data_R7D # _chem_comp.id R7D _chem_comp.name "N~2~-{(2R)-2-hydroxy-2-[4-(trifluoromethyl)phenyl]acetyl}-N-[(pyridin-2-yl)methyl]-L-cysteinamide" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C18 H18 F3 N3 O3 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2020-02-04 _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 413.414 _chem_comp.one_letter_code ? _chem_comp.three_letter_code R7D _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 6VPL _chem_comp.pdbx_subcomponent_list ? _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 R7D SD S1 S 0 1 N N N N N N -2.634 -9.254 -26.800 0.012 -1.154 -2.424 SD R7D 1 R7D CE C1 C 0 1 N N N N N N -2.890 -10.029 -28.454 1.161 -0.244 -1.356 CE R7D 2 R7D CAA C2 C 0 1 N N R N N N -5.468 -6.146 -28.804 -2.003 -2.429 1.018 CAA R7D 3 R7D CAB C3 C 0 1 N N N N N N -4.146 -6.819 -29.176 -0.691 -2.243 0.301 CAB R7D 4 R7D CAM C4 C 0 1 N N N N N N -4.356 -9.904 -33.003 4.520 0.740 1.248 CAM R7D 5 R7D CAN C5 C 0 1 Y N N N N N -5.307 -10.918 -33.007 5.832 0.927 0.530 CAN R7D 6 R7D CAP C6 C 0 1 Y N N N N N -6.615 -12.548 -31.867 7.902 0.092 -0.038 CAP R7D 7 R7D CAQ C7 C 0 1 Y N N N N N -7.201 -12.947 -33.061 8.210 1.234 -0.754 CAQ R7D 8 R7D CAR C8 C 0 1 Y N N N N N -6.827 -12.323 -34.246 7.281 2.261 -0.818 CAR R7D 9 R7D CAS C9 C 0 1 Y N N N N N -5.878 -11.307 -34.216 6.071 2.099 -0.162 CAS R7D 10 R7D CAY C10 C 0 1 Y N N N N N -5.296 -5.316 -27.690 -2.910 -1.264 0.718 CAY R7D 11 R7D CBA C11 C 0 1 Y N N N N N -5.162 -3.941 -27.828 -3.691 -1.272 -0.423 CBA R7D 12 R7D CBB C12 C 0 1 Y N N N N N -4.994 -3.132 -26.706 -4.523 -0.203 -0.698 CBB R7D 13 R7D CBC C13 C 0 1 Y N N N N N -4.955 -3.683 -25.426 -4.575 0.873 0.168 CBC R7D 14 R7D CBD C14 C 0 1 Y N N N N N -5.090 -5.059 -25.294 -3.795 0.881 1.309 CBD R7D 15 R7D CBE C15 C 0 1 Y N N N N N -5.257 -5.866 -26.416 -2.966 -0.190 1.586 CBE R7D 16 R7D CBF C16 C 0 1 N N N N N N -4.785 -2.884 -24.285 -5.482 2.039 -0.133 CBF R7D 17 R7D CX C17 C 0 1 N N N N N N -3.145 -9.623 -30.925 2.348 -0.279 0.821 CX R7D 18 R7D CXA C18 C 0 1 N N R N N N -3.027 -8.963 -29.545 1.393 -1.035 -0.066 CXA R7D 19 R7D FBG F1 F 0 1 N N N N N N -3.516 -2.433 -24.198 -6.736 1.815 0.443 FBG R7D 20 R7D FBH F2 F 0 1 N N N N N N -5.050 -3.605 -23.176 -4.928 3.209 0.397 FBH R7D 21 R7D FBI F3 F 0 1 N N N N N N -5.596 -1.836 -24.333 -5.622 2.175 -1.518 FBI R7D 22 R7D NAL N1 N 0 1 N N N N N N -4.211 -9.299 -31.671 3.592 0.005 0.385 NAL R7D 23 