data_LYB
#
_chem_comp.id LYB
_chem_comp.name
;2-{4-[4-(4-{4-[2-(2-AMINO-4-OXO-4,7-DIHYDRO-3H-PYRROLO[2,3-D]PYRIMIDIN-5-YL)-ETHYL]-BENZOYLAMINO}-4-CARBOXY-BUTYRYLAMIN
O)-4-CARBOXY-BUTYRYLAMINO}-PENTANEDIOIC ACID
;
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C35 H42 N8 O15"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "LY231514 TETRA GLU"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2001-08-27
_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 814.753
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code LYB
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag Y
_chem_comp.pdbx_ideal_coordinates_details ?
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 1JTU
_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
LYB N1 N1 N 0 1 Y N N 14.427 19.054 32.859 -1.697 -5.868 -6.609 N1 LYB 1
LYB C1 C1 C 0 1 Y N N 13.464 19.100 31.845 -0.448 -5.259 -6.849 C1 LYB 2
LYB N2 N2 N 0 1 Y N N 13.566 18.368 30.692 0.328 -4.831 -5.879 N2 LYB 3
LYB C3 C3 C 0 1 Y N N 14.699 17.519 30.570 -0.189 -5.032 -4.643 C3 LYB 4
LYB C4 C4 C 0 1 Y N N 15.615 17.349 31.604 -1.391 -5.612 -4.295 C4 LYB 5
LYB C5 C5 C 0 1 Y N N 15.529 18.160 32.795 -2.257 -6.088 -5.345 C5 LYB 6
LYB N3 N3 N 0 1 Y N N 14.968 16.616 29.546 0.446 -4.665 -3.488 N3 LYB 7
LYB C6 C6 C 0 1 Y N N 16.056 15.829 29.971 -0.338 -5.005 -2.412 C6 LYB 8
LYB C7 C7 C 0 1 Y N N 16.469 16.257 31.217 -1.465 -5.586 -2.906 C7 LYB 9
LYB C8 C8 C 0 1 N N N 17.598 15.637 32.009 -2.602 -6.114 -2.066 C8 LYB 10
LYB C9 C9 C 0 1 N N N 17.328 14.165 32.347 -2.430 -7.594 -1.672 C9 LYB 11
LYB C10 C10 C 0 1 Y N N 16.235 14.034 33.388 -3.554 -8.141 -0.859 C10 LYB 12
LYB C11 C11 C 0 1 Y N N 14.893 13.881 33.001 -3.511 -8.062 0.533 C11 LYB 13
LYB C12 C12 C 0 1 Y N N 13.896 13.737 33.970 -4.562 -8.574 1.294 C12 LYB 14
LYB C13 C13 C 0 1 Y N N 14.213 13.740 35.354 -5.633 -9.153 0.646 C13 LYB 15
LYB C14 C14 C 0 1 Y N N 15.568 13.901 35.733 -5.700 -9.244 -0.729 C14 LYB 16
LYB C15 C15 C 0 1 Y N N 16.564 14.045 34.755 -4.649 -8.733 -1.490 C15 LYB 17
LYB C16 C16 C 0 1 N N N 13.153 13.430 36.383 -6.752 -9.699 1.456 C16 LYB 18
LYB O1 O1 O 0 1 N N N 16.249 18.094 33.792 -3.344 -6.618 -5.145 O1 LYB 19
LYB N4 N4 N 0 1 N N N 12.309 20.027 31.983 -0.095 -5.143 -8.168 N4 LYB 20
LYB C17 C17 C 0 1 N N S 12.655 12.849 38.786 -9.180 -10.208 1.500 C17 LYB 21
LYB C18 C18 C 0 1 N N N 12.191 11.414 38.608 -10.457 -9.571 0.945 C18 LYB 22
LYB C19 C19 C 0 1 N N N 13.413 10.515 38.572 -10.512 -8.054 1.134 C19 LYB 23
LYB C20 C20 C 0 1 N N N 13.020 9.103 38.347 -11.794 -7.423 0.618 C20 LYB 24
