data_4D6
#

_chem_comp.id                                   4D6
_chem_comp.name                                 Vaborbactam
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C12 H16 B N O5 S"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        "{(3R,6S)-2-hydroxy-3-[(thiophen-2-ylacetyl)amino]-1,2-oxaborinan-6-yl}acetic acid;  2-((3R,6S)-2-hydroxy-3-(2-(thiophen-2-yl)acetamido)-1,2-oxaborinan-6-yl)acetic acid; 2-[(3R,6S)-2-hydroxy-3-[(2-thiophen-2-ylacetyl)amino]oxaborinan-6-yl]acetic acid; 1,2-Oxaborinane-6-acetic acid, 2-hydroxy-3-((2-(2-thienyl)acetyl)amino)-, (3R,6S)-"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2015-03-03
_chem_comp.pdbx_modified_date                   2020-11-04
_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                       297.135
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    4D6
_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       4XUX
_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.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
4D6  C1   C1   C  0  1  Y  N  N   8.110  25.002  22.224   6.247  -0.440  -0.079  C1   4D6   1  
4D6  C3   C2   C  0  1  Y  N  N   7.562  22.653  22.805   3.864  -0.091  -0.779  C3   4D6   2  
4D6  C5   C3   C  0  1  Y  N  N   7.815  24.836  23.576   5.619  -1.539  -0.501  C5   4D6   3  
4D6  C7   C4   C  0  1  N  N  N   6.605  20.794  21.455   1.581   0.261   0.069  C7   4D6   4  
4D6  C11  C5   C  0  1  N  N  N   6.702  21.231  18.426  -1.426   1.788   1.304  C11  4D6   5  
4D6  C12  C6   C  0  1  N  N  N   6.362  21.025  16.955  -2.430   1.855   0.149  C12  4D6   6  
4D6  C14  C7   C  0  1  N  N  S   7.356  20.074  16.301  -3.378   0.657   0.216  C14  4D6   7  
4D6  C17  C8   C  0  1  N  N  N   8.677  20.811  16.131  -4.434   0.782  -0.884  C17  4D6   8  
4D6  O20  O1   O  0  1  N  N  N   9.730  19.463  14.470  -5.324  -1.141   0.147  O20  4D6   9  
4D6  C18  C9   C  0  1  N  N  N   9.790  19.919  15.632  -5.440  -0.331  -0.743  C18  4D6  10  
4D6  O19  O2   O  0  1  N  N  N  10.751  19.678  16.398  -6.464  -0.423  -1.605  O19  4D6  11  
4D6  O16  O3   O  0  1  N  N  N   7.503  18.874  17.064  -2.638  -0.554   0.032  O16  4D6  12  
4D6  B15  B1   B  0  1  N  N  N   7.756  18.867  18.466  -1.574  -0.702   0.972  B15  4D6  13  
4D6  O27  O4   O  0  1  N  N  N   9.223  19.197  18.764  -1.411  -1.902   1.714  O27  4D6  14  
4D6  C34  C10  C  0  1  N  N  R   6.810  19.923  19.207  -0.585   0.513   1.157  C34  4D6  15  
4D6  N9   N1   N  0  1  N  N  N   7.364  20.284  20.488   0.286   0.626  -0.015  N9   4D6  16  
4D6  O8   O5   O  0  1  N  N  N   5.400  20.975  21.344   2.025  -0.161   1.116  O8   4D6  17  
4D6  C6   C11  C  0  1  N  N  N   7.314  21.163  22.731   2.477   0.377  -1.137  C6   4D6  18  
4D6  S2   S1   S  0  1  Y  N  N   8.020  23.496  21.350   5.152   0.933  -0.159  S2   4D6  19  
4D6  C4   C12  C  0  1  Y  N  N   7.514  23.513  23.910   4.305  -1.345  -0.892  C4   4D6  20  
4D6  H1   H1   H  0  1  N  N  N   8.364  25.949  21.772   7.271  -0.402   0.263  H1   4D6  21  
4D6  H2   H2   H  0  1  N  N  N   7.819  25.645  24.291   6.098  -2.506  -0.536  H2   4D6  22  
4D6  H3   H3   H  0  1  N  N  N   7.665  21.758  18.492  -0.774   2.661   1.272  H3   4D6  23  
4D6  H4   H4   H  0  1  N  N  N   5.915  21.848  18.884  -1.961   1.766   2.254  H4   4D6  24  
4D6  H5   H5   H  0  1  N  N  N   6.396  21.995  16.437  -3.006   2.778   0.223  H5   4D6  25  
4D6  H6   H6   H  0  1  N  N  N   5.350  20.601  16.874  -1.892   1.838  -0.799  H6   4D6  26  
4D6  H7   H7   H  0  1  N  N  N   6.976  19.822  15.300  -3.869   0.638   1.189  H7   4D6  27  
4D6  H8   H8   H  0  1  N  N  N   8.973  21.230  17.104  -4.940   1.743  -0.794  H8   4D6  28  
4D6  H9   H9   H  0  1  N  N  N   8.532  21.628  15.409  -3.952   0.715  -1.859  H9   4D6  29  
4D6  H10  H10  H  0  1  N  N  N  11.379  19.121  15.953  -7.084  -1.154  -1.474  H10  4D6  30  
4D6  H11  H11  H  0  1  N  N  N   9.687  19.344  17.948  -2.074  -2.578   1.519  H11  4D6  31  
4D6  H12  H12  H  0  1  N  N  N   5.810  19.479  19.324   0.018   0.364   2.053  H12  4D6  32  
