data_L4F
#
_chem_comp.id L4F
_chem_comp.name
'2-[4-[[(2~{S})-1-oxidanylidene-3-phenyl-1-[[(3~{S})-1-phenyl-5-(phenylsulfonyl)pentan-3-yl]amino]propan-2-yl]carbamoyl]piperazin-1-yl]ethyl 4-carbamimidamidobenzoate'
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula 'C41 H49 N7 O6 S'
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2022-11-10
_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 767.936
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code L4F
_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 8HEN
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBJ
_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
L4F C10 C1 C 0 1 N N N N N N -0.196 4.420 17.261 -2.638 -1.037 -2.477 C10 L4F 1
L4F C15 C2 C 0 1 N N N N N N -4.555 1.524 15.584 2.894 -0.694 -0.098 C15 L4F 2
L4F C17 C3 C 0 1 N N S N N N -6.617 2.147 16.846 5.099 -1.093 0.860 C17 L4F 3
L4F C21 C4 C 0 1 Y N N N N N -9.487 5.683 16.300 7.450 3.663 1.314 C21 L4F 4
L4F C22 C5 C 0 1 Y N N N N N -8.819 6.272 17.358 7.460 4.132 2.614 C22 L4F 5
L4F C24 C6 C 0 1 Y N N N N N -8.919 8.383 16.229 6.841 6.309 1.832 C24 L4F 6
L4F C26 C7 C 0 1 Y N N N N N -9.867 6.433 15.205 7.141 4.518 0.272 C26 L4F 7
L4F C02 C8 C 0 1 N N N N N N 0.164 5.360 22.315 -7.368 -1.622 1.355 C02 L4F 8
L4F C04 C9 C 0 1 N N N N N N 1.322 3.683 21.061 -5.609 -3.117 0.744 C04 L4F 9
L4F C05 C10 C 0 1 N N N N N N 0.722 2.606 20.151 -4.716 -3.439 -0.456 C05 L4F 10
L4F C07 C11 C 0 1 N N N N N N 0.429 1.873 18.127 -2.771 -2.157 0.206 C07 L4F 11
L4F C08 C12 C 0 1 N N N N N N 0.333 2.262 16.652 -2.024 -0.842 -0.036 C08 L4F 12
L4F C09 C13 C 0 1 N N N N N N -0.033 4.085 18.741 -3.362 -2.345 -2.139 C09 L4F 13
L4F C12 C14 C 0 1 N N N N N N -1.931 3.148 15.847 -0.341 -0.521 -1.791 C12 L4F 14
L4F C14 C15 C 0 1 N N S N N N -3.537 1.832 14.480 2.005 -0.204 -1.211 C14 L4F 15
L4F C18 C16 C 0 1 N N N N N N -7.996 1.862 16.249 6.446 -0.371 0.791 C18 L4F 16
L4F C19 C17 C 0 1 N N N N N N -8.553 3.029 15.412 6.240 1.120 1.065 C19 L4F 17
L4F C23 C18 C 0 1 Y N N N N N -8.533 7.627 17.318 7.156 5.456 2.873 C23 L4F 18
L4F C25 C19 C 0 1 Y N N N N N -9.584 7.788 15.174 6.837 5.841 0.531 C25 L4F 19
L4F C29 C20 C 0 1 N N N N N N -6.619 3.372 17.744 5.320 -2.600 0.711 C29 L4F 20
L4F C30 C21 C 0 1 N N N N N N -5.247 3.532 18.404 3.990 -3.331 0.904 C30 L4F 21
L4F C31 C22 C 0 1 Y N N N N N -5.128 4.850 19.162 4.207 -4.815 0.757 C31 L4F 22
L4F C32 C23 C 0 1 Y N N N N N -5.987 5.125 20.207 4.523 -5.581 1.864 C32 L4F 23
L4F C33 C24 C 0 1 Y N N N N N -5.878 6.320 20.889 4.723 -6.942 1.729 C33 L4F 24
L4F C34 C25 C 0 1 Y N N N N N -4.908 7.229 20.523 4.606 -7.538 0.488 C34 L4F 25
L4F C35 C26 C 0 1 Y N N N N N -4.051 6.952 19.474 4.289 -6.773 -0.619 C35 L4F 26
L4F C36 C27 C 0 1 Y N N N N N -4.161 5.759 18.795 4.084 -5.412 -0.484 C36 L4F 27
L4F C38 C28 C 0 1 N N N N N N -3.536 0.743 13.441 2.267 1.283 -1.457 C38 L4F 28
L4F C39 C29 C 0 1 Y N N N N N -2.773 1.158 12.186 1.469 1.744 -2.649 C39 L4F 29
L4F C40 C30 C 0 1 Y N N N N N -1.547 0.581 11.897 0.189 2.236 -2.474 C40 L4F 30
L4F C41 C31 C 0 1 Y N N N N N -0.858 0.954 10.760 -0.544 2.658 -3.568 C41 L4F 31
L4F C42 C32 C 0 1 Y N N N N N -1.389 1.906 9.913 0.003 2.588 -4.835 C42 L4F 32
L4F C43 C33 C 0 1 Y N N N N N -2.608 2.486 10.198 1.283 2.097 -5.009 C43 L4F 33
