data_2Y2 # _chem_comp.id 2Y2 _chem_comp.name ;N-[(2R)-1-{[(2S,3R,5R)-1-cyclohexyl-3-hydroxy-5-{[2-(morpholin-4-yl)ethyl]carbamoyl}oct-7-yn-2-yl]amino}-3-(methylsulfa nyl)-1-oxopropan-2-yl]-1H-benzimidazole-2-carboxamide ; _chem_comp.type peptide-like _chem_comp.pdbx_type HETAIN _chem_comp.formula "C33 H48 N6 O5 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "CP-108,420" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2010-11-10 _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 640.836 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 2Y2 _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 1FQ4 _chem_comp.pdbx_subcomponent_list "TRM SMC PCE EMR" _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 2Y2 N2 N2 N 0 1 Y N N -21.528 61.984 36.999 6.964 0.439 1.191 NG TRM 1 2Y2 C1 C1 C 0 1 Y N N -20.390 61.607 36.216 6.986 -0.273 0.092 CD1 TRM 2 2Y2 N1 N1 N 0 1 Y N N -20.555 60.316 35.888 8.279 -0.415 -0.340 NE1 TRM 3 2Y2 C7 C7 C 0 1 Y N N -21.739 59.858 36.471 9.081 0.252 0.556 CE2 TRM 4 2Y2 C6 C6 C 0 1 Y N N -22.423 58.640 36.472 10.451 0.463 0.655 CZ2 TRM 5 2Y2 C5 C5 C 0 1 Y N N -23.632 58.562 37.149 10.954 1.199 1.705 CH2 TRM 6 2Y2 C4 C4 C 0 1 Y N N -24.185 59.663 37.794 10.103 1.732 2.666 CZ3 TRM 7 2Y2 C3 C3 C 0 1 Y N N -23.497 60.869 37.777 8.755 1.537 2.588 CE3 TRM 8 2Y2 C2 C2 C 0 1 Y N N -22.318 60.945 37.124 8.217 0.792 1.529 CD2 TRM 9 2Y2 C8 C8 C 0 1 N N N -19.337 62.709 35.972 5.795 -0.832 -0.584 C TRM 10 2Y2 O1 O1 O 0 1 N N N -18.345 62.443 35.291 5.924 -1.481 -1.603 O TRM 11 2Y2 N3 N3 N 0 1 N N N -19.613 63.857 36.567 4.568 -0.623 -0.069 N SMC 12 2Y2 C9 C9 C 0 1 N N R -18.770 65.059 36.514 3.388 -1.177 -0.738 CA SMC 13 2Y2 C10 C10 C 0 1 N N N -19.449 66.166 35.738 3.174 -2.621 -0.280 CB SMC 14 2Y2 S1 S1 S 0 1 N N N -18.398 66.871 34.448 4.632 -3.613 -0.705 SG SMC 15 2Y2 C11 C11 C 0 1 N N N -17.086 67.470 35.551 4.195 -5.264 -0.094 CS SMC 16 2Y2 C12 C12 C 0 1 N N N -18.378 65.512 37.903 2.177 -0.353 -0.385 C SMC 17 2Y2 O2 O2 O 0 1 N N N -18.868 66.529 38.406 2.288 0.603 0.353 O SMC 18 2Y2 N4 N4 N 0 1 N N N -17.522 64.758 38.588 0.970 -0.679 -0.890 N PCE 19 2Y2 C13 C13 C 0 1 N N S -17.112 65.106 39.939 -0.207 0.122 -0.547 CA PCE 20 2Y2 C14 C14 C 0 1 N N N -17.482 64.094 40.989 -0.300 1.323 -1.491 CB PCE 21 2Y2 C15 C15 C 0 1 N N N -18.840 63.446 40.754 0.899 2.246 -1.261 CG PCE 22 2Y2 C16 C16 C 0 1 N N N -20.060 64.198 