data_O6K
#
_chem_comp.id O6K
_chem_comp.name "~{tert}-butyl ~{N}-[1-[(2~{S})-3-cyclopropyl-1-oxidanylidene-1-[[(2~{S},3~{R})-3-oxidanyl-4-oxidanylidene-1-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]-4-[(phenylmethyl)amino]butan-2-yl]amino]propan-2-yl]-2-oxidanylidene-pyridin-3-yl]carbamate"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C31 H41 N5 O7"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "(S,S,S)-13b; 13b-K; ketoamide inhibitor 13b (bound)"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2020-02-17
_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 595.687
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code O6K
_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 6Y2F
_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.pdbx_backbone_atom_flag
_chem_comp_atom.pdbx_n_terminal_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
O6K O26 O1 O 0 1 N N N N N N 11.831 -5.792 23.341 4.974 0.538 0.530 O26 O6K 1
O6K C24 C1 C 0 1 N N N N N N 11.055 -5.520 22.439 5.706 -0.404 0.758 C24 O6K 2
O6K O25 O2 O 0 1 N N N N N N 10.794 -6.486 21.388 7.042 -0.234 0.761 O25 O6K 3
O6K C27 C2 C 0 1 N N N N N N 11.592 -7.649 21.100 7.537 1.103 0.483 C27 O6K 4
O6K C31 C3 C 0 1 N N N N N N 11.566 -8.561 22.339 6.996 2.076 1.533 C31 O6K 5
O6K C32 C4 C 0 1 N N N N N N 11.003 -8.363 19.874 9.066 1.101 0.530 C32 O6K 6
O6K C33 C5 C 0 1 N N N N N N 13.034 -7.252 20.756 7.069 1.541 -0.906 C33 O6K 7
O6K N23 N1 N 0 1 N N N N N N 10.377 -4.374 22.318 5.181 -1.619 1.014 N23 O6K 8
O6K C19 C6 C 0 1 N N N N N N 10.511 -3.257 23.071 3.792 -1.773 1.123 C19 O6K 9
O6K C21 C7 C 0 1 N N N N N N 9.776 -2.076 22.588 2.950 -1.441 0.040 C21 O6K 10
O6K O22 O3 O 0 1 N N N N N N 9.071 -2.127 21.535 3.429 -1.017 -0.999 O22 O6K 11
O6K C18 C8 C 0 1 N N N N N N 11.312 -3.134 24.223 3.237 -2.253 2.277 C18 O6K 12
O6K C17 C9 C 0 1 N N N N N N 11.391 -1.923 24.880 1.845 -2.398 2.359 C17 O6K 13
O6K C16 C10 C 0 1 N N N N N N 10.667 -0.827 24.422 1.066 -2.066 1.304 C16 O6K 14
O6K N15 N2 N 0 1 N N N N N N 9.874 -0.879 23.325 1.617 -1.594 0.154 N15 O6K 15
O6K C20 C11 C 0 1 N N S N N N 9.148 0.279 22.802 0.749 -1.247 -0.975 C20 O6K 16
O6K C22 C12 C 0 1 N N N N N N 9.003 1.431 23.806 -0.035 -2.486 -1.414 C22 O6K 17
O6K C29 C13 C 0 1 N N N N N N 8.204 0.991 25.035 0.935 -3.537 -1.957 C29 O6K 18
