOUB Y N 31 XV9 C24 C25 SING Y N 32 XV9 C13 C14 DOUB Y N 33 XV9 C13 C12 SING N N 34 XV9 C15 C14 SING Y N 35 XV9 C23 C22 SING Y N 36 XV9 C25 C26 DOUB Y N 37 XV9 C12 C11 SING N N 38 XV9 C11 C19 SING N N 39 XV9 C22 C21 SING N N 40 XV9 C22 C27 DOUB Y N 41 XV9 C19 O3 DOUB N N 42 XV9 C19 N3 SING N N 43 XV9 C26 C27 SING Y N 44 XV9 N3 C20 SING N N 45 XV9 N3 N4 SING N N 46 XV9 C21 N4 SING N N 47 XV9 N4 C28 SING N N 48 XV9 C28 N6 DOUB N N 49 XV9 N1 H10 SING N N 50 XV9 C5 H1 SING N N 51 XV9 C7 H11 SING N N 52 XV9 C7 H12 SING N N 53 XV9 C7 H13 SING N N 54 XV9 C8 H15 SING N N 55 XV9 C8 H14 SING N N 56 XV9 C8 H16 SING N N 57 XV9 C15 H24 SING N N 58 XV9 C17 H26 SING N N 59 XV9 C20 H28 SING N N 60 XV9 C20 H30 SING N N 61 XV9 C20 H29 SING N N 62 XV9 C21 H31 SING N N 63 XV9 C21 H32 SING N N 64 XV9 C24 H34 SING N N 65 XV9 C26 H36 SING N N 66 XV9 C28 H3 SING N N 67 XV9 N H4 SING N N 68 XV9 C1 H SING N N 69 XV9 C11 H2 SING N N 70 XV9 C12 H21 SING N N 71 XV9 C12 H22 SING N N 72 XV9 C14 H23 SING N N 73 XV9 C16 H25 SING N N 74 XV9 C18 H27 SING N N 75 XV9 C2 H5 SING N N 76 XV9 C2 H6 SING N N 77 XV9 C23 H33 SING N N 78 XV9 C25 H35 SING N N 79 XV9 C27 H37 SING N N 80 XV9 C3 H7 SING N N 81 XV9 C3 H9 SING N N 82 XV9 C3 H8 SING N N 83 XV9 C32 H44 SING N N 84 XV9 C32 H45 SING N N 85 XV9 C34 H46 SING N N 86 XV9 C35 H47 SING N N 87 XV9 C36 H48 SING N N 88 XV9 C37 H49 SING N N 89 XV9 C38 H50 SING N N 90 XV9 C9 H19 SING N N 91 XV9 C9 H18 SING N N 92 XV9 C9 H17 SING N N 93 XV9 N2 H20 SING N N 94 XV9 N6 H43 SING N N 95 # 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 XV9 InChI InChI 1.06 "InChI=1S/C36H46N6O5/c1-6-29(39-35(46)47-24-28-20-14-9-15-21-28)32(43)40-31(36(2,3)4)33(44)38-30(22-26-16-10-7-11-17-26)34(45)41(5)42(25-37)23-27-18-12-8-13-19-27/h7-21,25,29-31,37H,6,22-24H2,1-5H3,(H,38,44)(H,39,46)(H,40,43)/b37-25-/t29-,30-,31+/m0/s1" XV9 InChIKey InChI 1.06 NHQUTJQVPJWESZ-YEPDJPBYSA-N XV9 SMILES_CANONICAL CACTVS 3.385 "CC[C@H](NC(=O)OCc1ccccc1)C(=O)N[C@H](C(=O)N[C@@H](Cc2ccccc2)C(=O)N(C)N(Cc3ccccc3)C=N)C(C)(C)C" XV9 SMILES CACTVS 3.385 "CC[CH](NC(=O)OCc1ccccc1)C(=O)N[CH](C(=O)N[CH](Cc2ccccc2)C(=O)N(C)N(Cc3ccccc3)C=N)C(C)(C)C" XV9 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "[H]/N=C\N(Cc1ccccc1)N(C)C(=O)[C@H](Cc2ccccc2)NC(=O)[C@H](C(C)(C)C)NC(=O)[C@H](CC)NC(=O)OCc3ccccc3" XV9 SMILES "OpenEye OEToolkits" 2.0.7 "CCC(C(=O)NC(C(=O)NC(Cc1ccccc1)C(=O)N(C)N(Cc2ccccc2)C=N)C(C)(C)C)NC(=O)OCc3ccccc3" # _pdbx_chem_comp_identifier.comp_id XV9 _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 "(phenylmethyl) ~{N}-[(2~{S})-1-[[(2~{S})-1-[[(2~{S})-1-[[iminomethyl-(phenylmethyl)amino]-methyl-amino]-1-oxidanylidene-3-phenyl-propan-2-yl]amino]-3,3-dimethyl-1-oxidanylidene-butan-2-yl]amino]-1-oxidanylidene-butan-2-yl]carbamate" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site XV9 "Create component" 2023-11-14 PDBE XV9 "Initial release" 2024-07-03 RCSB XV9 "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id XV9 _pdbx_chem_comp_pcm.modified_residue_id CYS _pdbx_chem_comp_pcm.type None _pdbx_chem_comp_pcm.category "Covalent chemical modification" _pdbx_chem_comp_pcm.position "Amino-acid side chain" _pdbx_chem_comp_pcm.polypeptide_position "Any position" _pdbx_chem_comp_pcm.comp_id_linking_atom C28 _pdbx_chem_comp_pcm.modified_residue_id_linking_atom SG _pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ? _pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ? #