LYB C21 C21 C 0 1 N N N 13.396 12.988 40.080 -9.212 -11.710 1.298 C21 LYB 25
LYB O2 O2 O 0 1 N N N 13.019 8.589 37.235 -12.692 -8.064 0.078 O2 LYB 26
LYB O3 O3 O 0 1 N N N 12.745 12.814 41.242 -8.843 -12.294 0.288 O3 LYB 27
LYB O4 O4 O 0 1 N N N 14.593 13.253 40.081 -9.753 -12.353 2.366 O4 LYB 28
LYB N5 N5 N 0 1 N N N 13.567 13.230 37.682 -7.994 -9.730 0.837 N5 LYB 29
LYB O5 O5 O 0 1 N N N 11.944 13.287 36.129 -6.535 -10.068 2.608 O5 LYB 30
LYB C22 C22 C 0 1 N N S 13.311 2.168 43.045 -13.912 -2.232 5.875 C22 LYB 31
LYB C23 C23 C 0 1 N N N 12.100 1.340 43.470 -14.808 -2.694 7.028 C23 LYB 32
LYB C24 C24 C 0 1 N N N 12.356 0.537 44.752 -16.236 -3.026 6.592 C24 LYB 33
LYB C25 C25 C 0 1 N N N 11.121 -0.266 45.103 -16.957 -1.862 5.931 C25 LYB 34
LYB C26 C26 C 0 1 N N N 14.548 1.327 42.821 -12.525 -1.900 6.389 C26 LYB 35
LYB O6 O6 O 0 1 N N N 9.985 0.041 44.734 -16.451 -0.753 5.782 O6 LYB 36
LYB N8 N8 N 0 1 N N N ? ? ? -18.246 -2.208 5.553 N8 LYB 37
LYB O8 O8 O 0 1 N N N 15.696 1.758 43.374 -12.413 -0.590 6.732 O8 LYB 38
LYB O9 O9 O 0 1 N N N 14.561 0.317 42.117 -11.613 -2.704 6.531 O9 LYB 39
LYB C27 C27 C 0 1 N N S 12.451 6.927 39.345 -12.893 -5.207 0.383 C27 LYB 40
LYB C28 C28 C 0 1 N N N 12.405 6.297 40.737 -13.016 -3.936 1.228 C28 LYB 41
LYB C29 C29 C 0 1 N N N 12.163 4.792 40.617 -13.314 -4.213 2.702 C29 LYB 42
LYB C30 C30 C 0 1 N N N 12.430 4.117 41.922 -13.474 -2.953 3.538 C30 LYB 43
LYB C31 C31 C 0 1 N N N 11.198 6.645 38.547 -12.623 -4.850 -1.066 C31 LYB 44
LYB O10 O10 O 0 1 N N N 12.260 4.632 43.030 -13.352 -1.820 3.080 O10 LYB 45
LYB N6 N6 N 0 1 N N N 12.950 2.871 41.815 -13.743 -3.252 4.866 N6 LYB 46
LYB O11 O11 O 0 1 N N N 11.199 5.532 37.792 -11.517 -4.644 -1.548 O11 LYB 47
LYB O12 O12 O 0 1 N N N 10.201 7.364 38.566 -13.773 -4.730 -1.781 O12 LYB 48
LYB N7 N7 N 0 1 N N N 12.735 8.368 39.453 -11.800 -6.049 0.809 N7 LYB 49
LYB O7 O7 O 0 1 N N N 11.302 -1.357 45.869 -21.569 0.667 8.011 O7 LYB 50
LYB O13 O13 O 0 1 N N N ? ? ? -22.244 -1.338 8.840 O13 LYB 51
LYB O14 O14 O 0 1 N N N ? ? ? -19.773 -3.377 3.988 O14 LYB 52
LYB O15 O15 O 0 1 N N N ? ? ? -20.836 -1.544 3.180 O15 LYB 53
LYB C32 C32 C 0 1 N N R ? ? ? -19.152 -1.273 4.927 C32 LYB 54
LYB C33 C33 C 0 1 N N N ? ? ? -19.994 -0.504 5.958 C33 LYB 55
LYB C34 C34 C 0 1 N N N ? ? ? -20.841 -1.355 6.909 C34 LYB 56
LYB C35 C35 C 0 1 N N N ? ? ? -21.570 -0.556 7.960 C35 LYB 57
LYB C36 C36 C 0 1 N N N ? ? ? -20.013 -2.040 3.940 C36 LYB 58
LYB HN1 HN1 H 0 1 N N N 14.337 19.664 33.646 -2.234 -6.170 -7.417 HN1 LYB 59
LYB HN3 HN3 H 0 1 N N N 14.482 16.540 28.675 1.350 -4.215 -3.434 HN3 LYB 60