O6K C34 C14 C 0 1 N N N N N N 7.462 2.042 25.855 0.356 -4.900 -2.342 C34 O6K 19
O6K C30 C15 C 0 1 N N N N N N 6.684 1.164 24.883 0.804 -3.924 -3.432 C30 O6K 20
O6K C36 C16 C 0 1 N N N N N N 9.908 0.711 21.576 -0.213 -0.166 -0.555 C36 O6K 21
O6K O37 O4 O 0 1 N N N N N N 11.128 0.554 21.519 -0.178 0.271 0.576 O37 O6K 22
O6K N38 N3 N 0 1 N N N N N N 9.195 1.270 20.584 -1.114 0.314 -1.435 N38 O6K 23
O6K C40 C17 C 0 1 N N S N N N 9.796 1.792 19.396 -1.975 1.438 -1.062 C40 O6K 24
O6K C42 C18 C 0 1 N N N N N N 9.250 1.152 18.080 -1.203 2.749 -1.224 C42 O6K 25
O6K C45 C19 C 0 1 N N S N N N 9.773 -0.250 17.989 -2.074 3.916 -0.755 C45 O6K 26
O6K C47 C20 C 0 1 N N N N N N 9.197 -1.141 16.910 -2.342 3.812 0.730 C47 O6K 27
O6K O48 O5 O 0 1 N N N N N N 8.004 -1.151 16.621 -3.147 3.062 1.240 O48 O6K 28
O6K N49 N4 N 0 1 N N N N N N 10.173 -1.911 16.400 -1.559 4.673 1.403 N49 O6K 29
O6K C51 C21 C 0 1 N N N N N N 11.469 -1.705 17.056 -0.690 5.427 0.491 C51 O6K 30
O6K C54 C22 C 0 1 N N N N N N 11.278 -0.341 17.708 -1.316 5.254 -0.914 C54 O6K 31
O6K C57 C23 C 0 1 N N R N N N 9.601 3.286 19.630 -3.208 1.458 -1.968 C57 O6K 32
O6K O40 O6 O 0 1 N N N N N N 9.919 3.762 20.992 -2.798 1.604 -3.329 O40 O6K 33
O6K C35 C24 C 0 1 N N N N N N 10.554 4.044 18.797 -3.970 0.167 -1.808 C35 O6K 34
O6K O41 O7 O 0 1 N N N N N N 10.478 3.883 17.593 -4.066 -0.600 -2.743 O41 O6K 35
O6K N36 N5 N 0 1 N N N N N N 11.356 4.866 19.534 -4.544 -0.135 -0.627 N36 O6K 36
O6K C13 C25 C 0 1 N N N N N N 12.370 5.770 18.992 -5.284 -1.390 -0.472 C13 O6K 37
O6K C14 C26 C 0 1 Y N N N N N 13.730 5.087 18.915 -5.822 -1.485 0.933 C14 O6K 38
O6K C28 C27 C 0 1 Y N N N N N 13.937 3.812 19.442 -7.074 -0.980 1.229 C28 O6K 39
O6K C26 C28 C 0 1 Y N N N N N 15.198 3.215 19.371 -7.567 -1.067 2.517 C26 O6K 40
O6K C25 C29 C 0 1 Y N N N N N 16.267 3.890 18.768 -6.809 -1.660 3.509 C25 O6K 41
O6K C23 C30 C 0 1 Y N N N N N 16.070 5.166 18.238 -5.557 -2.165 3.213 C23 O6K 42
O6K C15 C31 C 0 1 Y N N N N N 14.805 5.757 18.314 -5.066 -2.084 1.923 C15 O6K 43
O6K H1 H1 H 0 1 N N N N N N 11.993 -8.024 23.199 7.329 1.764 2.523 H1 O6K 44
O6K H2 H2 H 0 1 N N N N N N 10.527 -8.845 22.563 7.367 3.079 1.324 H2 O6K 45
O6K H3 H3 H 0 1 N N N N N N 12.159 -9.466 22.141 5.906 2.077 1.500 H3 O6K 46
O6K H4 H4 H 0 1 N N N N N N 9.966 -8.663 20.087 9.451 0.408 -0.218 H4 O6K 47
