6kw1

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==The structure of the metallo-beta-lactamase VIM-2 in complex with a triazolylthioacetamide 1b==
==The structure of the metallo-beta-lactamase VIM-2 in complex with a triazolylthioacetamide 1b==
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<StructureSection load='6kw1' size='340' side='right'caption='[[6kw1]]' scene=''>
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<StructureSection load='6kw1' size='340' side='right'caption='[[6kw1]], [[Resolution|resolution]] 1.78&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KW1 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6KW1 FirstGlance]. <br>
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<table><tr><td colspan='2'>[[6kw1]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_aeruginosus"_(schroeter_1872)_trevisan_1885 "bacillus aeruginosus" (schroeter 1872) trevisan 1885]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KW1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6KW1 FirstGlance]. <br>
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</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6kw1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kw1 OCA], [http://pdbe.org/6kw1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6kw1 RCSB], [http://www.ebi.ac.uk/pdbsum/6kw1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6kw1 ProSAT]</span></td></tr>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=9RX:2-[3-[2-(1H-benzimidazol-2-ylamino)-2-oxidanylidene-ethyl]sulfanyl-1H-1,2,4-triazol-5-yl]benzoic+acid'>9RX</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">blaVIM-2, bla vim-2, bla-VIM-2, blasVIM-2, blaVIM2, VIM-2, vim-2, IPC669_36195 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=287 "Bacillus aeruginosus" (Schroeter 1872) Trevisan 1885])</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6kw1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kw1 OCA], [https://pdbe.org/6kw1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6kw1 RCSB], [https://www.ebi.ac.uk/pdbsum/6kw1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6kw1 ProSAT]</span></td></tr>
</table>
</table>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Inhibition of beta-lactamases presents a promising strategy to restore the beta-lactams antibacterial activity to resistant bacteria. In this work, we found that aromatic carboxyl substituted 2-triazolylthioacetamides 1a-j inhibited VIM-2, exhibiting an IC50 value in the range of 20.6-58.6 muM. The structure-activity relationship study revealed that replacing the aliphatic carboxylic acid with aromatic carboxyl improved the inhibitory activity of 2-triazolylthioacetamides against VIM-2. 1a-j (16 mg/mL) restored the antibacterial activity of cefazolin against E. coli cell expressing VIM-2, resulting in a 4-8-fold reduction in MICs. The isothermal titration calorimetry (ITC) characterization suggested that the primary binding 2-triazolylthioacetamide (1b, 1c, or 1h) to VIM-2 was a combination of entropy and enthalpy contributions. Further, the crystal structure of VIM-2 in complex with 1b was obtained by co-crystallization with a hanging-drop vapour-diffusion method. The crystal structure analysis revealed that 1b bound to two Zn(II) ions of the enzyme active sites, formed H-bound with Asn233 and structure water molecule, and interacted with the hydrophobic pocket of enzyme activity center utilizing hydrophobic moieties; especially for the phenyl of aromatic carboxyl which formed pi-pi stacking with active residue His263. These studies confirmed that aromatic carboxyl substituted 2-triazolylthioacetamides are the potent VIM-2 inhibitors scaffold and provided help to further optimize 2-triazolylthioacetamides as VIM-2 even or broad-spectrum MbetaLs inhibitors.
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Kinetic, Thermodynamic, and Crystallographic Studies of 2-Triazolylthioacetamides as Verona Integron-Encoded Metallo-beta-Lactamase 2 (VIM-2) Inhibitor.,Xiang Y, Zhang YJ, Ge Y, Zhou Y, Chen C, Wahlgren WY, Tan X, Chen X, Yang KW Biomolecules. 2020 Jan 1;10(1). pii: biom10010072. doi: 10.3390/biom10010072. PMID:31906402<ref>PMID:31906402</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 6kw1" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Xiang Y]]
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[[Category: Xiang, Y]]
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[[Category: Yang KW]]
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[[Category: Yang, K W]]
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[[Category: Antibiotic resistant]]
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[[Category: Crystallographic study]]
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[[Category: Hydrolase]]
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[[Category: Metallo-beta-lactamase vim-2 inhibitor]]
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[[Category: Trizolylthioacetamide]]

Revision as of 06:47, 24 March 2021

The structure of the metallo-beta-lactamase VIM-2 in complex with a triazolylthioacetamide 1b

PDB ID 6kw1

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