LYB HC6 HC6 H 0 1 N N N 16.498 15.018 29.410 -0.003 -4.794 -1.406 HC6 LYB 61
LYB HC81 1HC8 H 0 0 N N N 18.519 15.696 31.411 -2.674 -5.498 -1.160 HC81 LYB 62
LYB HC82 2HC8 H 0 0 N N N 17.693 16.190 32.955 -3.553 -5.972 -2.596 HC82 LYB 63
LYB HC91 1HC9 H 0 0 N N N 17.014 13.641 31.432 -1.491 -7.692 -1.102 HC91 LYB 64
LYB HC92 2HC9 H 0 0 N N N 18.251 13.724 32.752 -2.273 -8.202 -2.580 HC92 LYB 65
LYB H11 H11 H 0 1 N N N 14.631 13.875 31.953 -2.662 -7.603 1.032 H11 LYB 66
LYB H12 H12 H 0 1 N N N 12.868 13.622 33.661 -4.518 -8.505 2.377 H12 LYB 67
LYB H14 H14 H 0 1 N N N 15.836 13.913 36.779 -6.548 -9.702 -1.232 H14 LYB 68
LYB H15 H15 H 0 1 N N N 17.594 14.166 35.056 -4.692 -8.799 -2.574 H15 LYB 69
LYB HN41 1HN4 H 0 0 N N N 12.368 20.512 32.855 -0.744 -5.446 -8.857 HN41 LYB 70
LYB HN42 2HN4 H 0 0 N N N 11.583 20.147 31.306 0.796 -4.761 -8.386 HN42 LYB 71
LYB H17 H17 H 0 1 N N N 11.771 13.503 38.784 -9.039 -9.991 2.564 H17 LYB 72
LYB H181 1H18 H 0 0 N N N 11.541 11.126 39.447 -10.534 -9.789 -0.129 H181 LYB 73
LYB H182 2H18 H 0 0 N N N 11.623 11.315 37.671 -11.336 -10.032 1.414 H182 LYB 74
LYB H191 1H19 H 0 0 N N N 14.073 10.839 37.754 -10.376 -7.790 2.189 H191 LYB 75
LYB H192 2H19 H 0 0 N N N 13.934 10.588 39.538 -9.685 -7.600 0.574 H192 LYB 76
LYB HO4 HO4 H 0 1 N N N 14.907 13.299 40.976 -9.830 -13.327 2.272 HO4 LYB 77
LYB HN5 HN5 H 0 1 N N N 14.538 13.349 37.891 -8.105 -9.348 -0.099 HN5 LYB 78
LYB H22 H22 H 0 1 N N N 13.563 2.870 43.854 -14.322 -1.360 5.357 H22 LYB 79
LYB H231 1H23 H 0 0 N N N 11.257 2.023 43.650 -14.371 -3.589 7.491 H231 LYB 80
LYB H232 2H23 H 0 0 N N N 11.884 0.624 42.663 -14.831 -1.926 7.811 H232 LYB 81
LYB H241 1H24 H 0 0 N N N 13.204 -0.146 44.593 -16.245 -3.889 5.917 H241 LYB 82
LYB H242 2H24 H 0 0 N N N 12.589 1.228 45.576 -16.820 -3.300 7.479 H242 LYB 83
LYB HN8 HN8 H 0 1 N N N ? ? ? -18.566 -3.157 5.723 HN8 LYB 84
LYB HO8 HO8 H 0 1 N N N 16.406 1.178 43.124 -11.544 -0.328 7.105 HO8 LYB 85
LYB H27 H27 H 0 1 N N N 13.272 6.459 38.782 -13.793 -5.828 0.438 H27 LYB 86
LYB H281 1H28 H 0 0 N N N 13.363 6.473 41.249 -12.079 -3.366 1.165 H281 LYB 87
LYB H282 2H28 H 0 0 N N N 11.587 6.752 41.315 -13.796 -3.286 0.810 H282 LYB 88
LYB H291 1H29 H 0 0 N N N 11.117 4.616 40.327 -14.211 -4.834 2.806 H291 LYB 89
LYB H292 2H29 H 0 0 N N N 12.842 4.380 39.856 -12.476 -4.775 3.132 H292 LYB 90
LYB HN6 HN6 H 0 1 N N N 13.083 2.444 40.921 -13.824 -4.226 5.140 HN6 LYB 91
LYB HO2 HO2 H 0 1 N N N 9.533 6.995 38.001 -13.657 -4.465 -2.718 HO2 LYB 92