41.281 0.826 2.834 0.150 CD1 PCE 23 2Y2 C17 C17 C 0 1 N N N -18.927 61.997 41.245 0.873 3.380 -2.287 CD2 PCE 24 2Y2 C18 C18 C 0 1 N N N -21.339 63.570 40.702 2.024 3.757 0.380 CE1 PCE 25 2Y2 C19 C19 C 0 1 N N N -20.170 61.354 40.606 2.072 4.303 -2.057 CE2 PCE 26 2Y2 C20 C20 C 0 1 N N N -21.444 62.089 41.027 1.999 4.891 -0.646 CZ PCE 27 2Y2 C21 C21 C 0 1 N N R -15.698 65.639 40.020 -1.466 -0.735 -0.688 CH PCE 28 2Y2 O3 O3 O 0 1 N N N -14.755 64.610 40.339 -1.643 -1.100 -2.058 OH PCE 29 2Y2 C22 C22 C 0 1 N N N -15.533 66.814 40.920 -2.682 0.061 -0.211 CM PCE 30 2Y2 C23 C23 C 0 1 N N R -15.548 68.228 40.579 -3.921 -0.836 -0.235 CA2 PCE 31 2Y2 C24 C24 C 0 1 N N N -15.079 68.714 39.269 -3.753 -1.965 0.784 CB2 PCE 32 2Y2 C25 C25 C 0 1 N N N -13.585 69.119 39.333 -4.888 -2.896 0.678 CG2 PCE 33 2Y2 C26 C26 C 0 1 N N N -12.457 68.808 39.634 -5.794 -3.638 0.593 CD3 PCE 34 2Y2 C27 C27 C 0 1 N N N -16.166 69.188 41.521 -5.139 -0.021 0.116 C PCE 35 2Y2 O4 O4 O 0 1 N N N -17.294 69.563 41.197 -5.027 1.162 0.361 O PCE 36 2Y2 O5 O5 O 0 1 N N N -15.913 72.790 46.942 -12.566 1.068 0.443 O1 EMR 37 2Y2 C28 C28 C 0 1 N N N -15.590 71.402 47.099 -12.327 0.081 1.450 C2 EMR 38 2Y2 C29 C29 C 0 1 N N N -15.763 70.720 45.766 -11.130 -0.781 1.038 C3 EMR 39 2Y2 N5 N5 N 0 1 N N N -14.877 71.285 44.737 -9.962 0.084 0.818 N4 EMR 40 2Y2 C30 C30 C 0 1 N N N -14.964 72.737 44.600 -10.244 1.085 -0.221 C5 EMR 41 2Y2 C31 C31 C 0 1 N N N -15.121 73.433 45.937 -11.449 1.928 0.203 C6 EMR 42 2Y2 C32 C32 C 0 1 N N N -14.953 70.536 43.469 -8.775 -0.711 0.476 "C1'" EMR 43 2Y2 C33 C33 C 0 1 N N N -15.755 69.241 43.781 -7.536 0.187 0.500 "C2'" EMR 44 2Y2 N6 N6 N 0 1 N N N -15.407 68.248 42.800 -6.353 -0.606 0.158 "N2'" EMR 45 2Y2 HN1 HN1 H 0 1 N N N -19.935 59.773 35.322 8.573 -0.897 -1.130 HE11 TRM 46 2Y2 H6 H6 H 0 1 N N N -22.021 57.780 35.958 11.118 0.053 -0.088 HZ21 TRM 47 2Y2 H5 H5 H 0 1 N N N -24.158 57.619 37.176 12.019 1.363 1.783 HH21 TRM 48 2Y2 H4 H4 H 0 1 N N N -25.135 59.581 38.301 10.513 2.307 3.483 HZ31 TRM 49 2Y2 H3 H3 H 0 1 N N N -23.900 61.736 38.280 8.103 1.957 3.340 HE31 TRM 50 2Y2 HN3 HN3 H 0 1 N N N -20.461 63.911 37.094 4.465 -0.105 0.745 H SMC 51 2Y2 H9 H9 H 0 1 N N N -17.844 64.801 35.979 3.540 -1.157 -1.817 HA SMC 52 2Y2 H10 H10 H 0 1 N N N -19.717 66.968 36.442 2.296 -3.034 -0.778 HB2 SMC 53 2Y2 H10A H10A H 0 0 N N N -20.350 65.752 35.262 3.022 -2.642 0.799 HB3 