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 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 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
_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
4D6 C1 C1 C 0 1 Y N N N 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 N 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 N 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 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 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 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 N N N 7.356 20.074 16.301 -3.378 0.657 0.216 C14 4D6 7
4D6 C17 C8 C 0 1 N N N 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 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 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 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 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 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 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 N N N 6.810 19.923 19.207 -0.585 0.513 1.157 C34 4D6 15
4D6 N9 N1 N 0 1 N N N 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 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 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 N 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 N 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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
4D6 "Modify PCM" 2024-09-27 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 ?
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id 4D6
_pdbx_chem_comp_pcm.modified_residue_id SER
_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 B15
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom OG
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ?
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ?
#