LYB HN7 HN7 H 0 1 N N N 12.718 8.810 40.350 -11.003 -5.617 1.269 HN7 LYB 93
LYB HO3 HO3 H 0 1 N N N ? ? ? -22.739 -0.853 9.534 HO3 LYB 94
LYB HO5 HO5 H 0 1 N N N ? ? ? -20.306 -3.921 3.369 HO5 LYB 95
LYB H32 H32 H 0 1 N N N ? ? ? -18.541 -0.562 4.357 H32 LYB 96
LYB H331 1H33 H 0 0 N N N ? ? ? -20.636 0.212 5.429 H331 LYB 97
LYB H332 2H33 H 0 0 N N N ? ? ? -19.316 0.099 6.576 H332 LYB 98
LYB H341 1H34 H 0 0 N N N ? ? ? -21.573 -1.956 6.360 H341 LYB 99
LYB H342 2H34 H 0 0 N N N ? ? ? -20.199 -2.074 7.433 H342 LYB 100
# #
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
LYB N1 C1 SING Y N 1
LYB N1 C5 SING Y N 2
LYB N1 HN1 SING N N 3
LYB C1 N2 DOUB Y N 4
LYB C1 N4 SING N N 5
LYB N2 C3 SING Y N 6
LYB C3 C4 DOUB Y N 7
LYB C3 N3 SING Y N 8
LYB C4 C5 SING Y N 9
LYB C4 C7 SING Y N 10
LYB C5 O1 DOUB N N 11
LYB N3 C6 SING Y N 12
LYB N3 HN3 SING N N 13
LYB C6 C7 DOUB Y N 14
LYB C6 HC6 SING N N 15
LYB C7 C8 SING N N 16
LYB C8 C9 SING N N 17
LYB C8 HC81 SING N N 18
LYB C8 HC82 SING N N 19
LYB C9 C10 SING N N 20
LYB C9 HC91 SING N N 21
LYB C9 HC92 SING N N 22
LYB C10 C11 DOUB Y N 23
LYB C10 C15 SING Y N 24
LYB C11 C12 SING Y N 25
LYB C11 H11 SING N N 26
LYB C12 C13 DOUB Y N 27
LYB C12 H12 SING N N 28
LYB C13 C14 SING Y N 29
LYB C13 C16 SING N N 30
LYB C14 C15 DOUB Y N 31
LYB C14 H14 SING N N 32
LYB C15 H15 SING N N 33
LYB C16 N5 SING N N 34
LYB C16 O5 DOUB N N 35
LYB N4 HN41 SING N N 36
LYB N4 HN42 SING N N 37
LYB C17 C18 SING N N 38
LYB C17 C21 SING N N 39
LYB C17 N5 SING N N 40
LYB C17 H17 SING N N 41
LYB C18 C19 SING N N 42
LYB C18 H181 SING N N 43
LYB C18 H182 SING N N 44
LYB C19 C20 SING N N 45
LYB C19 H191 SING N N 46
LYB C19 H192 SING N N 47
LYB C20 O2 DOUB N N 48
LYB C20 N7 SING N N 49
LYB C21 O3 DOUB N N 50
LYB C21 O4 SING N N 51
LYB O4 HO4 SING N N 52
LYB N5 HN5 SING N N 53
LYB C22 C23 SING N N 54
LYB C22 C26 SING N N 55
LYB C22 N6 SING N N 56
LYB C22 H22 SING N N 57
LYB C23 C24 SING N N 58
LYB C23 H231 SING N N 59
LYB C23 H232 SING N N 60
LYB C24 C25 SING N N 61
LYB C24 H241 SING N N 62
LYB C24 H242 SING N N 63
LYB C25 O6 DOUB N N 64
LYB C25 N8 SING N N 65
LYB C26 O8 SING N N 66
LYB C26 O9 DOUB N N 67
LYB N8 C32 SING N N 68
LYB N8 HN8 SING N N 69
LYB O8 HO8 SING N N 70
LYB C27 C28 SING N N 71
LYB C27 C31 SING N N 72
LYB C27 N7 SING N N 73
LYB C27 H27 SING N N 74
LYB C28 C29 SING N N 75
LYB C28 H281 SING N N 76
LYB C28 H282 SING N N 77
LYB C29 C30 SING N N 78
LYB C29 H291 SING N N 79
LYB C29 H292 SING N N 80
LYB C30 O10 DOUB N N 81
LYB C30 N6 SING N N 82
LYB C31 O11 DOUB N N 83
LYB C31 O12 SING N N 84
LYB N6 HN6 SING N N 85