SMC 54 2Y2 H11 H11 H 0 1 N N N -16.301 67.959 34.956 5.012 -5.956 -0.298 HCS1 SMC 55 2Y2 H11A H11A H 0 0 N N N -17.509 68.193 36.264 4.018 -5.218 0.981 HCS2 SMC 56 2Y2 H11B H11B H 0 0 N N N -16.654 66.621 36.101 3.292 -5.610 -0.596 HCS3 SMC 57 2Y2 HN4 HN4 H 0 1 N N N -17.152 63.932 38.163 0.882 -1.443 -1.480 H PCE 58 2Y2 H13 H13 H 0 1 N N N -17.738 65.968 40.213 -0.121 0.474 0.481 HA PCE 59 2Y2 H14 H14 H 0 1 N N N -16.719 63.302 40.986 -0.297 0.975 -2.523 HB2 PCE 60 2Y2 H14A H14A H 0 0 N N N -17.510 64.605 41.963 -1.222 1.869 -1.294 HB3 PCE 61 2Y2 H15 H15 H 0 1 N N N -18.888 63.483 39.656 1.822 1.677 -1.370 HG PCE 62 2Y2 H16 H16 H 0 1 N N N -20.084 64.133 42.379 -0.097 3.403 0.260 HD12 PCE 63 2Y2 H16A H16A H 0 0 N N N -20.000 65.253 40.977 0.844 2.026 0.882 HD13 PCE 64 2Y2 H17 H17 H 0 1 N N N -18.023 61.445 40.948 0.925 2.962 -3.292 HD23 PCE 65 2Y2 H17A H17A H 0 0 N N N -19.014 61.976 42.341 -0.050 3.949 -2.178 HD22 PCE 66 2Y2 H18 H18 H 0 1 N N N -22.210 64.087 41.132 1.973 4.175 1.385 HE12 PCE 67 2Y2 H18A H18A H 0 0 N N N -21.325 63.690 39.609 2.948 3.188 0.271 HE13 PCE 68 2Y2 H19 H19 H 0 1 N N N -20.075 61.402 39.511 2.995 3.734 -2.167 HE23 PCE 69 2Y2 H19A H19A H 0 0 N N N -20.238 60.305 40.932 2.053 5.111 -2.789 HE22 PCE 70 2Y2 H20 H20 H 0 1 N N N -21.588 61.968 42.111 1.076 5.460 -0.537 HZ2 PCE 71 2Y2 H20A H20A H 0 0 N N N -22.301 61.662 40.486 2.853 5.548 -0.482 HZ3 PCE 72 2Y2 H21 H21 H 0 1 N N N -15.482 66.008 39.007 -1.362 -1.636 -0.083 HH PCE 73 2Y2 HO3 HO3 H 0 1 N N N -13.882 64.982 40.381 -1.743 -0.347 -2.656 HO PCE 74 2Y2 H22 H22 H 0 1 N N N -16.366 66.712 41.631 -2.509 0.415 0.805 HM1 PCE 75 2Y2 H22A H22A H 0 0 N N N -14.534 66.665 41.357 -2.839 0.914 -0.871 HM2 PCE 76 2Y2 H23 H23 H 0 1 N N N -14.472 68.152 40.796 -4.043 -1.261 -1.231 HA2 PCE 77 2Y2 H24 H24 H 0 1 N N N -15.201 67.913 38.525 -2.824 -2.500 0.583 HB21 PCE 78 2Y2 H24A H24A H 0 0 N N N -15.676 69.591 38.978 -3.720 -1.546 1.789 HB22 PCE 79 2Y2 H26 H26 H 0 1 N N N -11.467 68.535 39.898 -6.604 -4.302 0.517 HD31 PCE 80 2Y2 H28 H28 H 0 1 N N N -14.549 71.297 47.440 -12.112 0.573 2.398 H21 EMR 81 2Y2 H28A H28A H 0 0 N N N -16.260 70.945 47.842 -13.210 -0.549 1.559 H22 EMR 82 2Y2 H29 H29 H 0 1 N N N -16.806 70.847 45.440 -11.366 -1.315 0.118 H31 EMR 83 2Y2 H29A H29A H 0 0 N N N -15.527 69.652 45.885 -10.909 -1.497 1.829 H32 EMR 84 2Y2 H30 H30 H 0 1 N N N -14.041 73.099 44.124 -9.375 1.731 -0.350 H51 EMR 85 2Y2 H30A H30A H 0 0 N N N -15.837 72.978 43.976 -10.465 0.581 -1.162 H52 EMR 86 2Y2 H31 H31 H 0 1 N N N -14.110 73.546 46.355 -11.697 2.634 -0.590 H61 EMR 87 2Y2 H31A H31A H 0 0 N N N -15.595 74.404 45.734 -11.209 2.475 1.115 H62 EMR 88 2Y2 H32 H32 H 0 1 N N N -15.463 71.131 42.698 -8.655 -1.515 1.202 "H1'1" EMR 89 2Y2 H32A H32A H 0 0 N N N -13.945 70.289 43.104 -8.897 -1.135 -0.520 "H1'2" EMR 90 2Y2 H33 H33 H 0 1 N N N -16.834 69.449 43.736 -7.414 0.612 1.496 "H2'1" EMR 91 2Y2 H33A H33A H 0 0 N N N -15.501 68.877 44.788 -7.657 0.991 -0.226 "H2'2" EMR 92 2Y2 HN6 HN6 H 0 1 N N N -14.925 67.372 42.832 -6.442 -1.551 -0.038 HN21 EMR 93 # # 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 2Y2 C1 N2 DOUB Y N 1 2Y2 N1 C1 SING Y N 2 2Y2 N1 C7 SING Y N 3 2Y2 N1 HN1 SING N N 4 2Y2 O1 C8 DOUB N N 5 2Y2 S1 C11 SING N N 6 2Y2 S1 C10 SING N N 7 2Y2 C2 C3 SING Y N 8 2Y2 N2 C2 SING Y N 9 2Y2 C3 C4 DOUB Y N 10 2Y2 C3 H3 SING N N 11 2Y2 N3 HN3 SING N N 12 2Y2 O3 HO3 SING N N 13 2Y2 C4 H4 SING N N 14 2Y2 N4 C13 SING N N 15 2Y2 N4 HN4 SING N N 16 2Y2 O4 C27 DOUB N N 17 2Y2 C5 C4 SING Y N 18 2Y2 C5 H5 SING N N 19 2Y2 C6 C5 DOUB Y N 20 2Y2 C6 H6 SING N N 21 2Y2 C7 C2 DOUB Y N 22 2Y2 C7 C6 SING Y N 23 2Y2 C8 C1 SING N N 24 2Y2 C8 N3 SING N N 25 2Y2 C9 N3 SING N N 26 2Y2 C9 C12 SING N N 27 2Y2 C9 H9 SING N N 28 2Y2 C10 C9 SING N N 29 2Y2 C10 H10 SING N N 30 2Y2 C10 H10A SING N N 31 2Y2 C11 H11 SING N N 32 2Y2 C11 H11A SING N N 33 2Y2 C11 H11B SING N N 34 2Y2 C12 O2 DOUB N N 35 2Y2 C12 N4 SING N N 36 2Y2 C13 C21 SING N N 37 2Y2 C13 C14 SING N N 38 2Y2 C13 H13 SING N N 39 2Y2 C14 H14 SING N N 40 2Y2 C14 H14A SING N N 41 2Y2 C15 C14 SING N N 42 2Y2 C15 C17 SING N N 43 2Y2 C15 C16 SING N N 44 2Y2 C15 H15 SING N N 45 2Y2 C16 H16 SING N N 46 2Y2 C16 H16A SING N N 47 2Y2 C17 H17 SING N N 48 2Y2 C17 H17A SING N N 49 2Y2 C18 C16 SING N N 50 2Y2 C18 C20 SING N N 51 2Y2 C18 H18 SING N N 52 2Y2 C18 H18A SING N N 53 2Y2 C19 C17 SING N N 54 2Y2 C19 C20 SING N N 55 2Y2 C19 H19 SING N N 56 2Y2 C19 H19A SING N N 57 2Y2 C20 H20 SING N N 58 2Y2 C20 H20A SING N N 59 2Y2 C21 O3 SING N N 60 2Y2 C21 C22 SING N N 61 2Y2 C21 H21 SING N N 62 2Y2 C22 H22 SING N N 63 2Y2 C22 H22A SING N N 64 2Y2 C23 C22 SING N N 65 2Y2 C23 C27 SING N N 66 2Y2 C23 H23 SING N N 67 2Y2 C24 C23 SING N N 68 2Y2 C24 C25 SING N N 69 2Y2 C24 H24 SING N N 70 2Y2 C24 H24A SING N N 71 