L4F C44 C34 C 0 1 Y N N N N N -3.300 2.111 11.342 2.018 1.680 -3.915 C44 L4F 34
L4F C46 C35 C 0 1 Y N N N N N -1.205 5.853 22.838 -8.311 -0.524 1.077 C46 L4F 35
L4F C47 C36 C 0 1 Y N N N N N -1.261 6.885 23.767 -9.203 -0.099 2.066 C47 L4F 36
L4F C48 C37 C 0 1 Y N N N N N -2.497 7.331 24.240 -10.082 0.927 1.804 C48 L4F 37
L4F C49 C38 C 0 1 Y N N N N N -3.667 6.745 23.791 -10.084 1.541 0.555 C49 L4F 38
L4F C51 C39 C 0 1 N N N N N N -5.612 6.551 25.139 -11.328 3.454 1.295 C51 L4F 39
L4F C54 C40 C 0 1 Y N N N N N -3.605 5.714 22.863 -9.197 1.121 -0.433 C54 L4F 40
L4F C55 C41 C 0 1 Y N N N N N -2.374 5.266 22.386 -8.311 0.100 -0.174 C55 L4F 41
L4F N06 N1 N 0 1 N N N N N N 0.759 2.956 18.943 -3.870 -2.278 -0.762 N06 L4F 42
L4F N11 N2 N 0 1 N N N N N N -0.636 3.280 16.548 -1.616 -0.789 -1.448 N11 L4F 43
L4F N13 N3 N 0 1 N N N N N N -2.258 1.908 15.154 0.602 -0.397 -0.835 N13 L4F 44
L4F N16 N4 N 0 1 N N N N N N -5.677 2.433 15.786 4.234 -0.617 -0.222 N16 L4F 45
L4F N50 N5 N 0 1 N N N N N N -4.961 7.212 24.287 -10.975 2.579 0.292 N50 L4F 46
L4F N52 N6 N 0 1 N N N N N N -6.898 7.037 25.613 -10.745 3.381 2.458 N52 L4F 47
L4F N53 N7 N 0 1 N N N N N N -5.086 5.296 25.660 -12.296 4.404 1.070 N53 L4F 48
L4F O01 O1 O 0 1 N N N N N N 1.026 6.145 22.135 -7.365 -2.160 2.445 O01 L4F 49
L4F O03 O2 O 0 1 N N N N N N 0.379 3.987 22.071 -6.509 -2.030 0.400 O03 L4F 50
L4F O27 O3 O 0 1 N N N N N N -11.166 3.534 15.998 8.332 1.984 -0.349 O27 L4F 51
L4F O28 O4 O 0 1 N N N N N N -9.809 3.508 17.760 8.667 1.588 2.070 O28 L4F 52
L4F O37 O5 O 0 1 N N N N N N -4.420 0.581 16.275 2.405 -1.159 0.910 O37 L4F 53
L4F O45 O6 O 0 1 N N N N N N -2.686 4.049 15.837 -0.040 -0.390 -2.962 O45 L4F 54
L4F S20 S1 S 0 1 N N N N N N -9.829 3.910 16.375 7.838 1.976 0.983 S20 L4F 55
L4F H1 H1 H 0 1 N N N N N N 0.771 4.752 16.855 -2.161 -1.125 -3.453 H1 L4F 56
L4F H2 H2 H 0 1 N N N N N N -0.936 5.226 17.150 -3.354 -0.216 -2.491 H2 L4F 57
L4F H3 H3 H 0 1 N N N N N N -6.286 1.272 17.425 4.626 -0.888 1.821 H3 L4F 58
L4F H4 H4 H 0 1 N N N N N N -8.522 5.679 18.210 7.706 3.466 3.427 H4 L4F 59
L4F H5 H5 H 0 1 N N N N N N -8.701 9.440 16.202 6.603 7.343 2.035 H5 L4F 60
L4F H6 H6 H 0 1 N N N N N N -10.382 5.966 14.378 7.137 4.152 -0.744 H6 L4F 61
L4F H7 H7 H 0 1 N N N N N N 2.250 3.309 21.519 -6.190 -4.000 1.011 H7 L4F 62
L4F H8 H8 H 0 1 N N N N N N 1.542 4.586 20.473 -4.988 -2.821 1.590 H8 L4F 63
L4F H9 H9 H 0 1 N N N N N N -0.325 2.433 20.442 -4.085 -4.296 -0.220 H9 L4F 64
L4F H10 H10 H 0 1 N N N N N N 1.295 1.675 20.272 -5.339 -3.672 -1.320 H10 L4F 65
L4F H11 H11 H 0 1 N N N N N N -0.542 1.471 18.450 -2.084 -2.994 0.083 H11 L4F 66
L4F H12 H12 H 0 1 N N N N N N 1.202 1.098 18.238 -3.176 -2.165 1.218 H12 L4F 67
L4F H13 H13 H 0 1 N N N N N N 0.030 1.391 16.052 -2.680 -0.001 0.188 H13 L4F 68
L4F H14 H14 H 0 1 N N N N N N 1.306 2.631 16.296 -1.143 -0.798 0.604 H14 L4F 69
L4F H15 H15 H 0 1 N N N N N N 0.436 4.941 19.248 -4.194 -2.489 -2.827 H15 L4F 70
L4F H16 H16 H 0 1 N N N N N N -1.027 3.902 19.174 -2.666 -3.179 -2.229 H16 L4F 71
L4F H17 H17 H 0 1 N N N N N N -3.786 2.795 14.011 2.218 -0.766 -2.120 H17 L4F 72
L4F H18 H18 H 0 1 N N N N N N -8.697 1.657 17.072 7.121 -0.788 1.540 H18 L4F 73
L4F H19 H19 H 0 1 N N N N N N -7.920 0.975 15.603 6.879 -0.503 -0.200 H19 L4F 74
L4F H20 H20 H 0 1 N N N N N N -7.737 3.723 15.162 5.566 1.537 0.316 H20 L4F 75