R7D NAO N2 N 0 1 Y N N N N N -5.662 -11.523 -31.864 6.740 -0.027 0.574 NAO R7D 24 R7D NX N3 N 0 1 N N N N N N -4.207 -8.151 -29.232 0.118 -1.216 0.631 NX R7D 25 R7D OAD O1 O 0 1 N N N N N N -3.128 -6.165 -29.407 -0.363 -3.015 -0.575 OAD R7D 26 R7D OAZ O2 O 0 1 N N N N N N -5.931 -5.402 -29.928 -2.620 -3.640 0.576 OAZ R7D 27 R7D OX O3 O 0 1 N N N N N N -2.282 -10.405 -31.307 1.998 0.073 1.928 OX R7D 28 R7D H1 H1 H 0 1 N N N N N N -2.542 -10.294 -26.025 -0.097 -0.355 -3.501 H1 R7D 29 R7D H2 H2 H 0 1 N N N N N N -3.806 -10.637 -28.428 2.110 -0.109 -1.875 H2 R7D 30 R7D H3 H3 H 0 1 N N N N N N -2.029 -10.673 -28.687 0.738 0.730 -1.113 H3 R7D 31 R7D H4 H4 H 0 1 N N N N N N -6.195 -6.937 -28.567 -1.825 -2.484 2.092 H4 R7D 32 R7D H5 H5 H 0 1 N N N N N N -3.387 -10.323 -33.311 4.685 0.177 2.167 H5 R7D 33 R7D H6 H6 H 0 1 N N N N N N -4.663 -9.125 -33.717 4.096 1.715 1.491 H6 R7D 34 R7D H7 H7 H 0 1 N N N N N N -6.895 -13.028 -30.941 8.622 -0.711 0.021 H7 R7D 35 R7D H8 H8 H 0 1 N N N N N N -7.940 -13.734 -33.069 9.163 1.326 -1.253 H8 R7D 36 R7D H9 H9 H 0 1 N N N N N N -7.270 -12.625 -35.183 7.496 3.167 -1.366 H9 R7D 37 R7D H10 H10 H 0 1 N N N N N N -5.583 -10.818 -35.133 5.324 2.879 -0.191 H10 R7D 38 R7D H11 H11 H 0 1 N N N N N N -5.188 -3.496 -28.811 -3.651 -2.113 -1.099 H11 R7D 39 R7D H12 H12 H 0 1 N N N N N N -4.893 -2.064 -26.830 -5.133 -0.209 -1.589 H12 R7D 40 R7D H13 H13 H 0 1 N N N N N N -5.065 -5.507 -24.312 -3.835 1.722 1.985 H13 R7D 41 R7D H14 H14 H 0 1 N N N N N N -5.358 -6.934 -26.294 -2.359 -0.186 2.480 H14 R7D 42 R7D H15 H15 H 0 1 N N N N N N -2.129 -8.328 -29.533 1.817 -2.009 -0.309 H15 R7D 43 R7D H16 H16 H 0 1 N N N N N N -4.896 -8.657 -31.327 3.872 -0.276 -0.500 H16 R7D 44 R7D H17 H17 H 0 1 N N N N N N -5.080 -8.607 -29.056 -0.144 -0.598 1.331 H17 R7D 45 R7D H18 H18 H 0 1 N N N N N N -5.196 -5.186 -30.490 -2.808 -3.661 -0.373 H18 R7D 46 # 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 R7D CAR CAS DOUB Y N 1 R7D CAR CAQ SING Y N 2 R7D CAS CAN SING Y N 3 R7D CAQ CAP DOUB Y N 4 R7D CAN CAM SING N N 5 R7D CAN NAO DOUB Y N 6 R7D CAM NAL SING N N 7 R7D CAP NAO SING Y N 8 R7D NAL CX SING N N 9 R7D OX CX DOUB N N 10 R7D CX CXA SING N N 11 R7D OAZ CAA SING N N 12 R7D CXA NX SING N N 13 R7D CXA CE SING N N 14 R7D OAD CAB DOUB N N 15 R7D NX CAB SING N N 16 R7D CAB CAA SING N N 17 R7D CAA CAY SING N N 18 R7D CE SD SING N N 19 R7D CBA CAY DOUB Y N 20 R7D CBA CBB SING Y N 21 R7D CAY CBE