2cni: Difference between revisions
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|PDB= 2cni |SIZE=350|CAPTION= <scene name='initialview01'>2cni</scene>, resolution 2.0Å | |PDB= 2cni |SIZE=350|CAPTION= <scene name='initialview01'>2cni</scene>, resolution 2.0Å | ||
|SITE= <scene name='pdbsite=AC1:Mo6+Binding+Site+For+Chain+A'>AC1</scene> | |SITE= <scene name='pdbsite=AC1:Mo6+Binding+Site+For+Chain+A'>AC1</scene> | ||
|LIGAND= | |LIGAND= <scene name='pdbligand=IZF:METHYL+2-{[5-({3-CHLORO-4-[(5S)-1,1-DIOXIDO-3-OXOISOTHIAZOLIDIN-5-YL]-N-(PHENYLSULFONYL)-L-PHENYLALANYL}AMINO)PENTYL]OXY}-6-HYDROXYBENZOATE'>IZF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene> | ||
|ACTIVITY= [http://en.wikipedia.org/wiki/Protein-tyrosine-phosphatase Protein-tyrosine-phosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.48 3.1.3.48] | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Protein-tyrosine-phosphatase Protein-tyrosine-phosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.48 3.1.3.48] </span> | ||
|GENE= | |GENE= | ||
|DOMAIN= | |||
|RELATEDENTRY= | |||
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2cni FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cni OCA], [http://www.ebi.ac.uk/pdbsum/2cni PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2cni RCSB]</span> | |||
}} | }} | ||
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==Overview== | ==Overview== | ||
Structural analyses of the protein-tyrosine phosphatase 1B (PTP1B) active site and inhibitor complexes have aided in optimization of a peptide inhibitor containing the novel (S)-isothiazolidinone (IZD) phosphonate mimetic. Potency and permeability were simultaneously improved by replacing the polar peptidic backbone of the inhibitor with nonpeptidic moieties. The C-terminal primary amide was replaced with a benzimidazole ring, which hydrogen bonds to the carboxylate of Asp(48), and the N terminus of the peptide was replaced with an aryl sulfonamide, which hydrogen bonds to Asp(48) and the backbone NH of Arg(47) via a water molecule. Although both substituents retain the favorable hydrogen bonding network of the peptide scaffold, their aryl rings interact weakly with the protein. The aryl ring of benzimidazole is partially solvent exposed and only participates in van der Waals interactions with Phe(182) of the flap. The aryl ring of aryl sulfonamide adopts an unexpected conformation and only participates in intramolecular pi-stacking interactions with the benzimidazole ring. These results explain the flat SAR for substitutions on both rings and the reason why unsubstituted moieties were selected as candidates. Finally, substituents ortho to the IZD heterocycle on the aryl ring of the IZD-phenyl moiety bind in a small narrow site adjacent to the primary phosphate binding pocket. The crystal structure of an o-chloro derivative reveals that chlorine interacts extensively with residues in the small site. The structural insights that have led to the discovery of potent benzimidazole aryl sulfonamide o-substituted derivatives are discussed in detail. | Structural analyses of the protein-tyrosine phosphatase 1B (PTP1B) active site and inhibitor complexes have aided in optimization of a peptide inhibitor containing the novel (S)-isothiazolidinone (IZD) phosphonate mimetic. Potency and permeability were simultaneously improved by replacing the polar peptidic backbone of the inhibitor with nonpeptidic moieties. The C-terminal primary amide was replaced with a benzimidazole ring, which hydrogen bonds to the carboxylate of Asp(48), and the N terminus of the peptide was replaced with an aryl sulfonamide, which hydrogen bonds to Asp(48) and the backbone NH of Arg(47) via a water molecule. Although both substituents retain the favorable hydrogen bonding network of the peptide scaffold, their aryl rings interact weakly with the protein. The aryl ring of benzimidazole is partially solvent exposed and only participates in van der Waals interactions with Phe(182) of the flap. The aryl ring of aryl sulfonamide adopts an unexpected conformation and only participates in intramolecular pi-stacking interactions with the benzimidazole ring. These results explain the flat SAR for substitutions on both rings and the reason why unsubstituted moieties were selected as candidates. Finally, substituents ortho to the IZD heterocycle on the aryl ring of the IZD-phenyl moiety bind in a small narrow site adjacent to the primary phosphate binding pocket. The crystal structure of an o-chloro derivative reveals that chlorine interacts extensively with residues in the small site. The structural insights that have led to the discovery of potent benzimidazole aryl sulfonamide o-substituted derivatives are discussed in detail. | ||
