data_012 # _chem_comp.id 012 _chem_comp.name "(4S)-N-[(1S,2R)-1-benzyl-3-{[3-(dimethylamino)benzyl]amino}-2-hydroxypropyl]-1-(3-methoxybenzyl)-2-oxoimidazolidine-4-carboxamide" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C31 H39 N5 O4" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "(S)-1-(3-methoxy-benzyl)-2-oxo-imidazolidine-4-carboxylic acid[(1S,2R)-1-benzyl-3-(3-dimethylamino-benzylamino)-2-hydroxy-propyl]-amide" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2008-03-17 _chem_comp.pdbx_modified_date 2021-03-13 _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 545.672 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 012 _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 3CKP _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ # # 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 012 C C C 0 1 N N N 30.098 7.404 10.486 -2.003 -1.433 -0.696 C 012 1 012 O O O 0 1 N N N 31.233 7.878 10.579 -2.337 -1.531 0.466 O 012 2 012 N N N 0 1 N N N 29.760 6.117 10.135 -0.696 -1.370 -1.019 N 012 3 012 CA CA C 0 1 N N S 30.717 5.053 9.801 0.322 -1.420 0.034 CA 012 4 012 CB CB C 0 1 N N N 30.775 4.059 10.990 0.628 -2.879 0.378 CB 012 5 012 CG CG C 0 1 Y N N 31.135 4.758 12.288 -0.596 -3.521 0.977 CG 012 6 012 CD1 CD1 C 0 1 Y N N 30.178 4.886 13.329 -1.517 -4.149 0.159 CD1 012 7 012 CD2 CD2 C 0 1 Y N N 32.421 5.311 12.487 -0.796 -3.488 2.344 CD2 012 8 012 CE1 CE1 C 0 1 Y N N 30.509 5.551 14.536 -2.641 -4.739 0.708 CE1 012 9 012 CE2 CE2 C 0 1 Y N N 32.748 5.977 13.693 -1.919 -4.077 2.893 CE2 012 10 012 CZ CZ C 0 1 Y N N 31.790 6.098 14.719 -2.843 -4.701 2.075 CZ 012 11 012 C1 C1 C 0 1 N N R 30.298 4.365 8.491 1.598 -0.733 -0.457 C1 012 12 012 OG OG O 0 1 N N N 31.234 3.352 8.192 2.147 -1.473 -1.550 OG 012 13 012 C2 C2 C 0 1 N N N 30.244 5.362 7.347 2.616 -0.674 0.682 C2 012 14 012 N2 N2 N 0 1 N N N 30.310 4.708 6.021 3.794 0.090 0.248 N2 012 15 012 C20 C20 C 0 1 N N N 30.752 5.576 4.897 4.796 0.167 1.319 C20 012 16 012 C21 C21 C 0 1 Y N N 32.179 6.031 5.080 5.986 0.956 0.838 C21 012 17 012 C22 C22 C 0 1 Y N N 32.488 7.387 5.374 6.025 2.326 1.019 C22 012 18 012 C23 C23 C 0 1 Y N N 33.831 7.788 5.559 7.115 3.054 0.579 C23 012 19 012 C24 C24 C 0 1 Y N N 34.871 6.838 5.452 8.170 2.414 -0.042 C24 012 20 012 C25 C25 C 0 1 Y N N 34.582 5.465 5.154 8.134 1.038 -0.225 C25 012 21 012 C26 C26 C 0 1 Y N N 33.227 5.089 4.973 7.039 0.309 0.222 C26 012 22 012 N27 N27 N 0 1 N N N 35.607 4.511 5.046 9.198 0.387 -0.854 N27 012 23 012 C28 C28 C 0 1 N N N 36.977 4.831 5.471 10.354 1.157 -1.321 C28 012 24 012 C29 C29 C 0 1 N N N 35.343 3.169 4.506 9.159 -1.065 -1.046 