L4F H21 H21 H 0 1 N N N N N N -8.998 2.637 14.486 5.808 1.251 2.056 H21 L4F 76
L4F H22 H22 H 0 1 N N N N N N -8.008 8.092 18.139 7.159 5.821 3.889 H22 L4F 77
L4F H23 H23 H 0 1 N N N N N N -9.884 8.381 14.323 6.596 6.509 -0.282 H23 L4F 78
L4F H24 H24 H 0 1 N N N N N N -6.842 4.266 17.142 5.711 -2.813 -0.284 H24 L4F 79
L4F H25 H25 H 0 1 N N N N N N -7.387 3.253 18.522 6.033 -2.939 1.462 H25 L4F 80
L4F H26 H26 H 0 1 N N N N N N -5.093 2.702 19.109 3.599 -3.118 1.899 H26 L4F 81
L4F H27 H27 H 0 1 N N N N N N -4.472 3.500 17.624 3.276 -2.993 0.153 H27 L4F 82
L4F H28 H28 H 0 1 N N N N N N -6.742 4.407 20.490 4.615 -5.115 2.834 H28 L4F 83
L4F H29 H29 H 0 1 N N N N N N -6.549 6.542 21.705 4.970 -7.540 2.594 H29 L4F 84
L4F H30 H30 H 0 1 N N N N N N -4.817 8.162 21.059 4.762 -8.601 0.382 H30 L4F 85
L4F H31 H31 H 0 1 N N N N N N -3.297 7.670 19.188 4.198 -7.239 -1.589 H31 L4F 86
L4F H32 H32 H 0 1 N N N N N N -3.491 5.537 17.977 3.833 -4.815 -1.348 H32 L4F 87
L4F H33 H33 H 0 1 N N N N N N -4.576 0.513 13.166 1.970 1.854 -0.577 H33 L4F 88
L4F H34 H34 H 0 1 N N N N N N -3.062 -0.154 13.866 3.329 1.437 -1.649 H34 L4F 89
L4F H35 H35 H 0 1 N N N N N N -1.130 -0.161 12.562 -0.239 2.290 -1.484 H35 L4F 90
L4F H36 H36 H 0 1 N N N N N N 0.096 0.501 10.533 -1.544 3.042 -3.432 H36 L4F 91
L4F H37 H37 H 0 1 N N N N N N -0.849 2.198 9.025 -0.571 2.914 -5.690 H37 L4F 92
L4F H38 H38 H 0 1 N N N N N N -3.023 3.229 9.533 1.711 2.042 -6.000 H38 L4F 93
L4F H39 H39 H 0 1 N N N N N N -4.252 2.567 11.570 3.019 1.296 -4.051 H39 L4F 94
L4F H40 H40 H 0 1 N N N N N N -0.349 7.342 24.123 -9.203 -0.576 3.036 H40 L4F 95
L4F H41 H41 H 0 1 N N N N N N -2.540 8.136 24.959 -10.771 1.255 2.567 H41 L4F 96
L4F H42 H42 H 0 1 N N N N N N -4.517 5.256 22.508 -9.202 1.599 -1.401 H42 L4F 97
L4F H43 H43 H 0 1 N N N N N N -2.333 4.463 21.665 -7.620 -0.223 -0.939 H43 L4F 98
L4F H45 H45 H 0 1 N N N N N N -1.621 1.137 15.144 0.351 -0.435 0.101 H45 L4F 99
L4F H46 H46 H 0 1 N N N N N N -5.794 3.237 15.203 4.626 -0.245 -1.028 H46 L4F 100
L4F H47 H47 H 0 1 N N N N N N -5.336 8.073 23.943 -11.347 2.685 -0.597 H47 L4F 101
L4F H48 H48 H 0 1 N N N N N N -7.307 6.420 26.286 -10.993 3.997 3.165 H48 L4F 102
L4F H49 H49 H 0 1 N N N N N N -5.608 4.778 26.337 -12.544 5.021 1.776 H49 L4F 103
L4F H50 H50 H 0 1 N N N N N N -4.203 4.953 25.341 -12.730 4.458 0.204 H50 L4F 104
#
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
L4F C42 C43 DOUB Y N 1
L4F C42 C41 SING Y N 2
L4F C43 C44 SING Y N 3
L4F C41 C40 DOUB Y N 4
L4F C44 C39 DOUB Y N 5
L4F C40 C39 SING Y N 6
L4F C39 C38 SING N N 7
L4F C38 C14 SING N N 8
L4F C14 N13 SING N N 9
L4F C14 C15 SING N N 10
L4F N13 C12 SING N N 11
L4F C25 C26 DOUB Y N 12
L4F C25 C24 SING Y N 13
L4F C26 C21 SING Y N 14
L4F C19 C18 SING N N 15
L4F C19 S20 SING N N 16
L4F C15 N16 SING N N 17
L4F C15 O37 DOUB N N 18
L4F N16 C17 SING N N 19
L4F O45 C12 DOUB N N 20
L4F C12 N11 SING N N 21
L4F O27 S20 DOUB N N 22
L4F C24 C23 DOUB Y N 23
L4F C18 C17 SING N N 24
L4F C21 S20 SING N N 25
L4F C21 C22 DOUB Y N 26
L4F S20 O28 DOUB N N 27
L4F N11 C08 SING N N 28
L4F N11 C10 SING N N 29
L4F C08 C07 SING N N 30
L4F C17 C29 SING N N 31
L4F C10 C09 SING N N 32
L4F C23 C22 SING Y N 33
L4F C29 C30 SING N N 34
L4F C07 N06 SING N N 35
L4F C30 C31 SING N N 36
L4F C09 N06 SING N N 37
L4F C36 C31 DOUB Y N 38
