data_Y3A # _chem_comp.id Y3A _chem_comp.name "N-[(benzyloxy)carbonyl]glycyl-N-[(2S,3R)-4-chloro-3-hydroxy-1-phenylbutan-2-yl]glycinamide" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C22 H26 Cl N3 O5" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "Z-Gly-Gly-Phe-Chloromethyl ketone (bound form)" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2013-01-28 _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 447.912 _chem_comp.one_letter_code ? _chem_comp.three_letter_code Y3A _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag Y _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 4HXF _chem_comp.pdbx_subcomponent_list "PHQ GLY GLY HPH 0QE" _chem_comp.pdbx_processing_site RCSB _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 Y3A C23 C23 C 0 1 N N N N N N -20.314 -32.847 -22.987 4.783 -0.497 0.831 C1 PHQ 1 Y3A O41 O41 O 0 1 N N N N N N -20.482 -33.520 -23.991 4.742 -1.018 1.928 O1 PHQ 2 Y3A O5 O5 O 0 1 N N N N N N -19.158 -32.022 -23.154 5.971 -0.208 0.268 O2 PHQ 3 Y3A C16 C16 C 0 1 N N N N N N -18.888 -30.792 -23.830 7.161 -0.547 1.027 C2 PHQ 4 Y3A C20 C20 C 0 1 Y N N N N N ? ? ? 8.387 -0.153 0.244 C3 PHQ 5 Y3A C19 C19 C 0 1 Y N N N N N ? ? ? 8.965 -1.052 -0.633 C4 PHQ 6 Y3A C18 C18 C 0 1 Y N N N N N ? ? ? 10.086 -0.689 -1.355 C5 PHQ 7 Y3A C17 C17 C 0 1 Y N N N N N ? ? ? 10.629 0.573 -1.201 C6 PHQ 8 Y3A C22 C22 C 0 1 Y N N N N N ? ? ? 10.051 1.472 -0.325 C7 PHQ 9 Y3A C21 C21 C 0 1 Y N N N N N ? ? ? 8.930 1.109 0.398 C8 PHQ 10 Y3A N31 N31 N 0 1 N N N N N N -20.120 -33.734 -21.830 3.640 -0.213 0.176 N GLY 11 Y3A C14 C14 C 0 1 N N N N N N -20.790 -35.041 -21.785 2.347 -0.533 0.787 CA GLY 12 Y3A C13 C13 C 0 1 N N N N N N -20.601 -35.962 -20.565 1.236 -0.118 -0.143 C GLY 13 Y3A O31 O31 O 0 1 N N N N N N -21.010 -37.066 -20.246 1.498 0.395 -1.210 O GLY 14 Y3A N3 N3 N 0 1 N N N N N N -19.732 -35.543 -19.456 -0.049 -0.316 0.212 N GLY 15 Y3A CA3 CA3 C 0 1 N N N N N N -19.923 -36.748 -18.626 -1.129 0.087 -0.692 CA GLY 16 Y3A C3 C3 C 0 1 N N N N N N -19.092 -36.499 -17.363 -2.459 -0.242 -0.063 C GLY 17 Y3A O3 O3 O 0 1 N N N N N N -18.706 -35.434 -16.926 -2.500 -0.762 1.031 O GLY 18 Y3A C4 C4 C 0 1 N N R N N N -16.168 -37.644 -16.057 -5.255 -1.734 -0.410 C HPH 19 Y3A O4 O4 O 0 1 N N N N N N -15.970 -38.751 -16.859 -4.249 -2.595 0.126 O HPH 20 Y3A CA4 CA4 C 0 1 N N S N N N -17.612 -37.659 -15.588 -4.895 -0.278 -0.108 CA HPH 21 Y3A N4 N4 N 0 1 N N N N N N -18.435 -37.795 -16.819 -3.602 0.042 -0.718 N HPH 22 Y3A CB4 CB4 C 0 1 N N N N N N -18.060 -38.932 -14.811 -5.972 0.644 -0.682 CB HPH 23 Y3A CG4 CG4 C 0 1 Y N N N N N -19.492 -38.907 -14.389 -5.682 2.067 -0.279 CG HPH 24 Y3A CD1 CD1 C 0 1 Y N N N N N -20.048 -37.988 -13.486 -4.895 2.867 -1.086 CD1 HPH 25 Y3A CD2 CD2 C 0 1 Y N N N N N -20.343 -39.900 -14.854 -6.208 2.574 0.894 CD2 HPH 26 Y3A CE1 CE1 C 0 1 Y N N N N N -21.375 -38.012 -13.098 -4.629 4.172 -0.717 CE1 HPH 27 Y3A CE2 CE2 C 0 1 Y N N N N N -21.679 -39.936 -14.482 -5.942 3.880 1.263 CE2 HPH 28 Y3A CZ4 CZ4 C 0 1 Y N N N N N -22.189 -38.994 -13.644 -5.150 4.678 0.459 CZ HPH 29 Y3A C15 C15 C 0 1 N N N N N N -15.584 -36.229 -16.425 -6.605 -2.068 0.228 C1 0QE 30 Y3A CL1 CL1 CL 0 0 N Y N N N N -15.290 -35.415 -14.810 -7.100 -3.734 -0.250 CL1 0QE 31 Y3A H21 H21 H 0 1 N N N N N N -18.228 -31.013 -24.682 7.150 -0.013 1.977 H21 PHQ 32 Y3A H22 H22 H 0 1 N N N N N N -19.844 -30.393 -24.201 7.179 -1.621 1.214 H22 PHQ 33 Y3A H25 H25 H 0 1 N N N N N N ? ? ? 