data_B3M # _chem_comp.id B3M _chem_comp.name "(3R)-3-amino-5-(methylsulfanyl)pentanoic acid" _chem_comp.type "L-peptide linking" _chem_comp.pdbx_type ATOMP _chem_comp.formula "C6 H13 N O2 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2008-11-19 _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 163.238 _chem_comp.one_letter_code X _chem_comp.three_letter_code B3M _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 3F86 _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 B3M N N N 0 1 N N N Y Y N 13.307 -14.126 17.722 -0.786 1.253 0.891 N B3M 1 B3M CB CA C 0 1 N N N Y N N 11.353 -15.203 17.177 -1.871 -0.818 0.161 CA B3M 2 B3M C C C 0 1 N N N Y N Y 10.190 -14.735 18.036 -3.161 -0.113 -0.173 C B3M 3 B3M O O O 0 1 N N N Y N Y 9.296 -14.096 17.561 -3.142 1.035 -0.548 O B3M 4 B3M CA CB C 0 1 N N R Y N N 12.341 -14.211 16.676 -0.696 0.137 -0.060 CB B3M 5 B3M CG CG C 0 1 N N N N N N 13.010 -14.704 15.390 0.619 -0.613 0.157 CG B3M 6 B3M CD CD C 0 1 N N N N N N 14.070 -13.721 14.913 1.793 0.306 -0.184 CD B3M 7 B3M SE SE S 0 1 N N N N N N 13.330 -12.121 14.515 3.353 -0.584 0.074 SE B3M 8 B3M CF CF C 0 1 N N N N N N 14.415 -10.951 15.338 4.606 0.649 -0.376 CF B3M 9 B3M H HN H 0 1 N N N Y Y N 14.226 -14.106 17.327 -1.616 1.803 0.725 HN B3M 10 B3M HB1 HA H 0 1 N N N Y N N 11.920 -15.919 17.790 -1.890 -1.136 1.203 HA B3M 11 B3M HB2 HAA H 0 1 N N N Y N N 10.871 -15.580 16.263 -1.756 -1.690 -0.484 HAA B3M 12 B3M HA HB H 0 1 N N N Y N N 11.873 -13.245 16.436 -0.729 0.524 -1.079 HB B3M 13 B3M HG HG H 0 1 N N N N N N 12.241 -14.797 14.609 0.692 -0.924 1.199 HG B3M 14 B3M HGA HGA H 0 1 N N N N N N 13.487 -15.676 15.585 0.647 -1.493 -0.487 HGA B3M 15 B3M HD HD H 0 1 N N N N N N 14.544 -14.126 14.007 1.721 0.616 -1.227 HD B3M 16 B3M HDA HDA H 0 1 N N N N N N 14.815 -13.583 15.710 1.766 1.185 0.459 HDA B3M 17 B3M HF HF H 0 1 N N N N N N 14.637 -11.308 16.354 4.462 0.951 -1.413 HF B3M 18 B3M HFA HFA H 0 1 N N N N N N 15.352 -10.858 14.770 4.508 1.519 0.273 HFA B3M 19 B3M HFB HFB H 0 1 N N N N N N 13.921 -9.970 15.394 5.599 0.217 -0.257 HFB B3M 20 B3M H2 HNA H 0 1 N Y N Y Y N 13.153 -13.291 18.250 -0.758 0.919 1.843 HNA B3M 21 B3M OXT OXT O 0 1 N Y N Y N Y 10.163 -15.062 19.428 -4.330 -0.761 -0.052 OXT B3M 22 B3M HXT HXT H 0 1 N Y N Y N Y 9.378 -14.701 19.823 -5.131 -0.268 -0.278 HXT B3M 23 # 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 B3M N H SING N N 1 B3M N H2 SING N N 2 B3M CB HB1 SING N N 3 B3M CB C SING N N 4 B3M C OXT SING N N 5 B3M O C DOUB N N 6 B3M CA N SING N N 7 B3M CA CB SING N N 8 B3M CG CA SING N N 9 B3M CG HGA SING N N 10 B3M CD CG SING N N 11 B3M CD HDA SING N N 12 B3M SE CD SING N N 13 B3M SE CF SING N N 14 B3M CF HF SING N N 15 B3M CF HFA SING N N 16 B3M HB2 CB SING N N 17 B3M HA CA SING N N 18 B3M HG CG SING N N 19 B3M HD CD SING N N 20 B3M HFB CF SING N N 21 B3M OXT HXT SING N N 22 # 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 B3M SMILES ACDLabs 10.04 "O=C(O)CC(N)CCSC" B3M SMILES_CANONICAL CACTVS 3.341 "CSCC[C@H](N)CC(O)=O" B3M SMILES CACTVS 3.341 "CSCC[CH](N)CC(O)=O" B3M SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CSCC[C@@H](CC(=O)O)N" B3M SMILES "OpenEye OEToolkits" 1.5.0 "CSCCC(CC(=O)O)N" B3M InChI InChI 1.03 "InChI=1S/C6H13NO2S/c1-10-3-2-5(7)4-6(8)9/h5H,2-4,7H2,1H3,(H,8,9)/t5-/m0/s1" B3M InChIKey InChI 1.03 QWVNCDVONVDGDV-YFKPBYRVSA-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 B3M "SYSTEMATIC NAME" ACDLabs 10.04 "(3R)-3-amino-5-(methylsulfanyl)pentanoic acid" B3M "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(3R)-3-amino-5-methylsulfanyl-pentanoic acid" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site B3M "Create component" 2008-11-19 RCSB B3M "Modify descriptor" 2011-06-04 RCSB B3M "Modify backbone" 2023-11-03 PDBE B3M "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id B3M _pdbx_chem_comp_pcm.modified_residue_id MET _pdbx_chem_comp_pcm.type "Beta-amino acid" _pdbx_chem_comp_pcm.category "Named protein modification" _pdbx_chem_comp_pcm.position "Amino-acid backbone" _pdbx_chem_comp_pcm.polypeptide_position "Any 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 ? #