L4F C36 C35 SING Y N 39
L4F N06 C05 SING N N 40
L4F C31 C32 SING Y N 41
L4F C35 C34 DOUB Y N 42
L4F C05 C04 SING N N 43
L4F C32 C33 DOUB Y N 44
L4F C34 C33 SING Y N 45
L4F C04 O03 SING N N 46
L4F O03 C02 SING N N 47
L4F O01 C02 DOUB N N 48
L4F C02 C46 SING N N 49
L4F C55 C46 DOUB Y N 50
L4F C55 C54 SING Y N 51
L4F C46 C47 SING Y N 52
L4F C54 C49 DOUB Y N 53
L4F C47 C48 DOUB Y N 54
L4F C49 C48 SING Y N 55
L4F C49 N50 SING N N 56
L4F N50 C51 SING N N 57
L4F C51 N52 DOUB N N 58
L4F C51 N53 SING N N 59
L4F C10 H1 SING N N 60
L4F C10 H2 SING N N 61
L4F C17 H3 SING N N 62
L4F C22 H4 SING N N 63
L4F C24 H5 SING N N 64
L4F C26 H6 SING N N 65
L4F C04 H7 SING N N 66
L4F C04 H8 SING N N 67
L4F C05 H9 SING N N 68
L4F C05 H10 SING N N 69
L4F C07 H11 SING N N 70
L4F C07 H12 SING N N 71
L4F C08 H13 SING N N 72
L4F C08 H14 SING N N 73
L4F C09 H15 SING N N 74
L4F C09 H16 SING N N 75
L4F C14 H17 SING N N 76
L4F C18 H18 SING N N 77
L4F C18 H19 SING N N 78
L4F C19 H20 SING N N 79
L4F C19 H21 SING N N 80
L4F C23 H22 SING N N 81
L4F C25 H23 SING N N 82
L4F C29 H24 SING N N 83
L4F C29 H25 SING N N 84
L4F C30 H26 SING N N 85
L4F C30 H27 SING N N 86
L4F C32 H28 SING N N 87
L4F C33 H29 SING N N 88
L4F C34 H30 SING N N 89
L4F C35 H31 SING N N 90
L4F C36 H32 SING N N 91
L4F C38 H33 SING N N 92
L4F C38 H34 SING N N 93
L4F C40 H35 SING N N 94
L4F C41 H36 SING N N 95
L4F C42 H37 SING N N 96
L4F C43 H38 SING N N 97
L4F C44 H39 SING N N 98
L4F C47 H40 SING N N 99
L4F C48 H41 SING N N 100
L4F C54 H42 SING N N 101
L4F C55 H43 SING N N 102
L4F N13 H45 SING N N 103
L4F N16 H46 SING N N 104
L4F N50 H47 SING N N 105
L4F N52 H48 SING N N 106
L4F N53 H49 SING N N 107
L4F N53 H50 SING N N 108
#
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
L4F InChI InChI 1.06 'InChI=1S/C41H49N7O6S/c42-40(43)45-34-20-17-33(18-21-34)39(50)54-28-27-47-23-25-48(26-24-47)41(51)46-37(30-32-12-6-2-7-13-32)38(49)44-35(19-16-31-10-4-1-5-11-31)22-29-55(52,53)36-14-8-3-9-15-36/h1-15,17-18,20-21,35,37H,16,19,22-30H2,(H,44,49)(H,46,51)(H4,42,43,45)/t35-,37-/m0/s1'
L4F InChIKey InChI 1.06 GRAYNEZFLQHYCO-JSXFGMRASA-N
L4F SMILES_CANONICAL CACTVS 3.385 'NC(=N)Nc1ccc(cc1)C(=O)OCCN2CCN(CC2)C(=O)N[C@@H](Cc3ccccc3)C(=O)N[C@@H](CCc4ccccc4)CC[S](=O)(=O)c5ccccc5'
L4F SMILES CACTVS 3.385 'NC(=N)Nc1ccc(cc1)C(=O)OCCN2CCN(CC2)C(=O)N[CH](Cc3ccccc3)C(=O)N[CH](CCc4ccccc4)CC[S](=O)(=O)c5ccccc5'
L4F SMILES_CANONICAL 'OpenEye OEToolkits' 2.0.7 '[H]/N=C(/N)\Nc1ccc(cc1)C(=O)OCCN2CCN(CC2)C(=O)N[C@@H](Cc3ccccc3)C(=O)N[C@@H](CCc4ccccc4)CCS(=O)(=O)c5ccccc5'
L4F SMILES 'OpenEye OEToolkits' 2.0.7 'c1ccc(cc1)CCC(CCS(=O)(=O)c2ccccc2)NC(=O)C(Cc3ccccc3)NC(=O)N4CCN(CC4)CCOC(=O)c5ccc(cc5)NC(=N)N'
#
_pdbx_chem_comp_identifier.comp_id L4F
_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
'2-[4-[[(2~{S})-1-oxidanylidene-3-phenyl-1-[[(3~{S})-1-phenyl-5-(phenylsulfonyl)pentan-3-yl]amino]propan-2-yl]carbamoyl]piperazin-1-yl]ethyl 4-carbamimidamidobenzoate'
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
L4F 'Create component' 2022-11-10 PDBJ
L4F 'Modify coordinates' 2022-12-21 PDBJ
L4F 'Initial release' 2023-12-13 RCSB
L4F 'Modify PCM' 2024-09-27 PDBE
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id L4F
_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 C18
_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 ?
