data_DB5
# 
_chem_comp.id                                    DB5 
_chem_comp.name                                  "[(4~{S})-4,5,6,7,8,9-hexahydro-1~{H}-cycloocta[d][1,2,3]triazol-4-yl] hydrogen carbonate" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C9 H13 N3 O3" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2018-01-11 
_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                        211.218 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     DB5 
_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        5NI3 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  EBI 
_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 
DB5 N03 N1  N 0 1 Y N N N N N -47.646 2.063 -53.776 1.669  2.181  0.334  N03 DB5 1  
DB5 N02 N2  N 0 1 Y N N N N N -48.059 2.528 -52.651 1.074  2.606  -0.733 N02 DB5 2  
DB5 N01 N3  N 0 1 Y N N N N N -47.037 2.861 -51.888 0.254  1.711  -1.175 N01 DB5 3  
DB5 OH  O1  O 0 1 N N N N N N -41.302 2.536 -52.029 -2.223 -0.217 1.465  OH  DB5 4  
DB5 CH  C1  C 0 1 N N N N N N -42.384 2.045 -51.789 -2.664 -0.171 0.335  CH  DB5 5  
DB5 OT  O2  O 0 1 N N N N N N -43.510 2.231 -52.761 -1.846 -0.373 -0.715 OT  DB5 6  
DB5 CI  C2  C 0 1 N N S N N N -44.552 3.027 -52.401 -0.450 -0.640 -0.421 CI  DB5 7  
DB5 CP  C3  C 0 1 Y N N N N N -45.967 2.705 -52.702 0.306  0.655  -0.369 CP  DB5 8  
DB5 CS  C4  C 0 1 Y N N N N N -46.326 2.147 -53.867 1.219  0.947  0.583  CS  DB5 9  
DB5 CK  C5  C 0 1 N N N N N N -45.351 1.686 -54.981 1.578  -0.041 1.671  CK  DB5 10 
DB5 CV  C6  C 0 1 N N N N N N -45.488 2.719 -56.028 2.429  -1.131 1.110  CV  DB5 11 
DB5 CM  C7  C 0 1 N N N N N N -44.952 4.056 -55.645 1.805  -2.206 0.237  CM  DB5 12 
DB5 CL  C8  C 0 1 N N N N N N -43.728 4.007 -54.667 1.689  -1.701 -1.215 CL  DB5 13 
DB5 CN  C9  C 0 1 N N N N N N -44.176 4.244 -53.211 0.156  -1.538 -1.524 CN  DB5 14 
DB5 H1  H1  H 0 1 N N N N N N -48.241 1.688 -54.487 2.326  2.667  0.857  H1  DB5 15 
DB5 H3  H3  H 0 1 N N N N N N -44.476 3.290 -51.336 -0.372 -1.144 0.543  H3  DB5 16 
DB5 H4  H4  H 0 1 N N N N N N -45.639 0.697 -55.368 2.125  0.474  2.461  H4  DB5 17 
DB5 H5  H5  H 0 1 N N N N N N -44.318 1.646 -54.604 0.666  -0.472 2.084  H5  DB5 18 
DB5 H6  H6  H 0 1 N N N N N N -46.557 2.831 -56.264 3.220  -0.658 0.528  H6  DB5 19 
DB5 H7  H7  H 0 1 N N N N N N -44.949 2.375 -56.923 2.909  -1.632 1.950  H7  DB5 20 
DB5 H8  H8  H 0 1 N N N N N N -44.639 4.577 -56.562 2.430  -3.099 0.261  H8  DB5 21 
DB5 H9  H9  H 0 1 N N N N N N -45.759 4.624 -55.158 0.813  -2.450 0.616  H9  DB5 22 
DB5 H10 H10 H 0 1 N N N N N N -43.248 3.020 -54.740 2.193  -0.740 -1.316 H10 DB5 23 
DB5 H11 H11 H 0 1 N N N N N N -43.007 4.787 -54.953 2.131  -2.427 -1.898 H11 DB5 24 
DB5 H12 H12 H 0 1 N N N N N N -43.350 4.748 -52.688 -0.330 -2.514 -1.512 H12 DB5 25 
