data_Y54 # _chem_comp.id Y54 _chem_comp.name "5-[(azetidin-3-yl)amino]-N-[(1R)-1-{3-[5-({[(1R,3S)-3-hydroxycyclopentyl]amino}methyl)thiophen-2-yl]phenyl}ethyl]-2-methylbenzamide" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C29 H36 N4 O2 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2021-02-04 _chem_comp.pdbx_modified_date 2021-02-19 _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 504.687 _chem_comp.one_letter_code ? _chem_comp.three_letter_code Y54 _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 7LLF _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 Y54 C01 C1 C 0 1 N N N 2.018 11.862 32.392 1.312 1.389 2.770 C01 Y54 1 Y54 C02 C2 C 0 1 N N R 1.679 11.740 33.822 1.365 0.953 1.304 C02 Y54 2 Y54 N03 N1 N 0 1 N N N 1.940 10.423 34.125 2.762 0.801 0.890 N03 Y54 3 Y54 C04 C3 C 0 1 N N N 1.638 9.751 35.189 3.458 1.872 0.462 C04 Y54 4 Y54 C05 C4 C 0 1 Y N N 1.867 8.408 35.522 4.868 1.719 0.044 C05 Y54 5 Y54 C06 C5 C 0 1 Y N N 0.873 7.555 35.430 5.553 2.798 -0.517 C06 Y54 6 Y54 C07 C6 C 0 1 N N N -0.439 7.923 34.978 4.856 4.121 -0.698 C07 Y54 7 Y54 C08 C7 C 0 1 Y N N 1.049 6.289 35.751 6.870 2.652 -0.906 C08 Y54 8 Y54 C09 C8 C 0 1 Y N N 2.191 5.825 36.157 7.514 1.441 -0.742 C09 Y54 9 Y54 C10 C9 C 0 1 Y N N 3.244 6.609 36.291 6.840 0.360 -0.185 C10 Y54 10 Y54 N11 N2 N 0 1 N N N 4.403 6.043 36.742 7.495 -0.863 -0.022 N11 Y54 11 Y54 C12 C10 C 0 1 N N N 5.682 6.459 36.919 8.893 -1.007 -0.437 C12 Y54 12 Y54 C13 C11 C 0 1 N N N 6.700 5.412 36.708 9.638 -2.148 0.278 C13 Y54 13 Y54 N14 N3 N 0 1 N N N 7.016 5.938 35.420 10.226 -2.460 -1.043 N14 Y54 14 Y54 C15 C12 C 0 1 N N N 6.375 7.153 35.756 9.075 -1.825 -1.728 C15 Y54 15 Y54 C16 C13 C 0 1 Y N N 3.069 7.950 35.964 5.519 0.497 0.214 C16 Y54 16 Y54 O17 O1 O 0 1 N N N 0.995 10.399 35.982 2.927 2.965 0.419 O17 Y54 17 Y54 C18 C14 C 0 1 Y N N 2.484 12.722 34.591 0.648 -0.363 1.146 C18 Y54 18 Y54 C19 C15 C 0 1 Y N N 3.820 12.669 34.547 1.285 -1.542 1.491 C19 Y54 19 Y54 C20 C16 C 0 1 Y N N 4.571 13.534 35.252 0.634 -2.755 1.348 C20 Y54 20 Y54 C21 C17 C 0 1 Y N N 3.982 14.461 36.013 -0.656 -2.795 0.861 C21 Y54 21 Y54 C22 C18 C 0 1 Y N N 2.651 14.571 36.124 -1.305 -1.610 0.512 C22 Y54 22 Y54 C23 C19 C 0 1 Y N N 2.057 15.561 36.965 -2.688 -1.646 -0.009 C23 Y54 23 Y54 C24 C20 C 0 1 Y N N 2.479 16.460 37.801 -3.424 -2.761 -0.186 C24 Y54 24 Y54 C25 C21 C 0 1 Y N N 1.499 17.248 38.403 -4.691 -2.542 -0.688 C25 Y54 25 Y54 C27 C22 C 0 1 N N N -1.001 17.492 38.370 -6.309 -0.767 -1.465 C27 Y54 26 Y54 C29 C23 C 0 1 N N R -1.670 18.950 36.369 -8.522 -0.003 -0.847 C29 Y54 27 Y54 C30 C24 C 0 1 N N N -0.497 19.567 35.679 -8.498 1.531 -1.010 C30 Y54 28 Y54 C32 C25 C 0 1 N N S -2.406 20.858 34.871 -10.704 0.796 -0.171 C32 Y54 29 Y54 C34 C26 C 0 1 N N N -2.810 20.009 36.062 -9.632 -0.259 0.202 C34 Y54 30 Y54 C26 C27 C 0 1 Y N N 0.286 16.967 38.045 -4.994 -1.262 -0.920 C26 Y54 31 Y54 N28 N4 N 0 1 N N N -1.303 18.787 37.802 -7.226 -0.488 -0.352 N28 Y54 32 Y54 C31 C28 C 0 1 N N N -0.951 20.919 35.115 -9.884 2.041 -0.581 C31 Y54 33 Y54 O33 O2 O 0 1 N N N -2.981 22.130 34.950 -11.531 1.090 0.957 O33 Y54 34 Y54 S35 S1 S 0 1 Y N N 0.404 15.773 37.002 -3.630 -0.239 -0.488 S35 Y54 35 Y54 C36 C29 C 0 1 Y N N 1.963 13.676 35.393 -0.645 -0.389 0.664 C36 Y54 36 Y54 H1 H1 H 0 1 N N N 1.838 12.895 32.059 1.830 2.341 2.884 H1 Y54 37 Y54 H2 H2 H 0 1 N N N 3.078 11.608 32.244 0.272 1.502 3.078 H2 Y54 38 Y54 H3 H3 H 0 1 N N N 1.391 11.173 31.807 1.795 0.635 3.391 H3 Y54 39 Y54 H4 H4 H 0 1 N N N 0.611 11.965 33.960 0.881 1.707 0.683 H4 Y54 40 Y54 H5 H5 H 0 1 N N N 2.434 9.912 33.422 3.185 -0.071 0.924 H5 Y54 41 Y54 H6 H6 H 0 1 N N N -0.498 7.805 33.886 4.896 4.683 0.235 H6 Y54 42 Y54 H7 H7 H 0 1 N N N -1.187 7.275 35.457 5.352 4.689 -1.486 H7 Y54 43 Y54 H8 H8 H 0 1 N N N -0.638 8.971 35.245 3.816 3.949 -0.975 H8 Y54 44 Y54 H9 H9 H 0 1 N N N 0.211 5.612 35.673 7.398 3.488 -1.340 H9 Y54 45 Y54 H10 H10 H 0 1 N N N 2.282 4.774 36.390 8.544 1.333 -1.048 H10 Y54 46 Y54 H11 H11 H 0 1 N N N 4.149 5.725 37.656 7.025 -1.617 0.367 H11 Y54 47 Y54 H12 H12 H 0 1 N N N 5.846 7.004 37.860 9.435 -0.061 -0.438 H12 Y54 48 Y54 H13 H13 H 0 1 N N N 6.290 4.392 36.683 10.366 -1.804 1.013 H13 Y54 49 Y54 H14 H14 H 0 1 N N N 7.535 5.454 37.422 8.981 -2.928 0.664 H14 Y54 50 Y54 H15 H15 H 0 1 N N N 6.587 5.446 34.662 10.240 -3.455 -1.208 H15 Y54 51 Y54 H17 H17 H 0 1 N N N 7.063 7.957 36.057 8.252 -2.511 -1.932 H17 Y54 52 Y54 H18 H18 H 0 1 N N N 5.689 7.529 34.983 9.355 -1.227 -2.595 H18 Y54 53 Y54 H19 H19 H 0 1 N N N 3.898 8.636 36.062 4.995 -0.340 0.651 H19 Y54 54 Y54 H20 H20 H 0 1 N N N 4.303 11.920 33.936 2.295 -1.516 1.872 H20 