_pdbx_chem_comp_pcm.first_instance_model_db_code 8HEN
#
loop_
_software.name
_software.version
_software.description
rdkit 2023.03.3 'Core functionality.'
pdbeccdutils 0.8.4 'Wrapper to provide 2D templates and molecular fragments.'
#
loop_
_pdbe_chem_comp_atom_depiction.comp_id
_pdbe_chem_comp_atom_depiction.atom_id
_pdbe_chem_comp_atom_depiction.element
_pdbe_chem_comp_atom_depiction.model_Cartn_x
_pdbe_chem_comp_atom_depiction.model_Cartn_y
_pdbe_chem_comp_atom_depiction.pdbx_ordinal
L4F C10 C 7.702 1.732 1
L4F C15 C 11.600 6.982 2
L4F C17 C 14.198 6.982 3
L4F C21 C 19.394 5.482 4
L4F C22 C 19.394 3.982 5
L4F C24 C 21.992 3.982 6
L4F C26 C 20.693 6.232 7
L4F C02 C 6.404 -5.018 8
L4F C04 C 7.702 -2.768 9
L4F C05 C 9.002 -2.018 10
L4F C07 C 10.301 0.233 11
L4F C08 C 10.301 1.732 12
L4F C09 C 7.702 0.233 13
L4F C12 C 9.002 3.982 14
L4F C14 C 10.301 6.232 15
L4F C18 C 15.497 6.232 16
L4F C19 C 16.796 6.982 17
L4F C23 C 20.693 3.232 18
L4F C25 C 21.992 5.482 19
L4F C29 C 14.198 8.482 20
L4F C30 C 15.497 9.232 21
L4F C31 C 15.497 10.732 22
L4F C32 C 16.796 11.482 23
L4F C33 C 16.796 12.982 24
L4F C34 C 15.497 13.732 25
L4F C35 C 14.198 12.982 26
L4F C36 C 14.198 11.482 27
L4F C38 C 9.002 6.982 28
L4F C39 C 9.002 8.482 29
L4F C40 C 10.301 9.232 30
L4F C41 C 10.301 10.732 31
L4F C42 C 9.002 11.482 32
L4F C43 C 7.702 10.732 33
L4F C44 C 7.702 9.232 34
L4F C46 C 6.404 -6.518 35
L4F C47 C 5.104 -7.268 36
L4F C48 C 5.104 -8.768 37
L4F C49 C 6.404 -9.518 38
L4F C51 C 5.104 -11.768 39
L4F C54 C 7.702 -8.768 40
L4F C55 C 7.702 -7.268 41
L4F N06 N 9.002 -0.517 42
L4F N11 N 9.002 2.482 43
L4F N13 N 10.301 4.732 44
L4F N16 N 12.899 6.232 45
L4F N50 N 6.404 -11.018 46
L4F N52 N 5.104 -13.268 47
L4F N53 N 3.805 -11.018 48
L4F O01 O 5.104 -4.268 49
L4F O03 O 7.702 -4.268 50
L4F O27 O 18.845 7.532 51
L4F O28 O 17.345 4.934 52
L4F O37 O 11.600 8.482 53
L4F O45 O 7.702 4.732 54
L4F S20 S 18.095 6.232 55
L4F H48 H 6.404 -14.018 56
#
loop_
_pdbe_chem_comp_bond_depiction.comp_id
_pdbe_chem_comp_bond_depiction.atom_id_1
_pdbe_chem_comp_bond_depiction.atom_id_2
_pdbe_chem_comp_bond_depiction.value_order
_pdbe_chem_comp_bond_depiction.bond_dir
_pdbe_chem_comp_bond_depiction.pdbx_ordinal
L4F C42 C43 DOUBLE NONE 1
L4F C42 C41 SINGLE NONE 2
L4F C43 C44 SINGLE NONE 3
L4F C41 C40 DOUBLE NONE 4
L4F C44 C39 DOUBLE NONE 5
L4F C40 C39 SINGLE NONE 6
L4F C39 C38 SINGLE NONE 7
L4F C14 C38 SINGLE BEGINWEDGE 8
L4F C14 N13 SINGLE NONE 9
L4F C14 C15 SINGLE NONE 10
L4F N13 C12 SINGLE NONE 11
L4F C25 C26 DOUBLE NONE 12
L4F C25 C24 SINGLE NONE 13
L4F C26 C21 SINGLE NONE 14
L4F C19 C18 SINGLE NONE 15
L4F C19 S20 SINGLE NONE 16
L4F C15 N16 SINGLE NONE 17
L4F C15 O37 DOUBLE NONE 18
L4F N16 C17 SINGLE NONE 19
L4F O45 C12 DOUBLE NONE 20
L4F C12 N11 SINGLE NONE 21
L4F O27 S20 DOUBLE NONE 22
L4F C24 C23 DOUBLE NONE 23
L4F C17 C18 SINGLE BEGINWEDGE 24
L4F C21 S20 SINGLE NONE 25
L4F C21 C22 DOUBLE NONE 26
L4F S20 O28 DOUBLE NONE 27
L4F N11 C08 SINGLE NONE 28
L4F N11 C10 SINGLE NONE 29
L4F C08 C07 SINGLE NONE 30
L4F C17 C29 SINGLE NONE 31
L4F C10 C09 SINGLE NONE 32
L4F C23 C22 SINGLE NONE 33
L4F C29 C30 SINGLE NONE 34
L4F C07 N06 SINGLE NONE 35