O6K H5 H5 H 0 1 N N N N N N 11.018 -7.682 19.011 9.437 2.104 0.321 H5 O6K 48
O6K H6 H6 H 0 1 N N N N N N 11.603 -9.256 19.647 9.399 0.789 1.520 H6 O6K 49
O6K H7 H7 H 0 1 N N N N N N 13.488 -6.736 21.615 5.980 1.543 -0.940 H7 O6K 50
O6K H8 H8 H 0 1 N N N N N N 13.617 -8.155 20.521 7.441 2.544 -1.115 H8 O6K 51
O6K H9 H9 H 0 1 N N N N N N 13.031 -6.580 19.885 7.455 0.848 -1.654 H9 O6K 52
O6K H10 H10 H 0 1 N N N N N N 9.694 -4.338 21.589 5.765 -2.386 1.124 H10 O6K 53
O6K H11 H11 H 0 1 N N N N N N 11.864 -3.986 24.592 3.864 -2.517 3.116 H11 O6K 54
O6K H12 H12 H 0 1 N N N N N N 12.018 -1.826 25.754 1.394 -2.776 3.265 H12 O6K 55
O6K H13 H13 H 0 1 N N N N N N 10.740 0.104 24.964 -0.005 -2.182 1.375 H13 O6K 56
O6K H14 H14 H 0 1 N N N N N N 8.140 -0.037 22.495 1.358 -0.889 -1.804 H14 O6K 57
O6K H15 H15 H 0 1 N N N N N N 10.004 1.758 24.126 -0.575 -2.896 -0.561 H15 O6K 58
O6K H16 H16 H 0 1 N N N N N N 8.482 2.269 23.319 -0.744 -2.208 -2.194 H16 O6K 59
O6K H17 H17 H 0 1 N N N N N N 8.554 0.093 25.566 1.937 -3.518 -1.528 H17 O6K 60
O6K H18 H18 H 0 1 N N N N N N 7.605 3.110 25.635 0.978 -5.778 -2.167 H18 O6K 61
O6K H19 H19 H 0 1 N N N N N N 7.337 1.904 26.939 -0.715 -5.048 -2.208 H19 O6K 62
O6K H20 H20 H 0 1 N N N N N N 6.269 1.597 23.961 0.027 -3.430 -4.015 H20 O6K 63
O6K H21 H21 H 0 1 N N N N N N 6.001 0.391 25.265 1.720 -4.160 -3.973 H21 O6K 64
O6K H22 H22 H 0 1 N N N N N N 8.201 1.323 20.681 -1.191 -0.085 -2.316 H22 O6K 65
O6K H23 H23 H 0 1 N N N N N N 10.877 1.590 19.429 -2.289 1.327 -0.024 H23 O6K 66
O6K H24 H24 H 0 1 N N N N N N 9.593 1.735 17.212 -0.293 2.711 -0.625 H24 O6K 67
O6K H25 H25 H 0 1 N N N N N N 8.150 1.139 18.101 -0.941 2.889 -2.273 H25 O6K 68
O6K H26 H26 H 0 1 N N N N N N 9.590 -0.740 18.957 -3.011 3.939 -1.312 H26 O6K 69
O6K H27 H27 H 0 1 N N N N N N 10.031 -2.558 15.651 -1.566 4.781 2.366 H27 O6K 70
O6K H28 H28 H 0 1 N N N N N N 11.665 -2.484 17.808 -0.675 6.481 0.770 H28 O6K 71
O6K H29 H29 H 0 1 N N N N N N 12.290 -1.687 16.324 0.320 5.018 0.507 H29 O6K 72
O6K H30 H30 H 0 1 N N N N N N 11.852 -0.275 18.644 -0.544 5.178 -1.679 H30 O6K 73
O6K H31 H31 H 0 1 N N N N N N 11.594 0.462 17.026 -2.005 6.070 -1.138 H31 O6K 74
O6K H34 H34 H 0 1 N N N N N N 11.241 4.849 20.527 -4.467 0.478 0.120 H34 O6K 75
O6K H35 H35 H 0 1 N N N N N N 12.448 6.653 19.643 -6.111 -1.414 -1.181 H35 O6K 76
O6K H36 H36 H 0 1 N N N N N N 12.068 6.084 17.982 -4.617 -2.231 -0.663 H36 O6K 77