Y54 55 Y54 H21 H21 H 0 1 N N N 5.649 13.479 35.203 1.137 -3.671 1.618 H21 Y54 56 Y54 H22 H22 H 0 1 N N N 4.605 15.151 36.562 -1.163 -3.743 0.750 H22 Y54 57 Y54 H23 H23 H 0 1 N N N 3.529 16.590 38.018 -3.052 -3.748 0.045 H23 Y54 58 Y54 H24 H24 H 0 1 N N N 1.732 18.030 39.111 -5.386 -3.346 -0.878 H24 Y54 59 Y54 H25 H25 H 0 1 N N N -1.066 17.578 39.465 -6.145 0.145 -2.038 H25 Y54 60 Y54 H26 H26 H 0 1 N N N -1.759 16.779 38.012 -6.744 -1.529 -2.112 H26 Y54 61 Y54 H27 H27 H 0 1 N N N -1.930 17.983 35.915 -8.772 -0.484 -1.792 H27 Y54 62 Y54 H28 H28 H 0 1 N N N -0.157 18.915 34.861 -7.727 1.962 -0.372 H28 Y54 63 Y54 H29 H29 H 0 1 N N N 0.324 19.716 36.395 -8.309 1.792 -2.052 H29 Y54 64 Y54 H30 H30 H 0 1 N N N -2.636 20.344 33.926 -11.311 0.446 -1.006 H30 Y54 65 Y54 H31 H31 H 0 1 N N N -2.956 20.655 36.940 -10.033 -1.268 0.105 H31 Y54 66 Y54 H32 H32 H 0 1 N N N -3.748 19.482 35.835 -9.256 -0.087 1.211 H32 Y54 67 Y54 H33 H33 H 0 1 N N N -0.493 19.354 37.950 -6.818 0.168 0.297 H33 Y54 68 Y54 H35 H35 H 0 1 N N N -0.424 21.123 34.171 -9.786 2.719 0.267 H35 Y54 69 Y54 H36 H36 H 0 1 N N N -0.729 21.717 35.839 -10.370 2.550 -1.413 H36 Y54 70 Y54 H37 H37 H 0 1 N N N -3.915 22.066 34.790 -12.182 1.786 0.796 H37 Y54 71 Y54 H38 H38 H 0 1 N N N 0.886 13.725 35.453 -1.143 0.532 0.399 H38 Y54 72 # # 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 Y54 C01 C02 SING N N 1 Y54 C02 N03 SING N N 2 Y54 C02 C18 SING N N 3 Y54 N03 C04 SING N N 4 Y54 C19 C18 DOUB Y N 5 Y54 C19 C20 SING Y N 6 Y54 C18 C36 SING Y N 7 Y54 C32 O33 SING N N 8 Y54 C32 C31 SING N N 9 Y54 C32 C34 SING N N 10 Y54 C07 C06 SING N N 11 Y54 C31 C30 SING N N 12 Y54 C04 C05 SING N N 13 Y54 C04 O17 DOUB N N 14 Y54 C20 C21 DOUB Y N 15 Y54 C36 C22 DOUB Y N 16 Y54 N14 C15 SING N N 17 Y54 N14 C13 SING N N 18 Y54 C06 C05 DOUB Y N 19 Y54 C06 C08 SING Y N 20 Y54 C05 C16 SING Y N 21 Y54 C30 C29 SING N N 22 Y54 C08 C09 DOUB Y N 23 Y54 C15 C12 SING N N 24 Y54 C16 C10 DOUB Y N 25 Y54 C21 C22 SING Y N 26 Y54 C34 C29 SING N N 27 Y54 C22 C23 SING N N 28 Y54 C09 C10 SING Y N 29 Y54 C10 N11 SING N N 30 Y54 C29 N28 SING N N 31 Y54 C13 C12 SING N N 32 Y54 N11 C12 SING N N 33 Y54 C23 S35 SING Y N 34 Y54 C23 C24 DOUB Y N 35 Y54 S35 C26 SING Y N 36 Y54 C24 C25 SING Y N 37 Y54 N28 C27 SING N N 38 Y54 C26 C27 SING N N 39 Y54 C26 C25 DOUB Y N 40 