8.541 -2.038 -0.753 H41 PHQ 34 Y3A H24 H24 H 0 1 N N N N N N ? ? ? 10.538 -1.391 -2.040 H51 PHQ 35 Y3A H23 H23 H 0 1 N N N N N N ? ? ? 11.506 0.857 -1.765 H61 PHQ 36 Y3A H27 H27 H 0 1 N N N N N N ? ? ? 10.475 2.458 -0.204 H71 PHQ 37 Y3A H26 H26 H 0 1 N N N N N N ? ? ? 8.475 1.813 1.079 H81 PHQ 38 Y3A H20 H20 H 0 1 N N N N N N -19.532 -33.448 -21.074 3.673 0.203 -0.699 H GLY 39 Y3A H18 H18 H 0 1 N N N N N N -20.446 -35.605 -22.665 2.287 -1.606 0.969 HA2 GLY 40 Y3A H19 H19 H 0 1 N N N N N N -21.869 -34.848 -21.873 2.250 0.002 1.732 HA3 GLY 41 Y3A HN3 HN3 H 0 1 N N N N N N -19.190 -34.715 -19.312 -0.258 -0.726 1.066 H GLY 42 Y3A HA3 HA3 H 0 1 N N N N N N -20.985 -36.876 -18.370 -1.069 1.160 -0.874 HA2 GLY 43 Y3A HA3A HA3A H 0 0 N N N N N N -19.563 -37.642 -19.155 -1.031 -0.448 -1.636 HA3 GLY 44 Y3A HO4 HO4 H 0 1 N N N N N N -15.071 -38.764 -17.166 -3.365 -2.439 -0.234 HO HPH 45 Y3A HA4 HA4 H 0 1 N N N N N N -17.862 -36.748 -15.025 -4.832 -0.136 0.971 HA HPH 46 Y3A HN4 HN4 H 0 1 N N N N N N -18.559 -38.677 -17.273 -3.569 0.458 -1.594 H HPH 47 Y3A HB4 HB4 H 0 1 N N N N N N -17.905 -39.807 -15.459 -5.974 0.567 -1.769 HB2 HPH 48 Y3A HB4A HB4A H 0 0 N N N N N N -17.435 -39.027 -13.911 -6.947 0.349 -0.295 HB3 HPH 49 Y3A HD1 HD1 H 0 1 N N N N N N -19.407 -37.223 -13.073 -4.487 2.472 -2.005 HD1 HPH 50 Y3A HD2 HD2 H 0 1 N N N N N N -19.958 -40.659 -15.518 -6.827 1.951 1.522 HD2 HPH 51 Y3A HE1 HE1 H 0 1 N N N N N N -21.764 -37.291 -12.394 -4.013 4.797 -1.347 HE1 HPH 52 Y3A HE2 HE2 H 0 1 N N N N N N -22.319 -40.719 -14.861 -6.354 4.276 2.180 HE2 HPH 53 Y3A HZ4 HZ4 H 0 1 N N N N N N -23.241 -39.011 -13.400 -4.942 5.698 0.748 HZ HPH 54 Y3A H4 H4 H 0 1 N N N N N N -15.617 -37.887 -15.136 -5.318 -1.876 -1.489 HC HPH 55 Y3A H15 H15 H 0 1 N N N N N N -14.643 -36.331 -16.985 -6.518 -2.011 1.313 H 0QE 56 Y3A H15A H15A H 0 0 N N N N N N -16.306 -35.655 -17.023 -7.355 -1.354 -0.114 HA 0QE 57 # 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 Y3A N3 CA3 SING N N 1 Y3A CA3 C3 SING N N 2 Y3A C3 O3 DOUB N N 3 Y3A C3 N4 SING N N 4 Y3A C4 O4 SING N N 5 Y3A C4 CA4 SING N N 6 Y3A C4 C15 SING N N 7 Y3A CA4 N4 SING N N 8 Y3A CA4 CB4 SING N N 9 Y3A CB4 CG4 SING N N 10 Y3A CG4 CD1 DOUB Y N 11 Y3A CG4 CD2 SING Y N 12 Y3A CD1 CE1 SING Y N 13 Y3A CD2 CE2 DOUB Y N 14 Y3A CE1 CZ4 DOUB Y N 15 Y3A CE2 CZ4 SING Y N 16 Y3A N3 C13 SING N N 17 Y3A C13 C14 SING N N 18 Y3A C13 O31 DOUB N N 19 Y3A C14 N31 SING N N 20 Y3A N31 C23 SING N N 21 Y3A C23 O41 DOUB N N 22 Y3A C23 O5 SING N N 23 Y3A O5 C16 SING N N 24 Y3A C17 C18 SING Y N 25 Y3A