DB5 H13 H13 H 0 1 N N N N N N -45.053 4.908 -53.238 0.023  -1.069 -2.499 H13 DB5 26 
DB5 OXT OXT O 0 1 N Y N N N N -42.457 1.519 -50.594 -3.969 0.081  0.132  OXT DB5 27 
DB5 H2  H2  H 0 1 N N N N N N -41.627 1.632 -50.147 -4.517 0.219  0.917  H2  DB5 28 
# 
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 
DB5 CV  CM  SING N N 1  
DB5 CV  CK  SING N N 2  
DB5 CM  CL  SING N N 3  
DB5 CK  CS  SING N N 4  
DB5 CL  CN  SING N N 5  
DB5 CS  N03 SING Y N 6  
DB5 CS  CP  DOUB Y N 7  
DB5 N03 N02 SING Y N 8  
DB5 CN  CI  SING N N 9  
DB5 OT  CI  SING N N 10 
DB5 OT  CH  SING N N 11 
DB5 CP  CI  SING N N 12 
DB5 CP  N01 SING Y N 13 
DB5 N02 N01 DOUB Y N 14 
DB5 OH  CH  DOUB N N 15 
DB5 N03 H1  SING N N 16 
DB5 CI  H3  SING N N 17 
DB5 CK  H4  SING N N 18 
DB5 CK  H5  SING N N 19 
DB5 CV  H6  SING N N 20 
DB5 CV  H7  SING N N 21 
DB5 CM  H8  SING N N 22 
DB5 CM  H9  SING N N 23 
DB5 CL  H10 SING N N 24 
DB5 CL  H11 SING N N 25 
DB5 CN  H12 SING N N 26 
DB5 CN  H13 SING N N 27 
DB5 CH  OXT SING N N 28 
DB5 OXT H2  SING N N 29 
# 
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 
DB5 InChI            InChI                1.03  "InChI=1S/C9H13N3O3/c13-9(14)15-7-5-3-1-2-4-6-8(7)11-12-10-6/h7H,1-5H2,(H,13,14)(H,10,11,12)/t7-/m0/s1" 
DB5 InChIKey         InChI                1.03  ZBJGIWFCJONVKZ-ZETCQYMHSA-N                                                                             
DB5 SMILES_CANONICAL CACTVS               3.385 "OC(=O)O[C@H]1CCCCCc2[nH]nnc12"                                                                         
DB5 SMILES           CACTVS               3.385 "OC(=O)O[CH]1CCCCCc2[nH]nnc12"                                                                          
DB5 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "C1CCc2c(nn[nH]2)[C@H](CC1)OC(=O)O"                                                                     
DB5 SMILES           "OpenEye OEToolkits" 2.0.6 "C1CCc2c(nn[nH]2)C(CC1)OC(=O)O"                                                                         
# 
_pdbx_chem_comp_identifier.comp_id           DB5 
_pdbx_chem_comp_identifier.type              "SYSTEMATIC NAME" 
_pdbx_chem_comp_identifier.program           "OpenEye OEToolkits" 
_pdbx_chem_comp_identifier.program_version   2.0.6 
_pdbx_chem_comp_identifier.identifier        "[(4~{S})-4,5,6,7,8,9-hexahydro-1~{H}-cycloocta[d][1,2,3]triazol-4-yl] hydrogen carbonate" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
DB5 "Create component" 2018-01-11 EBI  
DB5 "Initial release"  2018-09-12 RCSB 
DB5 "Modify PCM"       2024-09-27 PDBE 
# 
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 DB5 LYS None Crosslinker "Amino-acid side chain" "Any position" CH  NZ ? ? 
2 DB5 PHE None Crosslinker "Amino-acid side chain" "Any position" N01 CZ ? ? 
3 DB5 PHE None Crosslinker "Amino-acid side chain" "Any position" N03 CZ ? ? 
# 
