1xep
From Proteopedia
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|PDB= 1xep |SIZE=350|CAPTION= <scene name='initialview01'>1xep</scene>, resolution 1.55Å | |PDB= 1xep |SIZE=350|CAPTION= <scene name='initialview01'>1xep</scene>, resolution 1.55Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand= | + | |LIGAND= <scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=CAQ:CATECHOL'>CAQ</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene> |
| - | |ACTIVITY= [http://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] | + | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] </span> |
| - | |GENE= E ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id= | + | |GENE= E ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10665 Enterobacteria phage T4]) |
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[1lgu|1LGU]], [[1li2|1LI2]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1xep FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xep OCA], [http://www.ebi.ac.uk/pdbsum/1xep PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1xep RCSB]</span> | ||
}} | }} | ||
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==About this Structure== | ==About this Structure== | ||
| - | 1XEP is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/ | + | 1XEP is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t4 Enterobacteria phage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XEP OCA]. |
==Reference== | ==Reference== | ||
Decoys for docking., Graves AP, Brenk R, Shoichet BK, J Med Chem. 2005 Jun 2;48(11):3714-28. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15916423 15916423] | Decoys for docking., Graves AP, Brenk R, Shoichet BK, J Med Chem. 2005 Jun 2;48(11):3714-28. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15916423 15916423] | ||
| - | [[Category: | + | [[Category: Enterobacteria phage t4]] |
[[Category: Lysozyme]] | [[Category: Lysozyme]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
| Line 26: | Line 29: | ||
[[Category: Graves, A P.]] | [[Category: Graves, A P.]] | ||
[[Category: Shoichet, B K.]] | [[Category: Shoichet, B K.]] | ||
| - | [[Category: BME]] | ||
| - | [[Category: CAQ]] | ||
| - | [[Category: PO4]] | ||
[[Category: bacteriolytic enzyme]] | [[Category: bacteriolytic enzyme]] | ||
[[Category: glycosidase]] | [[Category: glycosidase]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 00:48:36 2008'' |
Revision as of 21:48, 30 March 2008
| |||||||
| , resolution 1.55Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , | ||||||
| Gene: | E (Enterobacteria phage T4) | ||||||
| Activity: | Lysozyme, with EC number 3.2.1.17 | ||||||
| Related: | 1LGU, 1LI2
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Catechol in complex with T4 lysozyme L99A/M102Q
Overview
Molecular docking is widely used to predict novel lead compounds for drug discovery. Success depends on the quality of the docking scoring function, among other factors. An imperfect scoring function can mislead by predicting incorrect ligand geometries or by selecting nonbinding molecules over true ligands. These false-positive hits may be considered "decoys". Although these decoys are frustrating, they potentially provide important tests for a docking algorithm; the more subtle the decoy, the more rigorous the test. Indeed, decoy databases have been used to improve protein structure prediction algorithms and protein-protein docking algorithms. Here, we describe 20 geometric decoys in five enzymes and 166 "hit list" decoys-i.e., molecules predicted to bind by our docking program that were tested and found not to do so-for beta-lactamase and two cavity sites in lysozyme. Especially in the cavity sites, which are very simple, these decoys highlight particular weaknesses in our scoring function. We also consider the performance of five other widely used docking scoring functions against our geometric and hit list decoys. Intriguingly, whereas many of these other scoring functions performed better on the geometric decoys, they typically performed worse on the hit list decoys, often highly ranking molecules that seemed to poorly complement the model sites. Several of these "hits"from the other scoring functions were tested experimentally and found, in fact, to be decoys. Collectively, these decoys provide a tool for the development and improvement of molecular docking scoring functions. Such improvements may, in turn, be rapidly tested experimentally against these and related experimental systems, which are well-behaved in assays and for structure determination.
About this Structure
1XEP is a Single protein structure of sequence from Enterobacteria phage t4. Full crystallographic information is available from OCA.
Reference
Decoys for docking., Graves AP, Brenk R, Shoichet BK, J Med Chem. 2005 Jun 2;48(11):3714-28. PMID:15916423
Page seeded by OCA on Mon Mar 31 00:48:36 2008