C29 012 25 012 C30 C30 C 0 1 N N S 28.885 8.245 10.802 -3.050 -1.388 -1.779 C30 012 26 012 N31 N31 N 0 1 N N N 27.672 7.694 10.223 -4.332 -1.908 -1.280 N31 012 27 012 C32 C32 C 0 1 N N N 26.735 8.176 11.140 -5.256 -0.942 -1.350 C32 012 28 012 O33 O33 O 0 1 N N N 25.547 8.070 10.906 -6.410 -1.101 -1.000 O33 012 29 012 N34 N34 N 0 1 N N N 27.233 8.789 12.317 -4.795 0.216 -1.840 N34 012 30 012 C35 C35 C 0 1 N N N 28.607 8.331 12.294 -3.368 0.070 -2.163 C35 012 31 012 C36 C36 C 0 1 N N N 26.444 8.553 13.567 -5.587 1.435 -2.025 C36 012 32 012 C41 C41 C 0 1 Y N N 26.570 7.233 14.298 -5.518 2.274 -0.775 C41 012 33 012 C42 C42 C 0 1 Y N N 26.001 6.055 13.761 -4.521 3.219 -0.633 C42 012 34 012 C43 C43 C 0 1 Y N N 26.097 4.819 14.429 -4.458 3.991 0.518 C43 012 35 012 C44 C44 C 0 1 Y N N 26.784 4.761 15.676 -5.396 3.811 1.523 C44 012 36 012 C45 C45 C 0 1 Y N N 27.358 5.931 16.231 -6.391 2.864 1.377 C45 012 37 012 C46 C46 C 0 1 Y N N 27.251 7.162 15.546 -6.455 2.100 0.226 C46 012 38 012 O47 O47 O 0 1 N N N 25.491 3.704 13.825 -3.478 4.922 0.660 O47 012 39 012 C48 C48 C 0 1 N N N 26.393 2.788 13.240 -3.474 5.681 1.872 C48 012 40 012 HN HN H 0 1 N N N 28.787 5.888 10.105 -0.429 -1.291 -1.948 HN 012 41 012 HA HA H 0 1 N N N 31.723 5.467 9.640 -0.048 -0.907 0.922 HA 012 42 012 HB HB H 0 1 N N N 29.788 3.587 11.105 0.913 -3.414 -0.528 HB 012 43 012 HBA HBA H 0 1 N N N 31.552 3.310 10.775 1.447 -2.918 1.096 HBA 012 44 012 HD1 HD1 H 0 1 N N N 29.189 4.473 13.200 -1.359 -4.179 -0.909 HD1 012 45 012 HD2 HD2 H 0 1 N N N 33.164 5.224 11.708 -0.074 -3.001 2.984 HD2 012 46 012 HE1 HE1 H 0 1 N N N 29.772 5.638 15.320 -3.360 -5.229 0.069 HE1 012 47 012 HE2 HE2 H 0 1 N N N 33.735 6.394 13.827 -2.075 -4.051 3.962 HE2 012 48 012 HZ HZ H 0 1 N N N 32.038 6.607 15.639 -3.721 -5.161 2.504 HZ 012 49 012 H1 H1 H 0 1 N N N 29.294 3.934 8.618 1.362 0.279 -0.786 H1 012 50 012 HOG HOG H 0 1 N N N 31.444 3.378 7.266 2.380 -2.385 -1.329 HOG 012 51 012 H2 H2 H 0 1 N N N 29.297 5.918 7.414 2.166 -0.188 1.548 H2 012 52 012 H2A H2A H 0 1 N N N 31.117 6.025 7.438 2.919 -1.686 0.951 H2A 012 53 012 HN2 HN2 H 0 1 N N N 30.961 3.952 6.091 4.191 -0.305 -0.591 HN2 012 54 012 H20 H20 H 0 1 N N N 30.679 5.007 3.959 4.361 0.660 2.189 H20 012 55 012 H20A H20A H 0 0 N N N 30.105 6.465 4.870 5.114 -0.839 1.593 H20A 012 56 012 H22 H22 H 0 1 N N N 31.694 8.114 5.456 5.201 2.829 1.504 H22 012 57 012 H23 H23 H 0 1 N N N 34.062 8.819 5.782 7.142 4.124 0.721 H23 012 58 012 H24 H24 H 0 1 N N N 35.895 7.149 5.596 9.021 2.984 -0.386 H24 012 59 012 H26 H26 H 0 1 N N N 32.990 4.059 4.748 7.010 -0.762 0.085 H26 012 60 012 H28 H28 H 0 1 N