4D6  H13  H13  H  0  1  N  N  N   8.341  20.148  20.654  -0.069   0.964  -0.853  H13  4D6  33  
4D6  H14  H14  H  0  1  N  N  N   6.694  20.859  23.587   2.517   1.418  -1.460  H14  4D6  34  
4D6  H15  H15  H  0  1  N  N  N   8.279  20.636  22.771   2.082  -0.239  -1.944  H15  4D6  35  
4D6  H16  H16  H  0  1  N  N  N   7.271  23.189  24.911   3.682  -2.149  -1.255  H16  4D6  36  
#   #
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
4D6  O20  C18  DOUB  N  N   1  
4D6  C18  C17  SING  N  N   2  
4D6  C18  O19  SING  N  N   3  
4D6  C17  C14  SING  N  N   4  
4D6  C14  C12  SING  N  N   5  
4D6  C14  O16  SING  N  N   6  
4D6  C12  C11  SING  N  N   7  
4D6  O16  B15  SING  N  N   8  
4D6  C11  C34  SING  N  N   9  
4D6  B15  O27  SING  N  N  10  
4D6  B15  C34  SING  N  N  11  
4D6  C34  N9   SING  N  N  12  
4D6  N9   C7   SING  N  N  13  
4D6  O8   C7   DOUB  N  N  14  
4D6  S2   C1   SING  Y  N  15  
4D6  S2   C3   SING  Y  N  16  
4D6  C7   C6   SING  N  N  17  
4D6  C1   C5   DOUB  Y  N  18  
4D6  C6   C3   SING  N  N  19  
4D6  C3   C4   DOUB  Y  N  20  
4D6  C5   C4   SING  Y  N  21  
4D6  C1   H1   SING  N  N  22  
4D6  C5   H2   SING  N  N  23  
4D6  C11  H3   SING  N  N  24  
4D6  C11  H4   SING  N  N  25  
4D6  C12  H5   SING  N  N  26  
4D6  C12  H6   SING  N  N  27  
4D6  C14  H7   SING  N  N  28  
4D6  C17  H8   SING  N  N  29  
4D6  C17  H9   SING  N  N  30  
4D6  O19  H10  SING  N  N  31  
4D6  O27  H11  SING  N  N  32  
4D6  C34  H12  SING  N  N  33  
4D6  N9   H13  SING  N  N  34  
4D6  C6   H14  SING  N  N  35  
4D6  C6   H15  SING  N  N  36  
4D6  C4   H16  SING  N  N  37  
#   #
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
4D6  SMILES            ACDLabs               12.01  "c2ccc(CC(NC1CCC(OB1O)CC(=O)O)=O)s2"  
4D6  InChI             InChI                 1.03   "InChI=1S/C12H16BNO5S/c15-11(7-9-2-1-5-20-9)14-10-4-3-8(6-12(16)17)19-13(10)18/h1-2,5,8,10,18H,3-4,6-7H2,(H,14,15)(H,16,17)/t8-,10-/m0/s1"  
4D6  InChIKey          InChI                 1.03   IOOWNWLVCOUUEX-WPRPVWTQSA-N  
4D6  SMILES_CANONICAL  CACTVS                3.385  "OB1O[C@@H](CC[C@@H]1NC(=O)Cc2sccc2)CC(O)=O"  
4D6  SMILES            CACTVS                3.385  "OB1O[CH](CC[CH]1NC(=O)Cc2sccc2)CC(O)=O"  
4D6  SMILES_CANONICAL  "OpenEye OEToolkits"  1.9.2  "B1([C@H](CC[C@H](O1)CC(=O)O)NC(=O)Cc2cccs2)O"  
4D6  SMILES            "OpenEye OEToolkits"  1.9.2  "B1(C(CCC(O1)CC(=O)O)NC(=O)Cc2cccs2)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
4D6  "SYSTEMATIC NAME"  ACDLabs               12.01  "{(3R,6S)-2-hydroxy-3-[(thiophen-2-ylacetyl)amino]-1,2-oxaborinan-6-yl}acetic acid"  
4D6  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.9.2  "2-[(3R,6S)-2-oxidanyl-3-(2-thiophen-2-ylethanoylamino)-1,2-oxaborinan-6-yl]ethanoic 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
4D6  "Create component"  2015-03-03  RCSB  
4D6  "Initial release"   2015-04-01  RCSB  
4D6  "Modify synonyms"   2020-11-04  PDBE  
#   #
loop_
_pdbx_chem_comp_synonyms.ordinal
_pdbx_chem_comp_synonyms.comp_id
_pdbx_chem_comp_synonyms.name
_pdbx_chem_comp_synonyms.provenance
_pdbx_chem_comp_synonyms.type
1  4D6  Vaborbactam                                                                            DRUGBANK  ?  
2  4D6  "2-((3R,6S)-2-hydroxy-3-(2-(thiophen-2-yl)acetamido)-1,2-oxaborinan-6-yl)acetic acid"  PUBCHEM   ?  
3  4D6  "2-[(3R,6S)-2-hydroxy-3-[(2-thiophen-2-ylacetyl)amino]oxaborinan-6-yl]acetic acid"     PUBCHEM   ?  
4  4D6  "1,2-Oxaborinane-6-acetic acid, 2-hydroxy-3-((2-(2-thienyl)acetyl)amino)-, (3R,6S)-"   PUBCHEM   ?  
5  4D6  56649692                                                                               PUBCHEM   ?  
6  4D6  CHEMBL3317857                                                                          CHEMBL    ?  
7  4D6  "{(3R,6S)-2-hydroxy-3-[(thiophen-2-ylacetyl)amino]-1,2-oxaborinan-6-yl}acetic acid"    PDB       ?  
8  4D6  " DB12107"                                                                             DRUGBANK  ?  
##