2Y2 C25 C26 TRIP N N 72 2Y2 C26 H26 SING N N 73 2Y2 C27 N6 SING N N 74 2Y2 N5 C29 SING N N 75 2Y2 O5 C28 SING N N 76 2Y2 N6 C33 SING N N 77 2Y2 N6 HN6 SING N N 78 2Y2 C28 H28 SING N N 79 2Y2 C28 H28A SING N N 80 2Y2 C29 C28 SING N N 81 2Y2 C29 H29 SING N N 82 2Y2 C29 H29A SING N N 83 2Y2 C30 N5 SING N N 84 2Y2 C30 C31 SING N N 85 2Y2 C30 H30 SING N N 86 2Y2 C30 H30A SING N N 87 2Y2 C31 O5 SING N N 88 2Y2 C31 H31 SING N N 89 2Y2 C31 H31A SING N N 90 2Y2 C32 N5 SING N N 91 2Y2 C32 C33 SING N N 92 2Y2 C32 H32 SING N N 93 2Y2 C32 H32A SING N N 94 2Y2 C33 H33 SING N N 95 2Y2 C33 H33A SING N N 96 # # 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 2Y2 SMILES ACDLabs 12.01 "O=C(c2nc1ccccc1n2)NC(C(=O)NC(CC3CCCCC3)C(O)CC(C(=O)NCCN4CCOCC4)CC#C)CSC" 2Y2 SMILES_CANONICAL CACTVS 3.370 "CSC[C@H](NC(=O)c1[nH]c2ccccc2n1)C(=O)N[C@@H](CC3CCCCC3)[C@H](O)C[C@@H](CC#C)C(=O)NCCN4CCOCC4" 2Y2 SMILES CACTVS 3.370 "CSC[CH](NC(=O)c1[nH]c2ccccc2n1)C(=O)N[CH](CC3CCCCC3)[CH](O)C[CH](CC#C)C(=O)NCCN4CCOCC4" 2Y2 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "CSC[C@@H](C(=O)N[C@@H](CC1CCCCC1)[C@@H](C[C@@H](CC#C)C(=O)NCCN2CCOCC2)O)NC(=O)c3[nH]c4ccccc4n3" 2Y2 SMILES "OpenEye OEToolkits" 1.7.0 "CSCC(C(=O)NC(CC1CCCCC1)C(CC(CC#C)C(=O)NCCN2CCOCC2)O)NC(=O)c3[nH]c4ccccc4n3" 2Y2 InChI InChI 1.03 "InChI=1S/C33H48N6O5S/c1-3-9-24(31(41)34-14-15-39-16-18-44-19-17-39)21-29(40)27(20-23-10-5-4-6-11-23)37-32(42)28(22-45-2)38-33(43)30-35-25-12-7-8-13-26(25)36-30/h1,7-8,12-13,23-24,27-29,40H,4-6,9-11,14-22H2,2H3,(H,34,41)(H,35,36)(H,37,42)(H,38,43)/t24-,27+,28+,29-/m1/s1" 2Y2 InChIKey InChI 1.03 MDCNERSXJOKFTF-ZLPBPMGLSA-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 2Y2 "SYSTEMATIC NAME" ACDLabs 12.01 "N-[(2R)-1-{[(2S,3R,5R)-1-cyclohexyl-3-hydroxy-5-{[2-(morpholin-4-yl)ethyl]carbamoyl}oct-7-yn-2-yl]amino}-3-(methylsulfanyl)-1-oxopropan-2-yl]-1H-benzimidazole-2-carboxamide" 2Y2 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.0 "N-[(2R)-1-[[(2S,3R,5R)-1-cyclohexyl-3-hydroxy-5-(2-morpholin-4-ylethylcarbamoyl)oct-7-yn-2-yl]amino]-3-methylsulfanyl-1-oxo-propan-2-yl]-1H-benzimidazole-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 2Y2 "Create component" 2010-11-10 RCSB 2Y2 "Modify descriptor" 2011-06-04 RCSB 2Y2 "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id 2Y2 _pdbx_chem_comp_synonyms.name "CP-108,420" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##