L4F C30 C31 SINGLE NONE 36
L4F C09 N06 SINGLE NONE 37
L4F C36 C31 SINGLE NONE 38
L4F C36 C35 DOUBLE NONE 39
L4F N06 C05 SINGLE NONE 40
L4F C31 C32 DOUBLE NONE 41
L4F C35 C34 SINGLE NONE 42
L4F C05 C04 SINGLE NONE 43
L4F C32 C33 SINGLE NONE 44
L4F C34 C33 DOUBLE NONE 45
L4F C04 O03 SINGLE NONE 46
L4F O03 C02 SINGLE NONE 47
L4F O01 C02 DOUBLE NONE 48
L4F C02 C46 SINGLE NONE 49
L4F C55 C46 SINGLE NONE 50
L4F C55 C54 DOUBLE NONE 51
L4F C46 C47 DOUBLE NONE 52
L4F C54 C49 SINGLE NONE 53
L4F C47 C48 SINGLE NONE 54
L4F C49 C48 DOUBLE NONE 55
L4F C49 N50 SINGLE NONE 56
L4F N50 C51 SINGLE ENDUPRIGHT 57
L4F C51 N52 DOUBLE NONE 58
L4F C51 N53 SINGLE ENDUPRIGHT 59
#
loop_
_pdbe_chem_comp_substructure.comp_id
_pdbe_chem_comp_substructure.substructure_name
_pdbe_chem_comp_substructure.id
_pdbe_chem_comp_substructure.substructure_type
_pdbe_chem_comp_substructure.substructure_smiles
_pdbe_chem_comp_substructure.substructure_inchis
_pdbe_chem_comp_substructure.substructure_inchikeys
L4F MurckoScaffold S1 scaffold 'O=C(OCCN1CCN(C(=O)N[C@@H](Cc2ccccc2)C(=O)N[C@@H](CCc2ccccc2)CCS(=O)(=O)c2ccccc2)CC1)c1ccccc1' InChI=1S/C40H46N4O6S/c45-38(41-35(22-21-32-13-5-1-6-14-32)23-30-51(48,49)36-19-11-4-12-20-36)37(31-33-15-7-2-8-16-33)42-40(47)44-26-24-43(25-27-44)28-29-50-39(46)34-17-9-3-10-18-34/h1-20,35,37H,21-31H2,(H,41,45)(H,42,47)/t35-,37-/m0/s1 BZDATQOFCGTKAO-JSXFGMRASA-N
L4F amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
L4F peptide F2 fragment NCC=O InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2 LYIIBVSRGJSHAV-UHFFFAOYSA-N
L4F phenyl F3 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
L4F piperazine F4 fragment C1CNCCN1 InChI=1S/C4H10N2/c1-2-6-4-3-5-1/h5-6H,1-4H2 GLUUGHFHXGJENI-UHFFFAOYSA-N
#
loop_
_pdbe_chem_comp_substructure_mapping.comp_id
_pdbe_chem_comp_substructure_mapping.atom_id
_pdbe_chem_comp_substructure_mapping.substructure_id
_pdbe_chem_comp_substructure_mapping.substructure_ordinal
L4F C10 S1 1
L4F C15 S1 1
L4F C17 S1 1
L4F C21 S1 1
L4F C22 S1 1
L4F C24 S1 1
L4F C26 S1 1
L4F C02 S1 1
L4F C04 S1 1
L4F C05 S1 1
L4F C07 S1 1
L4F C08 S1 1
L4F C09 S1 1
L4F C12 S1 1
L4F C14 S1 1
L4F C18 S1 1
L4F C19 S1 1
L4F C23 S1 1
L4F C25 S1 1
L4F C29 S1 1
L4F C30 S1 1
L4F C31 S1 1
L4F C32 S1 1
L4F C33 S1 1
L4F C34 S1 1
L4F C35 S1 1
L4F C36 S1 1
L4F C38 S1 1
L4F C39 S1 1
L4F C40 S1 1
L4F C41 S1 1
L4F C42 S1 1
L4F C43 S1 1
L4F C44 S1 1
L4F C46 S1 1
L4F C47 S1 1
L4F C48 S1 1
L4F C49 S1 1
L4F C54 S1 1
L4F C55 S1 1
L4F N06 S1 1
L4F N11 S1 1
L4F N13 S1 1
L4F N16 S1 1
L4F O01 S1 1
L4F O03 S1 1
L4F O27 S1 1
L4F O28 S1 1
L4F O37 S1 1
L4F O45 S1 1
L4F S20 S1 1
L4F N16 F1 1
L4F C15 F1 1
L4F O37 F1 1
L4F C14 F1 1
L4F O37 F2 1
L4F C15 F2 1
L4F C14 F2 1
L4F N13 F2 1
L4F C21 F3 1
L4F C26 F3 1
L4F C25 F3 1
L4F C24 F3 1
L4F C23 F3 1
L4F C22 F3 1
L4F C31 F3 2
L4F C36 F3 2
L4F C35 F3 2
L4F C34 F3 2
L4F C33 F3 2
L4F C32 F3 2
L4F C39 F3 3
L4F C44 F3 3
L4F C43 F3 3
L4F C42 F3 3
L4F C41 F3 3
L4F C40 F3 3
L4F C46 F3 4
L4F C55 F3 4
L4F C54 F3 4
L4F C49 F3 4
L4F C48 F3 4
L4F C47 F3 4
L4F N06 F4 1
L4F C07 F4 1
L4F C08 F4 1
L4F N11 F4 1
L4F C10 F4 1
L4F C09 F4 1
#
_pdbe_chem_comp_rdkit_properties.comp_id L4F