O6K H37 H37 H 0 1 N N N N N N 13.118 3.284 19.907 -7.666 -0.516 0.454 H37 O6K 78
O6K H38 H38 H 0 1 N N N N N N 15.349 2.228 19.783 -8.545 -0.671 2.749 H38 O6K 79
O6K H39 H39 H 0 1 N N N N N N 17.240 3.425 18.713 -7.194 -1.727 4.516 H39 O6K 80
O6K H40 H40 H 0 1 N N N N N N 16.889 5.694 17.772 -4.966 -2.633 3.987 H40 O6K 81
O6K H41 H41 H 0 1 N N N N N N 14.654 6.744 17.904 -4.088 -2.479 1.692 H41 O6K 82
O6K H32 H32 H 0 1 N N N N N N 8.569 3.563 19.367 -3.850 2.295 -1.691 H32 O6K 83
O6K H33 H33 H 0 1 N N N N N N 9.352 3.329 21.620 -2.223 0.893 -3.645 H33 O6K 84
#
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
O6K N49 C47 SING N N 1
O6K N49 C51 SING N N 2
O6K O48 C47 DOUB N N 3
O6K C47 C45 SING N N 4
O6K C51 C54 SING N N 5
O6K O41 C35 DOUB N N 6
O6K C54 C45 SING N N 7
O6K C45 C42 SING N N 8
O6K C42 C40 SING N N 9
O6K C23 C15 DOUB Y N 10
O6K C23 C25 SING Y N 11
O6K C15 C14 SING Y N 12
O6K C25 C26 DOUB Y N 13
O6K C35 N36 SING N N 14
O6K C35 C57 SING N N 15
O6K C14 C13 SING N N 16
O6K C14 C28 DOUB Y N 17
O6K C13 N36 SING N N 18
O6K C26 C28 SING Y N 19
O6K C40 C57 SING N N 20
O6K C40 N38 SING N N 21
O6K C57 O40 SING N N 22
O6K C32 C27 SING N N 23
O6K N38 C36 SING N N 24
O6K C33 C27 SING N N 25
O6K C27 O25 SING N N 26
O6K C27 C31 SING N N 27
O6K O25 C24 SING N N 28
O6K O37 C36 DOUB N N 29
O6K O22 C21 DOUB N N 30
O6K C36 C20 SING N N 31
O6K N23 C24 SING N N 32
O6K N23 C19 SING N N 33
O6K C24 O26 DOUB N N 34
O6K C21 C19 SING N N 35
O6K C21 N15 SING N N 36
O6K C20 N15 SING N N 37
O6K C20 C22 SING N N 38
O6K C19 C18 DOUB N N 39
O6K N15 C16 SING N N 40
O6K C22 C29 SING N N 41
O6K C18 C17 SING N N 42
O6K C16 C17 DOUB N N 43
O6K C30 C29 SING N N 44
O6K C30 C34 SING N N 45
O6K C29 C34 SING N N 46
O6K C31 H1 SING N N 47
O6K C31 H2 SING N N 48
O6K C31 H3 SING N N 49
O6K C32 H4 SING N N 50
O6K C32 H5 SING N N 51
O6K C32 H6 SING N N 52
O6K C33 H7 SING N N 53
O6K C33 H8 SING N N 54
O6K C33 H9 SING N N 55
O6K N23 H10 SING N N 56
O6K C18 H11 SING N N 57
O6K C17 H12 SING N N 58
O6K C16 H13 SING N N 59
O6K C20 H14 SING N N 60
O6K C22 H15 SING N N 61
O6K C22 H16 SING N N 62
O6K C29 H17 SING N N 63
O6K C34 H18 SING N N 64
O6K C34 H19 SING N N 65
O6K C30 H20 SING N N 66
O6K C30 H21 SING N N 67
O6K N38 H22 SING N N 68
O6K C40 H23 SING N N 69
O6K C42 H24 SING N N 70
O6K C42 H25 SING N N 71