Y54 C01 H1 SING N N 41 Y54 C01 H2 SING N N 42 Y54 C01 H3 SING N N 43 Y54 C02 H4 SING N N 44 Y54 N03 H5 SING N N 45 Y54 C07 H6 SING N N 46 Y54 C07 H7 SING N N 47 Y54 C07 H8 SING N N 48 Y54 C08 H9 SING N N 49 Y54 C09 H10 SING N N 50 Y54 N11 H11 SING N N 51 Y54 C12 H12 SING N N 52 Y54 C13 H13 SING N N 53 Y54 C13 H14 SING N N 54 Y54 N14 H15 SING N N 55 Y54 C15 H17 SING N N 56 Y54 C15 H18 SING N N 57 Y54 C16 H19 SING N N 58 Y54 C19 H20 SING N N 59 Y54 C20 H21 SING N N 60 Y54 C21 H22 SING N N 61 Y54 C24 H23 SING N N 62 Y54 C25 H24 SING N N 63 Y54 C27 H25 SING N N 64 Y54 C27 H26 SING N N 65 Y54 C29 H27 SING N N 66 Y54 C30 H28 SING N N 67 Y54 C30 H29 SING N N 68 Y54 C32 H30 SING N N 69 Y54 C34 H31 SING N N 70 Y54 C34 H32 SING N N 71 Y54 N28 H33 SING N N 72 Y54 C31 H35 SING N N 73 Y54 C31 H36 SING N N 74 Y54 O33 H37 SING N N 75 Y54 C36 H38 SING N N 76 # # 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 Y54 SMILES ACDLabs 12.01 "CC(NC(c1cc(ccc1C)NC2CNC2)=O)c3cc(ccc3)c4sc(cc4)CNC5CCC(O)C5" Y54 InChI InChI 1.03 "InChI=1S/C29H36N4O2S/c1-18-6-7-23(33-24-15-30-16-24)14-27(18)29(35)32-19(2)20-4-3-5-21(12-20)28-11-10-26(36-28)17-31-22-8-9-25(34)13-22/h3-7,10-12,14,19,22,24-25,30-31,33-34H,8-9,13,15-17H2,1-2H3,(H,32,35)/t19-,22-,25+/m1/s1" Y54 InChIKey InChI 1.03 IGVYCVBUHQMNRZ-QNIAMRLHSA-N Y54 SMILES_CANONICAL CACTVS 3.385 "C[C@@H](NC(=O)c1cc(NC2CNC2)ccc1C)c3cccc(c3)c4sc(CN[C@@H]5CC[C@H](O)C5)cc4" Y54 SMILES CACTVS 3.385 "C[CH](NC(=O)c1cc(NC2CNC2)ccc1C)c3cccc(c3)c4sc(CN[CH]5CC[CH](O)C5)cc4" Y54 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "Cc1ccc(cc1C(=O)N[C@H](C)c2cccc(c2)c3ccc(s3)CN[C@@H]4CC[C@@H](C4)O)NC5CNC5" Y54 SMILES "OpenEye OEToolkits" 2.0.7 "Cc1ccc(cc1C(=O)NC(C)c2cccc(c2)c3ccc(s3)CNC4CCC(C4)O)NC5CNC5" # # 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 Y54 "SYSTEMATIC NAME" ACDLabs 12.01 "5-[(azetidin-3-yl)amino]-N-[(1R)-1-{3-[5-({[(1R,3S)-3-hydroxycyclopentyl]amino}methyl)thiophen-2-yl]phenyl}ethyl]-2-methylbenzamide" Y54 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "5-(azetidin-3-ylamino)-2-methyl-~{N}-[(1~{R})-1-[3-[5-[[[(1~{R},3~{S})-3-oxidanylcyclopentyl]amino]methyl]thiophen-2-yl]phenyl]ethyl]benzamide" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site Y54 "Create component" 2021-02-04 RCSB Y54 "Initial release" 2021-02-24 RCSB ##