N N 37.627 4.911 4.587 11.097 1.215 -0.525 H28 012 61 012 H28A H28A H 0 0 N N N 36.978 5.787 6.014 10.790 0.666 -2.191 H28A 012 62 012 H28B H28B H 0 0 N N N 37.352 4.034 6.130 10.035 2.163 -1.593 H28B 012 63 012 H29 H29 H 0 1 N N N 35.277 3.221 3.409 8.294 -1.327 -1.654 H29 012 64 012 H29A H29A H 0 0 N N N 36.161 2.491 4.792 10.069 -1.389 -1.549 H29A 012 65 012 H29B H29B H 0 0 N N N 34.393 2.791 4.913 9.084 -1.558 -0.076 H29B 012 66 012 H30 H30 H 0 1 N N N 29.126 9.233 10.383 -2.721 -1.953 -2.651 H30 012 67 012 HN31 HN31 H 0 0 N N N 27.545 7.133 9.405 -4.483 -2.809 -0.953 HN31 012 68 012 H35 H35 H 0 1 N N N 28.727 7.358 12.793 -2.769 0.762 -1.571 H35 012 69 012 H35A H35A H 0 0 N N N 29.301 8.991 12.835 -3.198 0.231 -3.228 H35A 012 70 012 H36 H36 H 0 1 N N N 26.760 9.329 14.280 -5.189 2.003 -2.866 H36 012 71 012 H36A H36A H 0 0 N N N 25.399 8.563 13.223 -6.624 1.167 -2.226 H36A 012 72 012 H42 H42 H 0 1 N N N 25.480 6.104 12.816 -3.791 3.357 -1.417 H42 012 73 012 H44 H44 H 0 1 N N N 26.867 3.821 16.200 -5.349 4.411 2.421 H44 012 74 012 H45 H45 H 0 1 N N N 27.877 5.882 17.177 -7.122 2.724 2.159 H45 012 75 012 H46 H46 H 0 1 N N N 27.688 8.053 15.971 -7.236 1.363 0.112 H46 012 76 012 H48 H48 H 0 1 N N N 26.627 3.108 12.214 -4.413 6.227 1.961 H48 012 77 012 H48A H48A H 0 0 N N N 27.318 2.755 13.834 -3.365 5.007 2.722 H48A 012 78 012 H48B H48B H 0 0 N N N 25.936 1.788 13.216 -2.643 6.385 1.857 H48B 012 79 # # 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 012 C O DOUB N N 1 012 C N SING N N 2 012 C C30 SING N N 3 012 N CA SING N N 4 012 CA CB SING N N 5 012 CA C1 SING N N 6 012 CB CG SING N N 7 012 CG CD1 DOUB Y N 8 012 CG CD2 SING Y N 9 012 CD1 CE1 SING Y N 10 012 CD2 CE2 DOUB Y N 11 012 CE1 CZ DOUB Y N 12 012 CE2 CZ SING Y N 13 012 C1 OG SING N N 14 012 C1 C2 SING N N 15 012 C2 N2 SING N N 16 012 N2 C20 SING N N 17 012 C20 C21 SING N N 18 012 C21 C22 DOUB Y N 19 012 C21 C26 SING Y N 20 012 C22 C23 SING Y N 21 012 C23 C24 DOUB Y N 22 012 C24 C25 SING Y N 23 012 C25 C26 DOUB Y N 24 012 C25 N27 SING N N 25 012 N27 C28 SING N N 26 012 N27 C29 SING N N 27 012 C30 N31 SING N N 28 012 C30 C35 SING N N 29 012 N31 C32 SING N N 30 012 C32 O33 DOUB N N 31 012 C32 N34 SING N N 32 012 N34 C35 SING N N 33 012 N34 C36 SING N N 34 012 C36 C41 SING N N 35 012 C41 C42 DOUB Y N 36 012 C41 C46 SING Y N 37 012 C42 C43 SING Y N 38 012 C43 C44 DOUB Y N 39 012 C43 O47 SING N N 40 012 C44 C45 SING Y N 41 012 C45 C46 DOUB Y N 42 012 O47 C48 SING N N 43 012 N HN SING N N 44 012 CA HA SING N N 45 012 CB HB SING N N 46 012 CB HBA SING N N 47 012 CD1 HD1 SING N N 48 012 CD2 HD2 SING N N 49 012 CE1 