==About this Structure== | ==About this Structure== | ||
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[[Category: Wynn, R.]] | [[Category: Wynn, R.]] | ||
[[Category: Yue, E W.]] | [[Category: Yue, E W.]] | ||
[[Category: acetylation]] | [[Category: acetylation]] | ||
[[Category: endoplasmic reticulum]] | [[Category: endoplasmic reticulum]] | ||
| Line 54: | Line 52: | ||
[[Category: protein phosphatase]] | [[Category: protein phosphatase]] | ||
''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 02:24:01 2008'' | ||
Revision as of 02:24, 31 March 2008
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| , resolution 2.0Å | |||||||
|---|---|---|---|---|---|---|---|
| Sites: | |||||||
| Ligands: | , | ||||||
| Activity: | Protein-tyrosine-phosphatase, with EC number 3.1.3.48 | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
STRUCTURAL INSIGHTS INTO THE DESIGN OF NONPEPTIDIC ISOTHIAZOLIDINONE-CONTAINING INHIBITORS OF PROTEIN TYROSINE PHOSPHATASE 1B
OverviewOverview
Structural analyses of the protein-tyrosine phosphatase 1B (PTP1B) active site and inhibitor complexes have aided in optimization of a peptide inhibitor containing the novel (S)-isothiazolidinone (IZD) phosphonate mimetic. Potency and permeability were simultaneously improved by replacing the polar peptidic backbone of the inhibitor with nonpeptidic moieties. The C-terminal primary amide was replaced with a benzimidazole ring, which hydrogen bonds to the carboxylate of Asp(48), and the N terminus of the peptide was replaced with an aryl sulfonamide, which hydrogen bonds to Asp(48) and the backbone NH of Arg(47) via a water molecule. Although both substituents retain the favorable hydrogen bonding network of the peptide scaffold, their aryl rings interact weakly with the protein. The aryl ring of benzimidazole is partially solvent exposed and only participates in van der Waals interactions with Phe(182) of the flap. The aryl ring of aryl sulfonamide adopts an unexpected conformation and only participates in intramolecular pi-stacking interactions with the benzimidazole ring. These results explain the flat SAR for substitutions on both rings and the reason why unsubstituted moieties were selected as candidates. Finally, substituents ortho to the IZD heterocycle on the aryl ring of the IZD-phenyl moiety bind in a small narrow site adjacent to the primary phosphate binding pocket. The crystal structure of an o-chloro derivative reveals that chlorine interacts extensively with residues in the small site. The structural insights that have led to the discovery of potent benzimidazole aryl sulfonamide o-substituted derivatives are discussed in detail.
About this StructureAbout this Structure
2CNI is a Single protein structure of sequence from Homo sapiens. Full crystallographic information is available from OCA.
ReferenceReference
Structural insights into the design of nonpeptidic isothiazolidinone-containing inhibitors of protein-tyrosine phosphatase 1B., Ala PJ, Gonneville L, Hillman M, Becker-Pasha M, Yue EW, Douty B, Wayland B, Polam P, Crawley ML, McLaughlin E, Sparks RB, Glass B, Takvorian A, Combs AP, Burn TC, Hollis GF, Wynn R, J Biol Chem. 2006 Dec 8;281(49):38013-21. Epub 2006 Oct 6. PMID:17028182
Page seeded by OCA on Mon Mar 31 02:24:01 2008
Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)
OCA- Pages with broken file links
- Homo sapiens
- Protein-tyrosine-phosphatase
- Single protein
- Ala, P J.
- Becker-Pasha, M.
- Burn, T C.
- Combs, A P.
- Crawley, M L.
- Douty, B.
- Glass, B.
- Gonneville, L.
- Hillman, M.
- Hollis, G F.
- Mclaughlin, E.
- Polam, P.
- Sparks, R B.
- Takvorian, A.
- Wayland, B.
- Wynn, R.
- Yue, E W.
- Acetylation
- Endoplasmic reticulum
- Hydrolase
- Oxidation
- Phosphatase
- Phosphorylation
- Polymorphism
- Protein phosphatase