LYB O12 HO2 SING N N 86
LYB N7 HN7 SING N N 87
LYB O7 C35 DOUB N N 88
LYB O13 C35 SING N N 89
LYB O13 HO3 SING N N 90
LYB O14 C36 SING N N 91
LYB O14 HO5 SING N N 92
LYB O15 C36 DOUB N N 93
LYB C32 C33 SING N N 94
LYB C32 C36 SING N N 95
LYB C32 H32 SING N N 96
LYB C33 C34 SING N N 97
LYB C33 H331 SING N N 98
LYB C33 H332 SING N N 99
LYB C34 C35 SING N N 100
LYB C34 H341 SING N N 101
LYB C34 H342 SING N N 102
# #
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
LYB SMILES ACDLabs 10.04 "O=C(O)C(NC(=O)CCC(C(=O)O)NC(=O)CCC(C(=O)O)NC(=O)CCC(C(=O)O)NC(=O)c1ccc(cc1)CCc2cnc3N=C(NC(=O)c23)N)CCC(=O)O"
LYB SMILES_CANONICAL CACTVS 3.341 "NC1=Nc2[nH]cc(CCc3ccc(cc3)C(=O)N[C@@H](CCC(=O)N[C@@H](CCC(=O)N[C@@H](CCC(=O)NC(CCC(O)=O)C(O)=O)C(O)=O)C(O)=O)C(O)=O)c2C(=O)N1"
LYB SMILES CACTVS 3.341 "NC1=Nc2[nH]cc(CCc3ccc(cc3)C(=O)N[CH](CCC(=O)N[CH](CCC(=O)N[CH](CCC(=O)NC(CCC(O)=O)C(O)=O)C(O)=O)C(O)=O)C(O)=O)c2C(=O)N1"
LYB SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1cc(ccc1CCc2c[nH]c3c2C(=O)NC(=N3)N)C(=O)N[C@@H](CCC(=O)N[C@@H](CCC(=O)N[C@@H](CCC(=O)N[C@H](CCC(=O)O)C(=O)O)C(=O)O)C(=O)O)C(=O)O"
LYB SMILES "OpenEye OEToolkits" 1.5.0 "c1cc(ccc1CCc2c[nH]c3c2C(=O)NC(=N3)N)C(=O)NC(CCC(=O)NC(CCC(=O)NC(CCC(=O)NC(CCC(=O)O)C(=O)O)C(=O)O)C(=O)O)C(=O)O"
LYB InChI InChI 1.03 "InChI=1S/C35H42N8O15/c36-35-42-28-27(30(50)43-35)18(15-37-28)6-3-16-1-4-17(5-2-16)29(49)41-22(34(57)58)9-13-25(46)39-20(32(53)54)7-11-23(44)38-19(31(51)52)8-12-24(45)40-21(33(55)56)10-14-26(47)48/h1-2,4-5,15,19-22H,3,6-14H2,(H,38,44)(H,39,46)(H,40,45)(H,41,49)(H,47,48)(H,51,52)(H,53,54)(H,55,56)(H,57,58)(H4,36,37,42,43,50)/t19-,20-,21?,22-/m0/s1"
LYB InChIKey InChI 1.03 DICHBVJYDUDAIQ-QEGIFBSNSA-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
LYB "SYSTEMATIC NAME" ACDLabs 10.04 "N-({4-[2-(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-5-yl)ethyl]phenyl}carbonyl)-L-gamma-glutamyl-L-gamma-glutamyl-L-gamma-glutamylglutamic acid"
LYB "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2R)-2-[[(4S)-4-[[(4S)-4-[[(4S)-4-[[4-[2-(2-amino-4-oxo-3,7-dihydropyrrolo[5,4-d]pyrimidin-5-yl)ethyl]phenyl]carbonylamino]-5-hydroxy-5-oxo-pentanoyl]amino]-5-hydroxy-5-oxo-pentanoyl]amino]-5-hydroxy-5-oxo-pentanoyl]amino]pentanedioic acid"
# #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
LYB "Create component" 2001-08-27 RCSB
LYB "Modify descriptor" 2011-06-04 RCSB
LYB "Modify synonyms" 2020-06-05 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id LYB
_pdbx_chem_comp_synonyms.name "LY231514 TETRA GLU"
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
##