C18 C19 DOUB Y N 26 Y3A C19 C20 SING Y N 27 Y3A C20 C21 DOUB Y N 28 Y3A C21 C22 SING Y N 29 Y3A C17 C22 DOUB Y N 30 Y3A C20 C16 SING N N 31 Y3A N3 HN3 SING N N 32 Y3A CA3 HA3 SING N N 33 Y3A CA3 HA3A SING N N 34 Y3A C4 H4 SING N N 35 Y3A O4 HO4 SING N N 36 Y3A CA4 HA4 SING N N 37 Y3A N4 HN4 SING N N 38 Y3A CB4 HB4 SING N N 39 Y3A CB4 HB4A SING N N 40 Y3A CD1 HD1 SING N N 41 Y3A CD2 HD2 SING N N 42 Y3A CE1 HE1 SING N N 43 Y3A CE2 HE2 SING N N 44 Y3A CZ4 HZ4 SING N N 45 Y3A C15 H15 SING N N 46 Y3A C15 H15A SING N N 47 Y3A C15 CL1 SING N N 48 Y3A C14 H18 SING N N 49 Y3A C14 H19 SING N N 50 Y3A N31 H20 SING N N 51 Y3A C16 H21 SING N N 52 Y3A C16 H22 SING N N 53 Y3A C17 H23 SING N N 54 Y3A C18 H24 SING N N 55 Y3A C19 H25 SING N N 56 Y3A C21 H26 SING N N 57 Y3A C22 H27 SING N N 58 # 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 Y3A SMILES ACDLabs 12.01 "ClCC(O)C(NC(=O)CNC(=O)CNC(=O)OCc1ccccc1)Cc2ccccc2" Y3A InChI InChI 1.03 "InChI=1S/C22H26ClN3O5/c23-12-19(27)18(11-16-7-3-1-4-8-16)26-21(29)14-24-20(28)13-25-22(30)31-15-17-9-5-2-6-10-17/h1-10,18-19,27H,11-15H2,(H,24,28)(H,25,30)(H,26,29)/t18-,19-/m0/s1" Y3A InChIKey InChI 1.03 WLEADEPGUSFGIL-OALUTQOASA-N Y3A SMILES_CANONICAL CACTVS 3.385 "O[C@@H](CCl)[C@H](Cc1ccccc1)NC(=O)CNC(=O)CNC(=O)OCc2ccccc2" Y3A SMILES CACTVS 3.385 "O[CH](CCl)[CH](Cc1ccccc1)NC(=O)CNC(=O)CNC(=O)OCc2ccccc2" Y3A SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "c1ccc(cc1)C[C@@H]([C@H](CCl)O)NC(=O)CNC(=O)CNC(=O)OCc2ccccc2" Y3A SMILES "OpenEye OEToolkits" 1.7.6 "c1ccc(cc1)CC(C(CCl)O)NC(=O)CNC(=O)CNC(=O)OCc2ccccc2" # 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 Y3A "SYSTEMATIC NAME" ACDLabs 12.01 "N-[(benzyloxy)carbonyl]glycyl-N-[(2S,3R)-4-chloro-3-hydroxy-1-phenylbutan-2-yl]glycinamide" Y3A "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "(phenylmethyl) N-[2-[[2-[[(2S,3R)-4-chloranyl-3-oxidanyl-1-phenyl-butan-2-yl]amino]-2-oxidanylidene-ethyl]amino]-2-oxidanylidene-ethyl]carbamate" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site Y3A "Create component" 2013-01-28 RCSB Y3A "Initial release" 2013-05-08 RCSB Y3A "Other modification" 2014-09-28 RCSB Y3A "Modify synonyms" 2021-03-01 PDBE Y3A "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id Y3A _pdbx_chem_comp_synonyms.name "Z-Gly-Gly-Phe-Chloromethyl ketone (bound form)" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? # loop_ _pdbx_chem_comp_pcm.pcm_id _pdbx_chem_comp_pcm.comp_id _pdbx_chem_comp_pcm.modified_residue_id _pdbx_chem_comp_pcm.type _pdbx_chem_comp_pcm.category _pdbx_chem_comp_pcm.position _pdbx_chem_comp_pcm.polypeptide_position _pdbx_chem_comp_pcm.comp_id_linking_atom _pdbx_chem_comp_pcm.modified_residue_id_linking_atom _pdbx_chem_comp_pcm.uniprot_specific_ptm_accession _pdbx_chem_comp_pcm.uniprot_generic_ptm_accession 1 Y3A HIS None "Covalent chemical modification" "Amino-acid side chain" "Any position" C15 NE2 ? ? 2 Y3A SER None "Covalent chemical modification" "Amino-acid side chain" "Any position" C4 OG ? ? #