_pdbe_chem_comp_rdkit_properties.exactmw 767.347
_pdbe_chem_comp_rdkit_properties.amw 767.953
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 13
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 6
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 17
_pdbe_chem_comp_rdkit_properties.NumHBD 5
_pdbe_chem_comp_rdkit_properties.NumHBA 8
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 55
_pdbe_chem_comp_rdkit_properties.NumAtoms 104
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 14
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 3
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.317
_pdbe_chem_comp_rdkit_properties.NumRings 5
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 4
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 1
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 2
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 391.411
_pdbe_chem_comp_rdkit_properties.tpsa 187.020
_pdbe_chem_comp_rdkit_properties.CrippenClogP 3.416
_pdbe_chem_comp_rdkit_properties.CrippenMR 211.493
_pdbe_chem_comp_rdkit_properties.chi0v 27.305
_pdbe_chem_comp_rdkit_properties.chi1v 15.376
_pdbe_chem_comp_rdkit_properties.chi2v 6.402
_pdbe_chem_comp_rdkit_properties.chi3v 6.402
_pdbe_chem_comp_rdkit_properties.chi4v 3.762
_pdbe_chem_comp_rdkit_properties.chi0n 75.488
_pdbe_chem_comp_rdkit_properties.chi1n 38.076
_pdbe_chem_comp_rdkit_properties.chi2n 5.290
_pdbe_chem_comp_rdkit_properties.chi3n 5.290
_pdbe_chem_comp_rdkit_properties.chi4n 3.058
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -5.730
_pdbe_chem_comp_rdkit_properties.kappa1 10.976
_pdbe_chem_comp_rdkit_properties.kappa2 20.091
_pdbe_chem_comp_rdkit_properties.kappa3 12.968
_pdbe_chem_comp_rdkit_properties.Phi 4.009
#
_pdbe_chem_comp_external_mappings.comp_id L4F
_pdbe_chem_comp_external_mappings.source UniChem
_pdbe_chem_comp_external_mappings.resource PDBe
_pdbe_chem_comp_external_mappings.resource_id L4F
#
loop_
_pdbe_chem_comp_rdkit_conformer.comp_id
_pdbe_chem_comp_rdkit_conformer.atom_id
_pdbe_chem_comp_rdkit_conformer.Cartn_x_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_y_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_z_rdkit
_pdbe_chem_comp_rdkit_conformer.rdkit_method
_pdbe_chem_comp_rdkit_conformer.rdkit_ordinal
L4F C10 3.449 3.005 -0.757 ETKDGv3 1
L4F C15 -2.607 1.802 0.033 ETKDGv3 2
L4F C17 -4.985 2.248 0.831 ETKDGv3 3
L4F C21 -8.190 -1.380 0.073 ETKDGv3 4
L4F C22 -7.908 -1.819 1.311 ETKDGv3 5
L4F C24 -10.270 -2.180 1.807 ETKDGv3 6
L4F C26 -9.602 -1.304 -0.371 ETKDGv3 7
L4F C02 8.370 -1.808 0.204 ETKDGv3 8
L4F C04 6.773 -0.097 1.053 ETKDGv3 9
L4F C05 6.233 0.491 -0.255 ETKDGv3 10
L4F C07 3.822 0.219 -0.048 ETKDGv3 11
L4F C08 2.508 0.924 0.292 ETKDGv3 12
L4F C09 4.729 2.219 -1.052 ETKDGv3 13
L4F C12 1.000 2.475 -1.028 ETKDGv3 14
L4F C14 -1.510 2.073 -0.973 ETKDGv3 15
L4F C18 -5.682 0.883 0.619 ETKDGv3 16
L4F C19 -6.340 0.729 -0.760 ETKDGv3 17
L4F C23 -8.998 -2.233 2.219 ETKDGv3 18
L4F C25 -10.587 -1.692 0.449 ETKDGv3 19
L4F C29 -5.936 3.468 0.753 ETKDGv3 20
L4F C30 -6.869 3.629 1.969 ETKDGv3 21
L4F C31 -8.132 2.810 1.871 ETKDGv3 22
L4F C32 -8.441 1.907 2.821 ETKDGv3 23
