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                    2023-11-03 
_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 
# 
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 
# 