SING Y N 22 R7D CBB CBC DOUB Y N 23 R7D CBE CBD DOUB Y N 24 R7D CBC CBD SING Y N 25 R7D CBC CBF SING N N 26 R7D FBI CBF SING N N 27 R7D CBF FBG SING N N 28 R7D CBF FBH SING N N 29 R7D SD H1 SING N N 30 R7D CE H2 SING N N 31 R7D CE H3 SING N N 32 R7D CAA H4 SING N N 33 R7D CAM H5 SING N N 34 R7D CAM H6 SING N N 35 R7D CAP H7 SING N N 36 R7D CAQ H8 SING N N 37 R7D CAR H9 SING N N 38 R7D CAS H10 SING N N 39 R7D CBA H11 SING N N 40 R7D CBB H12 SING N N 41 R7D CBD H13 SING N N 42 R7D CBE H14 SING N N 43 R7D CXA H15 SING N N 44 R7D NAL H16 SING N N 45 R7D NX H17 SING N N 46 R7D OAZ H18 SING N N 47 # 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 R7D SMILES ACDLabs 12.01 "SCC(C(NCc1ncccc1)=O)NC(C(c2ccc(cc2)C(F)(F)F)O)=O" R7D InChI InChI 1.03 "InChI=1S/C18H18F3N3O3S/c19-18(20,21)12-6-4-11(5-7-12)15(25)17(27)24-14(10-28)16(26)23-9-13-3-1-2-8-22-13/h1-8,14-15,25,28H,9-10H2,(H,23,26)(H,24,27)/t14-,15+/m0/s1" R7D InChIKey InChI 1.03 MMSMEDXVHMERGZ-LSDHHAIUSA-N R7D SMILES_CANONICAL CACTVS 3.385 "O[C@@H](C(=O)N[C@@H](CS)C(=O)NCc1ccccn1)c2ccc(cc2)C(F)(F)F" R7D SMILES CACTVS 3.385 "O[CH](C(=O)N[CH](CS)C(=O)NCc1ccccn1)c2ccc(cc2)C(F)(F)F" R7D SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1ccnc(c1)CNC(=O)[C@H](CS)NC(=O)[C@@H](c2ccc(cc2)C(F)(F)F)O" R7D SMILES "OpenEye OEToolkits" 2.0.7 "c1ccnc(c1)CNC(=O)C(CS)NC(=O)C(c2ccc(cc2)C(F)(F)F)O" # 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 R7D "SYSTEMATIC NAME" ACDLabs 12.01 "N~2~-{(2R)-2-hydroxy-2-[4-(trifluoromethyl)phenyl]acetyl}-N-[(pyridin-2-yl)methyl]-L-cysteinamide" R7D "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(2~{R})-2-[[(2~{R})-2-oxidanyl-2-[4-(trifluoromethyl)phenyl]ethanoyl]amino]-~{N}-(pyridin-2-ylmethyl)-3-sulfanyl-propanamide" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site R7D "Create component" 2020-02-04 RCSB R7D "Modify formula" 2020-02-04 RCSB R7D "Initial release" 2020-08-05 RCSB R7D "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id R7D _pdbx_chem_comp_pcm.modified_residue_id CYS _pdbx_chem_comp_pcm.type None _pdbx_chem_comp_pcm.category "Covalent chemical modification" _pdbx_chem_comp_pcm.position "Amino-acid side chain" _pdbx_chem_comp_pcm.polypeptide_position "Any position" _pdbx_chem_comp_pcm.comp_id_linking_atom SD _pdbx_chem_comp_pcm.modified_residue_id_linking_atom SG _pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ? _pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ? #