HE1 SING N N 50 012 CE2 HE2 SING N N 51 012 CZ HZ SING N N 52 012 C1 H1 SING N N 53 012 OG HOG SING N N 54 012 C2 H2 SING N N 55 012 C2 H2A SING N N 56 012 N2 HN2 SING N N 57 012 C20 H20 SING N N 58 012 C20 H20A SING N N 59 012 C22 H22 SING N N 60 012 C23 H23 SING N N 61 012 C24 H24 SING N N 62 012 C26 H26 SING N N 63 012 C28 H28 SING N N 64 012 C28 H28A SING N N 65 012 C28 H28B SING N N 66 012 C29 H29 SING N N 67 012 C29 H29A SING N N 68 012 C29 H29B SING N N 69 012 C30 H30 SING N N 70 012 N31 HN31 SING N N 71 012 C35 H35 SING N N 72 012 C35 H35A SING N N 73 012 C36 H36 SING N N 74 012 C36 H36A SING N N 75 012 C42 H42 SING N N 76 012 C44 H44 SING N N 77 012 C45 H45 SING N N 78 012 C46 H46 SING N N 79 012 C48 H48 SING N N 80 012 C48 H48A SING N N 81 012 C48 H48B SING N N 82 # # 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 012 SMILES ACDLabs 10.04 "O=C3NC(C(=O)NC(Cc1ccccc1)C(O)CNCc2cccc(N(C)C)c2)CN3Cc4cc(OC)ccc4" 012 SMILES_CANONICAL CACTVS 3.341 "COc1cccc(CN2C[C@H](NC2=O)C(=O)N[C@@H](Cc3ccccc3)[C@H](O)CNCc4cccc(c4)N(C)C)c1" 012 SMILES CACTVS 3.341 "COc1cccc(CN2C[CH](NC2=O)C(=O)N[CH](Cc3ccccc3)[CH](O)CNCc4cccc(c4)N(C)C)c1" 012 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CN(C)c1cccc(c1)CNC[C@H]([C@H](Cc2ccccc2)NC(=O)[C@@H]3CN(C(=O)N3)Cc4cccc(c4)OC)O" 012 SMILES "OpenEye OEToolkits" 1.5.0 "CN(C)c1cccc(c1)CNCC(C(Cc2ccccc2)NC(=O)C3CN(C(=O)N3)Cc4cccc(c4)OC)O" 012 InChI InChI 1.03 "InChI=1S/C31H39N5O4/c1-35(2)25-13-7-11-23(15-25)18-32-19-29(37)27(17-22-9-5-4-6-10-22)33-30(38)28-21-36(31(39)34-28)20-24-12-8-14-26(16-24)40-3/h4-16,27-29,32,37H,17-21H2,1-3H3,(H,33,38)(H,34,39)/t27-,28-,29+/m0/s1" 012 InChIKey InChI 1.03 MCBWJRZWLSXSBN-YTCPBCGMSA-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 012 "SYSTEMATIC NAME" ACDLabs 10.04 "(4S)-N-[(1S,2R)-1-benzyl-3-{[3-(dimethylamino)benzyl]amino}-2-hydroxypropyl]-1-(3-methoxybenzyl)-2-oxoimidazolidine-4-carboxamide" 012 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(4S)-N-[(2S,3R)-4-[(3-dimethylaminophenyl)methylamino]-3-hydroxy-1-phenyl-butan-2-yl]-1-[(3-methoxyphenyl)methyl]-2-oxo-imidazolidine-4-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 012 "Create component" 2008-03-17 PDBJ 012 "Modify aromatic_flag" 2011-06-04 RCSB 012 "Modify descriptor" 2011-06-04 RCSB 012 "Modify synonyms" 2021-03-13 RCSB # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id 012 _pdbx_chem_comp_synonyms.name "(S)-1-(3-methoxy-benzyl)-2-oxo-imidazolidine-4-carboxylic acid[(1S,2R)-1-benzyl-3-(3-dimethylamino-benzylamino)-2-hydroxy-propyl]-amide" _pdbx_chem_comp_synonyms.provenance PDB _pdbx_chem_comp_synonyms.type ? ##