L4F C33 -9.720 1.170 2.762 ETKDGv3 24
L4F C34 -10.584 1.405 1.769 ETKDGv3 25
L4F C35 -10.257 2.394 0.724 ETKDGv3 26
L4F C36 -9.101 3.067 0.775 ETKDGv3 27
L4F C38 -1.625 1.124 -2.184 ETKDGv3 28
L4F C39 -1.316 -0.311 -1.834 ETKDGv3 29
L4F C40 -2.395 -1.194 -1.327 ETKDGv3 30
L4F C41 -2.125 -2.457 -0.975 ETKDGv3 31
L4F C42 -0.749 -2.980 -1.095 ETKDGv3 32
L4F C43 0.229 -2.191 -1.557 ETKDGv3 33
L4F C44 -0.066 -0.796 -1.945 ETKDGv3 34
L4F C46 9.775 -2.223 0.002 ETKDGv3 35
L4F C47 10.079 -3.375 -0.626 ETKDGv3 36
L4F C48 11.489 -3.773 -0.822 ETKDGv3 37
L4F C49 12.486 -3.000 -0.355 ETKDGv3 38
L4F C51 14.391 -4.682 -0.520 ETKDGv3 39
L4F C54 12.154 -1.722 0.315 ETKDGv3 40
L4F C55 10.878 -1.357 0.489 ETKDGv3 41
L4F N06 4.945 1.181 -0.023 ETKDGv3 42
L4F N11 2.317 2.088 -0.582 ETKDGv3 43
L4F N13 -0.177 1.992 -0.359 ETKDGv3 44
L4F N16 -3.895 2.413 -0.138 ETKDGv3 45
L4F N50 13.868 -3.344 -0.560 ETKDGv3 46
L4F N52 13.684 -5.652 -0.032 ETKDGv3 47
L4F N53 15.728 -4.928 -0.966 ETKDGv3 48
L4F O01 7.424 -2.535 -0.210 ETKDGv3 49
L4F O03 8.093 -0.604 0.865 ETKDGv3 50
L4F O27 -7.391 -1.065 -2.450 ETKDGv3 51
L4F O28 -5.750 -1.909 -0.859 ETKDGv3 52
L4F O37 -2.412 0.999 0.987 ETKDGv3 53
L4F O45 0.879 3.245 -2.019 ETKDGv3 54
L4F S20 -6.892 -0.949 -1.036 ETKDGv3 55
L4F H1 3.270 3.714 -1.593 ETKDGv3 56
L4F H2 3.584 3.596 0.175 ETKDGv3 57
L4F H3 -4.540 2.245 1.852 ETKDGv3 58
L4F H4 -6.883 -1.887 1.652 ETKDGv3 59
L4F H5 -11.070 -2.483 2.470 ETKDGv3 60
L4F H6 -9.843 -0.937 -1.361 ETKDGv3 61
L4F H7 6.816 0.708 1.818 ETKDGv3 62
L4F H8 6.114 -0.901 1.440 ETKDGv3 63
L4F H9 6.132 -0.306 -1.026 ETKDGv3 64
L4F H10 7.002 1.206 -0.625 ETKDGv3 65
L4F H11 3.732 -0.261 -1.050 ETKDGv3 66
L4F H12 3.980 -0.583 0.703 ETKDGv3 67
L4F H13 2.522 1.257 1.352 ETKDGv3 68
L4F H14 1.686 0.188 0.160 ETKDGv3 69
L4F H15 5.575 2.942 -1.051 ETKDGv3 70
L4F H16 4.663 1.763 -2.067 ETKDGv3 71
L4F H17 -1.658 3.113 -1.340 ETKDGv3 72
L4F H18 -6.438 0.720 1.411 ETKDGv3 73
L4F H19 -4.921 0.083 0.746 ETKDGv3 74
L4F H20 -7.221 1.396 -0.844 ETKDGv3 75
L4F H21 -5.616 0.989 -1.561 ETKDGv3 76
L4F H22 -8.764 -2.583 3.216 ETKDGv3 77
L4F H23 -11.618 -1.638 0.124 ETKDGv3 78
L4F H24 -5.298 4.379 0.726 ETKDGv3 79
L4F H25 -6.504 3.476 -0.200 ETKDGv3 80
L4F H26 -7.174 4.696 2.035 ETKDGv3 81
L4F H27 -6.311 3.409 2.905 ETKDGv3 82
L4F H28 -7.766 1.714 3.645 ETKDGv3 83
L4F H29 -9.959 0.446 3.530 ETKDGv3 84
L4F H30 -11.525 0.870 1.729 ETKDGv3 85
L4F H31 -10.961 2.582 -0.077 ETKDGv3 86
L4F H32 -8.882 3.805 0.015 ETKDGv3 87
L4F H33 -2.652 1.188 -2.607 ETKDGv3 88
L4F H34 -0.941 1.470 -2.989 ETKDGv3 89
L4F H35 -3.403 -0.813 -1.235 ETKDGv3 90
L4F H36 -2.914 -3.097 -0.602 ETKDGv3 91
L4F H37 -0.534 -4.001 -0.809 ETKDGv3 92
L4F H38 1.239 -2.571 -1.643 ETKDGv3 93
L4F H39 0.741 -0.172 -2.309 ETKDGv3 94
L4F H40 9.302 -4.028 -1.003 ETKDGv3 95
L4F H41 11.698 -4.681 -1.371 ETKDGv3 96
L4F H42 12.949 -1.080 0.675 ETKDGv3 97
L4F H43 10.660 -0.420 0.987 ETKDGv3 98
L4F H45 -0.071 1.597 0.602 ETKDGv3 99
L4F H46 -4.048 3.015 -0.979 ETKDGv3 100
L4F H47 14.553 -2.561 -0.655 ETKDGv3 101
L4F H48 14.054 -6.627 0.026 ETKDGv3 102
L4F H49 16.309 -4.149 -1.346 ETKDGv3 103
L4F H50 16.140 -5.887 -0.925 ETKDGv3 104
#