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| | <StructureSection load='4lv3' size='340' side='right'caption='[[4lv3]], [[Resolution|resolution]] 1.42Å' scene=''> | | <StructureSection load='4lv3' size='340' side='right'caption='[[4lv3]], [[Resolution|resolution]] 1.42Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4lv3]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LV3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4LV3 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4lv3]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LV3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4LV3 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=25N:(3,5-DI-TERT-BUTYLPHENYL)BORONIC+ACID'>25N</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=25N:(3,5-DI-TERT-BUTYLPHENYL)BORONIC+ACID'>25N</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4lv0|4lv0]], [[4lv1|4lv1]], [[4lv2|4lv2]]</td></tr>
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4lv3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lv3 OCA], [https://pdbe.org/4lv3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4lv3 RCSB], [https://www.ebi.ac.uk/pdbsum/4lv3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4lv3 ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ampA, ampC, b4150, JW4111 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
| + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-lactamase Beta-lactamase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.6 3.5.2.6] </span></td></tr>
| + | |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4lv3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lv3 OCA], [http://pdbe.org/4lv3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4lv3 RCSB], [http://www.ebi.ac.uk/pdbsum/4lv3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4lv3 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/AMPC_ECOLI AMPC_ECOLI]] This protein is a serine beta-lactamase with a substrate specificity for cephalosporins. | + | [https://www.uniprot.org/uniprot/AMPC_ECOLI AMPC_ECOLI] This protein is a serine beta-lactamase with a substrate specificity for cephalosporins. |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | | | |
| | ==See Also== | | ==See Also== |
| - | *[[Beta-lactamase|Beta-lactamase]] | + | *[[Beta-lactamase 3D structures|Beta-lactamase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Beta-lactamase]] | + | [[Category: Escherichia coli K-12]] |
| - | [[Category: Ecoli]]
| + | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Eidam, O]] | + | [[Category: Eidam O]] |
| - | [[Category: London, N]] | + | [[Category: London N]] |
| - | [[Category: Shoichet, B K]] | + | [[Category: Shoichet BK]] |
| - | [[Category: Ampc beta-lactamase]]
| + | |
| - | [[Category: Boronic acid]]
| + | |
| - | [[Category: Class c]]
| + | |
| - | [[Category: Covalent inhibitor]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Hydrolase-hydrolase inhibitor complex]]
| + | |
| Structural highlights
Function
AMPC_ECOLI This protein is a serine beta-lactamase with a substrate specificity for cephalosporins.
Publication Abstract from PubMed
Chemical probes that form a covalent bond with a protein target often show enhanced selectivity, potency and utility for biological studies. Despite these advantages, protein-reactive compounds are usually avoided in high-throughput screening campaigns. Here we describe a general method (DOCKovalent) for screening large virtual libraries of electrophilic small molecules. We apply this method prospectively to discover reversible covalent fragments that target distinct protein nucleophiles, including the catalytic serine of AmpC beta-lactamase and noncatalytic cysteines in RSK2, MSK1 and JAK3 kinases. We identify submicromolar to low-nanomolar hits with high ligand efficiency, cellular activity and selectivity, including what are to our knowledge the first reported reversible covalent inhibitors of JAK3. Crystal structures of inhibitor complexes with AmpC and RSK2 confirm the docking predictions and guide further optimization. As covalent virtual screening may have broad utility for the rapid discovery of chemical probes, we have made the method freely available through an automated web server (http://covalent.docking.org/).
Covalent docking of large libraries for the discovery of chemical probes.,London N, Miller RM, Krishnan S, Uchida K, Irwin JJ, Eidam O, Gibold L, Cimermancic P, Bonnet R, Shoichet BK, Taunton J Nat Chem Biol. 2014 Oct 26. doi: 10.1038/nchembio.1666. PMID:25344815[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ London N, Miller RM, Krishnan S, Uchida K, Irwin JJ, Eidam O, Gibold L, Cimermancic P, Bonnet R, Shoichet BK, Taunton J. Covalent docking of large libraries for the discovery of chemical probes. Nat Chem Biol. 2014 Oct 26. doi: 10.1038/nchembio.1666. PMID:25344815 doi:http://dx.doi.org/10.1038/nchembio.1666
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