1q2p

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
(New page: 200px<br /><applet load="1q2p" size="450" color="white" frame="true" align="right" spinBox="true" caption="1q2p, resolution 2.00&Aring;" /> '''SHV-1 class A beta-l...)
Current revision (07:14, 30 October 2024) (edit) (undo)
 
(16 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1q2p.gif|left|200px]]<br /><applet load="1q2p" size="450" color="white" frame="true" align="right" spinBox="true"
 
-
caption="1q2p, resolution 2.00&Aring;" />
 
-
'''SHV-1 class A beta-lactamase complexed with penem WAY185229'''<br />
 
-
==Overview==
+
==SHV-1 class A beta-lactamase complexed with penem WAY185229==
-
The design and synthesis of a series of seven tricyclic 6-methylidene, penems as novel class A and C serine beta-lactamase inhibitors is, described. These compounds proved to be very potent inhibitors of the, TEM-1 and AmpC beta-lactamases and less so against the class B, metallo-beta-lactamase CcrA. In combination with piperacillin, their in, vitro activities enhanced susceptibility of all class C resistant strains, from various bacteria. Crystallographic structures of a serine-bound, reaction intermediate of 17 with the class A SHV-1 and class C GC1 enzymes, have been established to resolutions of 2.0 and 1.4 A, respectively, and, refined to R-factors equal 0.163 and 0.145. In both beta-lactamases, a, seven-membered 1,4-thiazepine ring has formed. The stereogenic C7 atom in, the ring has the R configuration in the SHV-1 intermediate and has both R, and S configurations in the GC1 intermediate. Hydrophobic stacking, interactions between the tricyclic C7 substituent and a tyrosine side, chain, rather than electrostatic or hydrogen bonding by the C3 carboxylic, acid group, dominate in both complexes. The formation of the 1,4-, thiazepine ring structures is proposed based on a 7-endo-trig cyclization.
+
<StructureSection load='1q2p' size='340' side='right'caption='[[1q2p]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[1q2p]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Klebsiella_pneumoniae Klebsiella pneumoniae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q2P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Q2P FirstGlance]. <br>
 +
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2&#8491;</td></tr>
 +
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MA4:CYCLOHEXYL-HEXYL-BETA-D-MALTOSIDE'>MA4</scene>, <scene name='pdbligand=WY2:(6,7-DIHYDRO-5H-CYCLOPENTA[D]IMIDAZO[2,1-B]THIAZOL-2-YL]-4,7-DIHYDRO[1,4]THIAZEPINE-3,6-DICARBOXYLIC+ACID'>WY2</scene></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=1q2p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q2p OCA], [https://pdbe.org/1q2p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1q2p RCSB], [https://www.ebi.ac.uk/pdbsum/1q2p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1q2p ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/BLA1_KLEPN BLA1_KLEPN]
 +
== Evolutionary Conservation ==
 +
[[Image:Consurf_key_small.gif|200px|right]]
 +
Check<jmol>
 +
<jmolCheckbox>
 +
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/q2/1q2p_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
 +
<text>to colour the structure by Evolutionary Conservation</text>
 +
</jmolCheckbox>
 +
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1q2p ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
The design and synthesis of a series of seven tricyclic 6-methylidene penems as novel class A and C serine beta-lactamase inhibitors is described. These compounds proved to be very potent inhibitors of the TEM-1 and AmpC beta-lactamases and less so against the class B metallo-beta-lactamase CcrA. In combination with piperacillin, their in vitro activities enhanced susceptibility of all class C resistant strains from various bacteria. Crystallographic structures of a serine-bound reaction intermediate of 17 with the class A SHV-1 and class C GC1 enzymes have been established to resolutions of 2.0 and 1.4 A, respectively, and refined to R-factors equal 0.163 and 0.145. In both beta-lactamases, a seven-membered 1,4-thiazepine ring has formed. The stereogenic C7 atom in the ring has the R configuration in the SHV-1 intermediate and has both R and S configurations in the GC1 intermediate. Hydrophobic stacking interactions between the tricyclic C7 substituent and a tyrosine side chain, rather than electrostatic or hydrogen bonding by the C3 carboxylic acid group, dominate in both complexes. The formation of the 1,4- thiazepine ring structures is proposed based on a 7-endo-trig cyclization.
-
==About this Structure==
+
Structure-activity relationship of 6-methylidene penems bearing tricyclic heterocycles as broad-spectrum beta-lactamase inhibitors: crystallographic structures show unexpected binding of 1,4-thiazepine intermediates.,Venkatesan AM, Gu Y, Dos Santos O, Abe T, Agarwal A, Yang Y, Petersen PJ, Weiss WJ, Mansour TS, Nukaga M, Hujer AM, Bonomo RA, Knox JR J Med Chem. 2004 Dec 16;47(26):6556-68. PMID:15588091<ref>PMID:15588091</ref>
-
1Q2P is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Klebsiella_pneumoniae Klebsiella pneumoniae] with MA4 and WY2 as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1Q2P OCA].
+
-
==Reference==
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
Structure-activity relationship of 6-methylidene penems bearing tricyclic heterocycles as broad-spectrum beta-lactamase inhibitors: crystallographic structures show unexpected binding of 1,4-thiazepine intermediates., Venkatesan AM, Gu Y, Dos Santos O, Abe T, Agarwal A, Yang Y, Petersen PJ, Weiss WJ, Mansour TS, Nukaga M, Hujer AM, Bonomo RA, Knox JR, J Med Chem. 2004 Dec 16;47(26):6556-68. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15588091 15588091]
+
</div>
-
[[Category: Beta-lactamase]]
+
<div class="pdbe-citations 1q2p" style="background-color:#fffaf0;"></div>
-
[[Category: Klebsiella pneumoniae]]
+
-
[[Category: Single protein]]
+
-
[[Category: Bonomo, R.A.]]
+
-
[[Category: Hujer, A.]]
+
-
[[Category: Knox, J.R.]]
+
-
[[Category: Mansour, T.S.]]
+
-
[[Category: Nukaga, M.]]
+
-
[[Category: Venkatesan, A.M.]]
+
-
[[Category: MA4]]
+
-
[[Category: WY2]]
+
-
[[Category: beta-lactam antibiotics]]
+
-
[[Category: drug design]]
+
-
[[Category: hydrolase]]
+
-
[[Category: inhibition]]
+
-
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 00:20:15 2007''
+
==See Also==
 +
*[[Beta-lactamase 3D structures|Beta-lactamase 3D structures]]
 +
== References ==
 +
<references/>
 +
__TOC__
 +
</StructureSection>
 +
[[Category: Klebsiella pneumoniae]]
 +
[[Category: Large Structures]]
 +
[[Category: Bonomo RA]]
 +
[[Category: Hujer A]]
 +
[[Category: Knox JR]]
 +
[[Category: Mansour TS]]
 +
[[Category: Nukaga M]]
 +
[[Category: Venkatesan AM]]

Current revision

SHV-1 class A beta-lactamase complexed with penem WAY185229

PDB ID 1q2p

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Personal tools