O6K C45 H26 SING N N 72
O6K N49 H27 SING N N 73
O6K C51 H28 SING N N 74
O6K C51 H29 SING N N 75
O6K C54 H30 SING N N 76
O6K C54 H31 SING N N 77
O6K N36 H34 SING N N 78
O6K C13 H35 SING N N 79
O6K C13 H36 SING N N 80
O6K C28 H37 SING N N 81
O6K C26 H38 SING N N 82
O6K C25 H39 SING N N 83
O6K C23 H40 SING N N 84
O6K C15 H41 SING N N 85
O6K C57 H32 SING N N 86
O6K O40 H33 SING N N 87
#
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
O6K InChI InChI 1.06 "InChI=1S/C31H41N5O7/c1-31(2,3)43-30(42)35-22-10-7-15-36(29(22)41)24(16-19-11-12-19)27(39)34-23(17-21-13-14-32-26(21)38)25(37)28(40)33-18-20-8-5-4-6-9-20/h4-10,15,19,21,23-25,37H,11-14,16-18H2,1-3H3,(H,32,38)(H,33,40)(H,34,39)(H,35,42)/t21-,23-,24-,25+/m0/s1"
O6K InChIKey InChI 1.06 FRACPXUHUTXLCX-BELIEFIBSA-N
O6K SMILES_CANONICAL CACTVS 3.385 "CC(C)(C)OC(=O)NC1=CC=CN([C@@H](CC2CC2)C(=O)N[C@@H](C[C@@H]3CCNC3=O)[C@@H](O)C(=O)NCc4ccccc4)C1=O"
O6K SMILES CACTVS 3.385 "CC(C)(C)OC(=O)NC1=CC=CN([CH](CC2CC2)C(=O)N[CH](C[CH]3CCNC3=O)[CH](O)C(=O)NCc4ccccc4)C1=O"
O6K SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC(C)(C)OC(=O)NC1=CC=CN(C1=O)[C@@H](CC2CC2)C(=O)N[C@@H](C[C@@H]3CCNC3=O)[C@H](C(=O)NCc4ccccc4)O"
O6K SMILES "OpenEye OEToolkits" 2.0.7 "CC(C)(C)OC(=O)NC1=CC=CN(C1=O)C(CC2CC2)C(=O)NC(CC3CCNC3=O)C(C(=O)NCc4ccccc4)O"
#
_pdbx_chem_comp_identifier.comp_id O6K
_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 "~{tert}-butyl ~{N}-[1-[(2~{S})-3-cyclopropyl-1-oxidanylidene-1-[[(2~{S},3~{R})-3-oxidanyl-4-oxidanylidene-1-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]-4-[(phenylmethyl)amino]butan-2-yl]amino]propan-2-yl]-2-oxidanylidene-pyridin-3-yl]carbamate"
#
loop_
_pdbx_chem_comp_synonyms.ordinal
_pdbx_chem_comp_synonyms.comp_id
_pdbx_chem_comp_synonyms.name
_pdbx_chem_comp_synonyms.provenance
_pdbx_chem_comp_synonyms.type
1 O6K "(S,S,S)-13b" AUTHOR ?
2 O6K 13b-K AUTHOR ?
3 O6K "ketoamide inhibitor 13b (bound)" AUTHOR ?
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
O6K "Create component" 2020-02-17 PDBE
O6K "Initial release" 2020-03-04 RCSB
O6K "Modify synonyms" 2023-02-28 PDBE
O6K "Modify synonyms" 2023-08-13 PDBE
O6K "Modify PCM" 2024-09-27 PDBE
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id O6K
_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 C57
_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 ?
#